Secondary Structure Graphs & Chain Graphs#

In this tutorial, we’ll be looking at higher-order graphs - that is graphs of Secondary Structure Elements and interacting chains (quaternary structure) - as well as assorted visualisation tools.

Graphein provides utilities for computing these graphs from residue-level graphs. I’d recommend checking out `this tutorial <>`__ for more information.

Open In Colab

First, we’ll construct a graph to work with

# Install Graphein if necessary
# !pip install graphein

# Install DSSP if necessary
# !sudo apt-get install dssp (better for colab) OR !conda install -c salilab dssp
import logging
import networkx as nx
import matplotlib.pyplot as plt

import graphein.protein as gp

new_funcs = {"keep_hets": False,
             "edge_construction_functions": [gp.add_peptide_bonds,
             "dssp_config": gp.DSSPConfig()
config = gp.ProteinGraphConfig(**new_funcs)
g = gp.construct_graph(config=config, pdb_code='4hhb')
gp.plotly_protein_structure_graph(g, node_size_multiplier=1)
INFO:graphein.protein.edges.distance:Found 208 hbond interactions.
INFO:graphein.protein.edges.distance:Found 12 hbond interactions.
INFO:graphein.protein.edges.distance:Found 6 disulfide interactions.
INFO:graphein.protein.edges.distance:Found 4566 ionic interactions.
INFO:graphein.protein.edges.distance:Found: 84 aromatic-aromatic interactions

Secondary Structure Graphs#

We use [DSSP] to compute secondary structures. This is stored under d["ss"] in the node attributes. Eg:

g = gp.secondary_structure(g)
for n, d in g.nodes(data=True):
    if d["ss"] == "T":
Downloading PDB structure '4hhb'...
INFO:graphein.protein.utils:Downloaded PDB file for: 4hhb

We can compute either a multigraph, where each edge in the selection is preserved (e.g. multiple edges between nodes H1 and H2 are permitted), or a weighted graph where we aggregate multiple edges between a pair of nodes into and preserve the edge information as metadata.


ss_graph = gp.compute_secondary_structure_graph(g, remove_self_loops=True)

for u, v, d in g.edges(data=True):
    print(u, v, d)
Name: 4hhb
Type: MultiGraph
Number of nodes: 80
Number of edges: 107
Average degree:   2.6750
A:VAL:1 A:LEU:2 {'kind': {'peptide_bond'}}
A:LEU:2 A:SER:3 {'kind': {'peptide_bond'}}
A:SER:3 A:PRO:4 {'kind': {'peptide_bond'}}
A:SER:3 A:ASP:6 {'kind': {'hbond'}}
A:PRO:4 A:ALA:5 {'kind': {'peptide_bond'}}
A:ALA:5 A:ASP:6 {'kind': {'peptide_bond'}}
A:ASP:6 A:LYS:7 {'kind': {'peptide_bond', 'ionic'}}
A:ASP:6 A:LYS:127 {'kind': {'ionic', 'hbond'}}
A:ASP:6 A:SER:124 {'kind': {'hbond'}}
A:ASP:6 C:ARG:141 {'kind': {'ionic'}}
A:LYS:7 A:THR:8 {'kind': {'peptide_bond'}}
A:LYS:7 A:ASP:74 {'kind': {'ionic', 'hbond'}}
A:THR:8 A:ASN:9 {'kind': {'peptide_bond'}}
A:ASN:9 A:VAL:10 {'kind': {'peptide_bond'}}
A:VAL:10 A:LYS:11 {'kind': {'peptide_bond'}}
A:LYS:11 A:ALA:12 {'kind': {'peptide_bond'}}
A:LYS:11 A:ASP:74 {'kind': {'ionic'}}
A:ALA:12 A:ALA:13 {'kind': {'peptide_bond'}}
A:ALA:13 A:TRP:14 {'kind': {'peptide_bond'}}
A:TRP:14 A:GLY:15 {'kind': {'peptide_bond'}}
A:GLY:15 A:LYS:16 {'kind': {'peptide_bond'}}
A:LYS:16 A:VAL:17 {'kind': {'peptide_bond'}}
A:LYS:16 A:GLU:116 {'kind': {'ionic'}}
A:VAL:17 A:GLY:18 {'kind': {'peptide_bond'}}
A:GLY:18 A:ALA:19 {'kind': {'peptide_bond'}}
A:ALA:19 A:HIS:20 {'kind': {'peptide_bond'}}
A:HIS:20 A:ALA:21 {'kind': {'peptide_bond'}}
A:HIS:20 A:GLU:23 {'kind': {'ionic'}}
A:HIS:20 A:HIS:112 {'kind': {'aromatic'}}
A:ALA:21 A:GLY:22 {'kind': {'peptide_bond'}}
A:GLY:22 A:GLU:23 {'kind': {'peptide_bond'}}
A:GLU:23 A:TYR:24 {'kind': {'peptide_bond'}}
A:GLU:23 A:HIS:112 {'kind': {'ionic'}}
A:TYR:24 A:GLY:25 {'kind': {'peptide_bond'}}
A:GLY:25 A:ALA:26 {'kind': {'peptide_bond'}}
A:ALA:26 A:GLU:27 {'kind': {'peptide_bond'}}
A:GLU:27 A:ALA:28 {'kind': {'peptide_bond'}}
A:GLU:27 A:ARG:31 {'kind': {'ionic'}}
A:GLU:27 A:HIS:112 {'kind': {'ionic'}}
A:ALA:28 A:LEU:29 {'kind': {'peptide_bond'}}
A:LEU:29 A:GLU:30 {'kind': {'peptide_bond'}}
A:GLU:30 A:ARG:31 {'kind': {'peptide_bond', 'ionic'}}
A:GLU:30 A:HIS:50 {'kind': {'ionic'}}
A:ARG:31 A:MET:32 {'kind': {'peptide_bond'}}
A:MET:32 A:PHE:33 {'kind': {'peptide_bond'}}
A:PHE:33 A:LEU:34 {'kind': {'peptide_bond'}}
A:PHE:33 A:PHE:43 {'kind': {'aromatic'}}
A:LEU:34 A:SER:35 {'kind': {'peptide_bond'}}
A:SER:35 A:PHE:36 {'kind': {'peptide_bond'}}
A:PHE:36 A:PRO:37 {'kind': {'peptide_bond'}}
A:PHE:36 A:HIS:103 {'kind': {'aromatic'}}
A:PRO:37 A:THR:38 {'kind': {'peptide_bond'}}
A:THR:38 A:THR:39 {'kind': {'peptide_bond'}}
A:THR:39 A:LYS:40 {'kind': {'peptide_bond'}}
A:LYS:40 A:THR:41 {'kind': {'peptide_bond'}}
A:THR:41 A:TYR:42 {'kind': {'peptide_bond'}}
A:TYR:42 A:PHE:43 {'kind': {'peptide_bond'}}
A:TYR:42 D:ASP:99 {'kind': {'hbond'}}
A:PHE:43 A:PRO:44 {'kind': {'peptide_bond'}}
A:PHE:43 A:HIS:58 {'kind': {'aromatic'}}
A:PHE:43 A:PHE:46 {'kind': {'aromatic'}}
A:PRO:44 A:HIS:45 {'kind': {'peptide_bond'}}
A:HIS:45 A:PHE:46 {'kind': {'aromatic', 'peptide_bond'}}
A:PHE:46 A:ASP:47 {'kind': {'peptide_bond'}}
A:PHE:46 A:HIS:58 {'kind': {'aromatic'}}
A:ASP:47 A:LEU:48 {'kind': {'peptide_bond'}}
A:ASP:47 A:SER:49 {'kind': {'hbond'}}
A:LEU:48 A:SER:49 {'kind': {'peptide_bond'}}
A:SER:49 A:HIS:50 {'kind': {'peptide_bond'}}
A:HIS:50 A:GLY:51 {'kind': {'peptide_bond'}}
A:GLY:51 A:SER:52 {'kind': {'peptide_bond'}}
A:SER:52 A:ALA:53 {'kind': {'peptide_bond'}}
A:ALA:53 A:GLN:54 {'kind': {'peptide_bond'}}
A:GLN:54 A:VAL:55 {'kind': {'peptide_bond'}}
A:VAL:55 A:LYS:56 {'kind': {'peptide_bond'}}
A:LYS:56 A:GLY:57 {'kind': {'peptide_bond'}}
A:GLY:57 A:HIS:58 {'kind': {'peptide_bond'}}
A:HIS:58 A:GLY:59 {'kind': {'peptide_bond'}}
A:GLY:59 A:LYS:60 {'kind': {'peptide_bond'}}
A:LYS:60 A:LYS:61 {'kind': {'peptide_bond'}}
A:LYS:60 A:ASP:64 {'kind': {'ionic'}}
A:LYS:61 A:VAL:62 {'kind': {'peptide_bond'}}
A:LYS:61 A:ASP:64 {'kind': {'ionic'}}
A:VAL:62 A:ALA:63 {'kind': {'peptide_bond'}}
A:ALA:63 A:ASP:64 {'kind': {'peptide_bond'}}
A:ASP:64 A:ALA:65 {'kind': {'peptide_bond'}}
A:ALA:65 A:LEU:66 {'kind': {'peptide_bond'}}
A:LEU:66 A:THR:67 {'kind': {'peptide_bond'}}
A:THR:67 A:ASN:68 {'kind': {'peptide_bond'}}
A:ASN:68 A:ALA:69 {'kind': {'peptide_bond'}}
A:ALA:69 A:VAL:70 {'kind': {'peptide_bond'}}
A:VAL:70 A:ALA:71 {'kind': {'peptide_bond'}}
A:ALA:71 A:HIS:72 {'kind': {'peptide_bond'}}
A:HIS:72 A:VAL:73 {'kind': {'peptide_bond'}}
A:HIS:72 A:ASP:75 {'kind': {'ionic'}}
A:VAL:73 A:ASP:74 {'kind': {'peptide_bond'}}
A:ASP:74 A:ASP:75 {'kind': {'peptide_bond'}}
A:ASP:75 A:MET:76 {'kind': {'peptide_bond'}}
A:ASP:75 A:ASN:78 {'kind': {'hbond'}}
A:MET:76 A:PRO:77 {'kind': {'peptide_bond'}}
A:PRO:77 A:ASN:78 {'kind': {'peptide_bond'}}
A:ASN:78 A:ALA:79 {'kind': {'peptide_bond'}}
A:ALA:79 A:LEU:80 {'kind': {'peptide_bond'}}
A:LEU:80 A:SER:81 {'kind': {'peptide_bond'}}
A:SER:81 A:ALA:82 {'kind': {'peptide_bond'}}
A:SER:81 A:LYS:139 {'kind': {'hbond'}}
A:ALA:82 A:LEU:83 {'kind': {'peptide_bond'}}
A:LEU:83 A:SER:84 {'kind': {'peptide_bond'}}
A:SER:84 A:ASP:85 {'kind': {'peptide_bond'}}
A:ASP:85 A:LEU:86 {'kind': {'peptide_bond'}}
A:ASP:85 A:LYS:139 {'kind': {'ionic', 'hbond'}}
A:ASP:85 A:HIS:89 {'kind': {'ionic'}}
A:LEU:86 A:HIS:87 {'kind': {'peptide_bond'}}
A:HIS:87 A:ALA:88 {'kind': {'peptide_bond'}}
A:HIS:87 A:PHE:98 {'kind': {'aromatic'}}
A:HIS:87 A:TYR:140 {'kind': {'aromatic'}}
A:ALA:88 A:HIS:89 {'kind': {'peptide_bond'}}
A:HIS:89 A:LYS:90 {'kind': {'peptide_bond'}}
A:LYS:90 A:LEU:91 {'kind': {'peptide_bond'}}
A:LEU:91 A:ARG:92 {'kind': {'peptide_bond'}}
A:ARG:92 A:VAL:93 {'kind': {'peptide_bond'}}
A:ARG:92 D:GLU:43 {'kind': {'ionic'}}
A:VAL:93 A:ASP:94 {'kind': {'peptide_bond'}}
A:ASP:94 A:PRO:95 {'kind': {'peptide_bond'}}
A:PRO:95 A:VAL:96 {'kind': {'peptide_bond'}}
A:VAL:96 A:ASN:97 {'kind': {'peptide_bond'}}
A:ASN:97 A:PHE:98 {'kind': {'peptide_bond'}}
A:PHE:98 A:LYS:99 {'kind': {'peptide_bond'}}
A:PHE:98 A:TYR:140 {'kind': {'aromatic'}}
A:LYS:99 A:LEU:100 {'kind': {'peptide_bond'}}
A:LEU:100 A:LEU:101 {'kind': {'peptide_bond'}}
A:LEU:101 A:SER:102 {'kind': {'peptide_bond'}}
A:SER:102 A:HIS:103 {'kind': {'peptide_bond'}}
A:SER:102 A:SER:133 {'kind': {'hbond'}}
A:HIS:103 A:CYS:104 {'kind': {'peptide_bond'}}
A:CYS:104 A:LEU:105 {'kind': {'peptide_bond'}}
A:LEU:105 A:LEU:106 {'kind': {'peptide_bond'}}
A:LEU:106 A:VAL:107 {'kind': {'peptide_bond'}}
A:VAL:107 A:THR:108 {'kind': {'peptide_bond'}}
A:THR:108 A:LEU:109 {'kind': {'peptide_bond'}}
A:LEU:109 A:ALA:110 {'kind': {'peptide_bond'}}
A:ALA:110 A:ALA:111 {'kind': {'peptide_bond'}}
A:ALA:111 A:HIS:112 {'kind': {'peptide_bond'}}
A:HIS:112 A:LEU:113 {'kind': {'peptide_bond'}}
A:LEU:113 A:PRO:114 {'kind': {'peptide_bond'}}
A:PRO:114 A:ALA:115 {'kind': {'peptide_bond'}}
A:ALA:115 A:GLU:116 {'kind': {'peptide_bond'}}
A:GLU:116 A:PHE:117 {'kind': {'peptide_bond'}}
A:PHE:117 A:THR:118 {'kind': {'peptide_bond'}}
A:PHE:117 B:HIS:116 {'kind': {'aromatic'}}
A:THR:118 A:PRO:119 {'kind': {'peptide_bond'}}
A:PRO:119 A:ALA:120 {'kind': {'peptide_bond'}}
A:ALA:120 A:VAL:121 {'kind': {'peptide_bond'}}
A:VAL:121 A:HIS:122 {'kind': {'peptide_bond'}}
A:HIS:122 A:ALA:123 {'kind': {'peptide_bond'}}
A:HIS:122 A:ASP:126 {'kind': {'ionic'}}
A:ALA:123 A:SER:124 {'kind': {'peptide_bond'}}
A:SER:124 A:LEU:125 {'kind': {'peptide_bond'}}
A:LEU:125 A:ASP:126 {'kind': {'peptide_bond'}}
A:ASP:126 A:LYS:127 {'kind': {'peptide_bond', 'ionic'}}
A:ASP:126 B:TYR:35 {'kind': {'hbond'}}
A:ASP:126 C:ARG:141 {'kind': {'ionic'}}
A:LYS:127 A:PHE:128 {'kind': {'peptide_bond'}}
A:PHE:128 A:LEU:129 {'kind': {'peptide_bond'}}
A:LEU:129 A:ALA:130 {'kind': {'peptide_bond'}}
A:ALA:130 A:SER:131 {'kind': {'peptide_bond'}}
A:SER:131 A:VAL:132 {'kind': {'peptide_bond'}}
A:VAL:132 A:SER:133 {'kind': {'peptide_bond'}}
A:SER:133 A:THR:134 {'kind': {'peptide_bond'}}
A:THR:134 A:VAL:135 {'kind': {'peptide_bond'}}
A:VAL:135 A:LEU:136 {'kind': {'peptide_bond'}}
A:LEU:136 A:THR:137 {'kind': {'peptide_bond'}}
A:THR:137 A:SER:138 {'kind': {'peptide_bond'}}
A:SER:138 A:LYS:139 {'kind': {'peptide_bond'}}
A:LYS:139 A:TYR:140 {'kind': {'peptide_bond'}}
A:TYR:140 A:ARG:141 {'kind': {'peptide_bond'}}
A:ARG:141 C:ASP:6 {'kind': {'ionic'}}
A:ARG:141 C:ASP:126 {'kind': {'ionic'}}
B:VAL:1 B:HIS:2 {'kind': {'peptide_bond'}}
B:HIS:2 B:LEU:3 {'kind': {'peptide_bond'}}
B:HIS:2 B:GLU:7 {'kind': {'ionic'}}
B:LEU:3 B:THR:4 {'kind': {'peptide_bond'}}
B:THR:4 B:PRO:5 {'kind': {'peptide_bond'}}
B:PRO:5 B:GLU:6 {'kind': {'peptide_bond'}}
B:GLU:6 B:GLU:7 {'kind': {'peptide_bond'}}
B:GLU:7 B:LYS:8 {'kind': {'peptide_bond', 'ionic'}}
B:GLU:7 B:LYS:132 {'kind': {'ionic'}}
B:LYS:8 B:SER:9 {'kind': {'peptide_bond'}}
B:SER:9 B:ALA:10 {'kind': {'peptide_bond'}}
B:ALA:10 B:VAL:11 {'kind': {'peptide_bond'}}
B:VAL:11 B:THR:12 {'kind': {'peptide_bond'}}
B:THR:12 B:ALA:13 {'kind': {'peptide_bond'}}
B:ALA:13 B:LEU:14 {'kind': {'peptide_bond'}}
B:LEU:14 B:TRP:15 {'kind': {'peptide_bond'}}
B:TRP:15 B:GLY:16 {'kind': {'peptide_bond'}}
B:GLY:16 B:LYS:17 {'kind': {'peptide_bond'}}
B:LYS:17 B:VAL:18 {'kind': {'peptide_bond'}}
B:LYS:17 B:GLU:121 {'kind': {'ionic'}}
B:VAL:18 B:ASN:19 {'kind': {'peptide_bond'}}
B:ASN:19 B:VAL:20 {'kind': {'peptide_bond'}}
B:VAL:20 B:ASP:21 {'kind': {'peptide_bond'}}
B:ASP:21 B:GLU:22 {'kind': {'peptide_bond'}}
B:ASP:21 B:LYS:65 {'kind': {'ionic'}}
B:GLU:22 B:VAL:23 {'kind': {'peptide_bond'}}
B:GLU:22 B:HIS:117 {'kind': {'ionic'}}
B:VAL:23 B:GLY:24 {'kind': {'peptide_bond'}}
B:GLY:24 B:GLY:25 {'kind': {'peptide_bond'}}
B:GLY:25 B:GLU:26 {'kind': {'peptide_bond'}}
B:GLU:26 B:ALA:27 {'kind': {'peptide_bond'}}
B:GLU:26 B:HIS:117 {'kind': {'ionic'}}
B:GLU:26 B:ARG:30 {'kind': {'ionic'}}
B:GLU:26 B:HIS:116 {'kind': {'ionic'}}
B:ALA:27 B:LEU:28 {'kind': {'peptide_bond'}}
B:LEU:28 B:GLY:29 {'kind': {'peptide_bond'}}
B:GLY:29 B:ARG:30 {'kind': {'peptide_bond'}}
B:ARG:30 B:LEU:31 {'kind': {'peptide_bond'}}
B:LEU:31 B:LEU:32 {'kind': {'peptide_bond'}}
B:LEU:32 B:VAL:33 {'kind': {'peptide_bond'}}
B:VAL:33 B:VAL:34 {'kind': {'peptide_bond'}}
B:VAL:34 B:TYR:35 {'kind': {'peptide_bond'}}
B:TYR:35 B:PRO:36 {'kind': {'peptide_bond'}}
B:PRO:36 B:TRP:37 {'kind': {'peptide_bond'}}
B:TRP:37 B:THR:38 {'kind': {'peptide_bond'}}
B:THR:38 B:GLN:39 {'kind': {'peptide_bond'}}
B:GLN:39 B:ARG:40 {'kind': {'peptide_bond'}}
B:ARG:40 B:PHE:41 {'kind': {'peptide_bond'}}
B:PHE:41 B:PHE:42 {'kind': {'aromatic', 'peptide_bond'}}
B:PHE:42 B:GLU:43 {'kind': {'peptide_bond'}}
B:PHE:42 B:HIS:63 {'kind': {'aromatic'}}
B:PHE:42 B:PHE:45 {'kind': {'aromatic'}}
B:GLU:43 B:SER:44 {'kind': {'peptide_bond'}}
B:GLU:43 C:ARG:92 {'kind': {'ionic'}}
B:SER:44 B:PHE:45 {'kind': {'peptide_bond'}}
B:PHE:45 B:GLY:46 {'kind': {'peptide_bond'}}
B:PHE:45 B:HIS:63 {'kind': {'aromatic'}}
B:GLY:46 B:ASP:47 {'kind': {'peptide_bond'}}
B:ASP:47 B:LEU:48 {'kind': {'peptide_bond'}}
B:ASP:47 B:SER:49 {'kind': {'hbond'}}
B:LEU:48 B:SER:49 {'kind': {'peptide_bond'}}
B:SER:49 B:THR:50 {'kind': {'peptide_bond'}}
B:THR:50 B:PRO:51 {'kind': {'peptide_bond'}}
B:PRO:51 B:ASP:52 {'kind': {'peptide_bond'}}
B:ASP:52 B:ALA:53 {'kind': {'peptide_bond'}}
B:ALA:53 B:VAL:54 {'kind': {'peptide_bond'}}
B:VAL:54 B:MET:55 {'kind': {'peptide_bond'}}
B:MET:55 B:GLY:56 {'kind': {'peptide_bond'}}
B:GLY:56 B:ASN:57 {'kind': {'peptide_bond'}}
B:ASN:57 B:PRO:58 {'kind': {'peptide_bond'}}
B:PRO:58 B:LYS:59 {'kind': {'peptide_bond'}}
B:LYS:59 B:VAL:60 {'kind': {'peptide_bond'}}
B:VAL:60 B:LYS:61 {'kind': {'peptide_bond'}}
B:LYS:61 B:ALA:62 {'kind': {'peptide_bond'}}
B:ALA:62 B:HIS:63 {'kind': {'peptide_bond'}}
B:HIS:63 B:GLY:64 {'kind': {'peptide_bond'}}
B:GLY:64 B:LYS:65 {'kind': {'peptide_bond'}}
B:LYS:65 B:LYS:66 {'kind': {'peptide_bond'}}
B:LYS:66 B:VAL:67 {'kind': {'peptide_bond'}}
B:VAL:67 B:LEU:68 {'kind': {'peptide_bond'}}
B:LEU:68 B:GLY:69 {'kind': {'peptide_bond'}}
B:GLY:69 B:ALA:70 {'kind': {'peptide_bond'}}
B:ALA:70 B:PHE:71 {'kind': {'peptide_bond'}}
B:PHE:71 B:SER:72 {'kind': {'peptide_bond'}}
B:SER:72 B:ASP:73 {'kind': {'peptide_bond'}}
B:ASP:73 B:GLY:74 {'kind': {'peptide_bond'}}
B:ASP:73 B:HIS:77 {'kind': {'ionic'}}
B:GLY:74 B:LEU:75 {'kind': {'peptide_bond'}}
B:LEU:75 B:ALA:76 {'kind': {'peptide_bond'}}
B:ALA:76 B:HIS:77 {'kind': {'peptide_bond'}}
B:HIS:77 B:LEU:78 {'kind': {'peptide_bond'}}
B:LEU:78 B:ASP:79 {'kind': {'peptide_bond'}}
B:ASP:79 B:ASN:80 {'kind': {'peptide_bond'}}
B:ASN:80 B:LEU:81 {'kind': {'peptide_bond'}}
B:LEU:81 B:LYS:82 {'kind': {'peptide_bond'}}
B:LYS:82 B:GLY:83 {'kind': {'peptide_bond'}}
B:GLY:83 B:THR:84 {'kind': {'peptide_bond'}}
B:THR:84 B:PHE:85 {'kind': {'peptide_bond'}}
B:PHE:85 B:ALA:86 {'kind': {'peptide_bond'}}
B:ALA:86 B:THR:87 {'kind': {'peptide_bond'}}
B:THR:87 B:LEU:88 {'kind': {'peptide_bond'}}
B:LEU:88 B:SER:89 {'kind': {'peptide_bond'}}
B:SER:89 B:GLU:90 {'kind': {'peptide_bond'}}
B:GLU:90 B:LEU:91 {'kind': {'peptide_bond'}}
B:GLU:90 B:LYS:144 {'kind': {'ionic'}}
B:LEU:91 B:HIS:92 {'kind': {'peptide_bond'}}
B:HIS:92 B:CYS:93 {'kind': {'peptide_bond'}}
B:HIS:92 B:PHE:103 {'kind': {'aromatic'}}
B:HIS:92 B:TYR:145 {'kind': {'aromatic'}}
B:CYS:93 B:ASP:94 {'kind': {'peptide_bond'}}
B:ASP:94 B:LYS:95 {'kind': {'peptide_bond', 'ionic'}}
B:ASP:94 B:HIS:146 {'kind': {'ionic'}}
B:ASP:94 B:HIS:97 {'kind': {'ionic'}}
B:LYS:95 B:LEU:96 {'kind': {'peptide_bond'}}
B:LEU:96 B:HIS:97 {'kind': {'peptide_bond'}}
B:HIS:97 B:VAL:98 {'kind': {'peptide_bond'}}
B:VAL:98 B:ASP:99 {'kind': {'peptide_bond'}}
B:ASP:99 B:PRO:100 {'kind': {'peptide_bond'}}
B:ASP:99 C:TYR:42 {'kind': {'hbond'}}
B:PRO:100 B:GLU:101 {'kind': {'peptide_bond'}}
B:GLU:101 B:ASN:102 {'kind': {'peptide_bond'}}
B:GLU:101 B:ARG:104 {'kind': {'ionic'}}
B:ASN:102 B:PHE:103 {'kind': {'peptide_bond'}}
B:PHE:103 B:ARG:104 {'kind': {'peptide_bond'}}
B:PHE:103 B:TYR:145 {'kind': {'aromatic'}}
B:ARG:104 B:LEU:105 {'kind': {'peptide_bond'}}
B:LEU:105 B:LEU:106 {'kind': {'peptide_bond'}}
B:LEU:106 B:GLY:107 {'kind': {'peptide_bond'}}
B:GLY:107 B:ASN:108 {'kind': {'peptide_bond'}}
B:ASN:108 B:VAL:109 {'kind': {'peptide_bond'}}
B:VAL:109 B:LEU:110 {'kind': {'peptide_bond'}}
B:LEU:110 B:VAL:111 {'kind': {'peptide_bond'}}
B:VAL:111 B:CYS:112 {'kind': {'peptide_bond'}}
B:CYS:112 B:VAL:113 {'kind': {'peptide_bond'}}
B:VAL:113 B:LEU:114 {'kind': {'peptide_bond'}}
B:LEU:114 B:ALA:115 {'kind': {'peptide_bond'}}
B:ALA:115 B:HIS:116 {'kind': {'peptide_bond'}}
B:HIS:116 B:HIS:117 {'kind': {'aromatic', 'peptide_bond'}}
B:HIS:117 B:PHE:118 {'kind': {'aromatic', 'peptide_bond'}}
B:PHE:118 B:GLY:119 {'kind': {'peptide_bond'}}
B:GLY:119 B:LYS:120 {'kind': {'peptide_bond'}}
B:LYS:120 B:GLU:121 {'kind': {'peptide_bond', 'ionic'}}
B:GLU:121 B:PHE:122 {'kind': {'peptide_bond'}}
B:PHE:122 B:THR:123 {'kind': {'peptide_bond'}}
B:PHE:122 B:TYR:130 {'kind': {'aromatic'}}
B:THR:123 B:PRO:124 {'kind': {'peptide_bond'}}
B:PRO:124 B:PRO:125 {'kind': {'peptide_bond'}}
B:PRO:125 B:VAL:126 {'kind': {'peptide_bond'}}
B:VAL:126 B:GLN:127 {'kind': {'peptide_bond'}}
B:GLN:127 B:ALA:128 {'kind': {'peptide_bond'}}
B:ALA:128 B:ALA:129 {'kind': {'peptide_bond'}}
B:ALA:129 B:TYR:130 {'kind': {'peptide_bond'}}
B:TYR:130 B:GLN:131 {'kind': {'peptide_bond'}}
B:GLN:131 B:LYS:132 {'kind': {'peptide_bond'}}
B:LYS:132 B:VAL:133 {'kind': {'peptide_bond'}}
B:VAL:133 B:VAL:134 {'kind': {'peptide_bond'}}
B:VAL:134 B:ALA:135 {'kind': {'peptide_bond'}}
B:ALA:135 B:GLY:136 {'kind': {'peptide_bond'}}
B:GLY:136 B:VAL:137 {'kind': {'peptide_bond'}}
B:VAL:137 B:ALA:138 {'kind': {'peptide_bond'}}
B:ALA:138 B:ASN:139 {'kind': {'peptide_bond'}}
B:ASN:139 B:ALA:140 {'kind': {'peptide_bond'}}
B:ALA:140 B:LEU:141 {'kind': {'peptide_bond'}}
B:LEU:141 B:ALA:142 {'kind': {'peptide_bond'}}
B:ALA:142 B:HIS:143 {'kind': {'peptide_bond'}}
B:HIS:143 B:LYS:144 {'kind': {'peptide_bond'}}
B:LYS:144 B:TYR:145 {'kind': {'peptide_bond'}}
B:TYR:145 B:HIS:146 {'kind': {'peptide_bond'}}
C:VAL:1 C:LEU:2 {'kind': {'peptide_bond'}}
C:LEU:2 C:SER:3 {'kind': {'peptide_bond'}}
C:SER:3 C:PRO:4 {'kind': {'peptide_bond'}}
C:SER:3 C:ASP:6 {'kind': {'hbond'}}
C:PRO:4 C:ALA:5 {'kind': {'peptide_bond'}}
C:ALA:5 C:ASP:6 {'kind': {'peptide_bond'}}
C:ASP:6 C:LYS:7 {'kind': {'peptide_bond', 'ionic'}}
C:ASP:6 C:SER:124 {'kind': {'hbond'}}
C:ASP:6 C:LYS:127 {'kind': {'ionic', 'hbond'}}
C:LYS:7 C:THR:8 {'kind': {'peptide_bond'}}
C:LYS:7 C:ASP:74 {'kind': {'ionic', 'hbond'}}
C:THR:8 C:ASN:9 {'kind': {'peptide_bond'}}
C:ASN:9 C:VAL:10 {'kind': {'peptide_bond'}}
C:VAL:10 C:LYS:11 {'kind': {'peptide_bond'}}
C:LYS:11 C:ALA:12 {'kind': {'peptide_bond'}}
C:LYS:11 C:ASP:74 {'kind': {'ionic'}}
C:ALA:12 C:ALA:13 {'kind': {'peptide_bond'}}
C:ALA:13 C:TRP:14 {'kind': {'peptide_bond'}}
C:TRP:14 C:GLY:15 {'kind': {'peptide_bond'}}
C:GLY:15 C:LYS:16 {'kind': {'peptide_bond'}}
C:LYS:16 C:VAL:17 {'kind': {'peptide_bond'}}
C:LYS:16 C:GLU:116 {'kind': {'ionic'}}
C:VAL:17 C:GLY:18 {'kind': {'peptide_bond'}}
C:GLY:18 C:ALA:19 {'kind': {'peptide_bond'}}
C:ALA:19 C:HIS:20 {'kind': {'peptide_bond'}}
C:HIS:20 C:ALA:21 {'kind': {'peptide_bond'}}
C:HIS:20 C:GLU:23 {'kind': {'ionic'}}
C:HIS:20 C:HIS:112 {'kind': {'aromatic'}}
C:HIS:20 C:TYR:24 {'kind': {'aromatic'}}
C:ALA:21 C:GLY:22 {'kind': {'peptide_bond'}}
C:GLY:22 C:GLU:23 {'kind': {'peptide_bond'}}
C:GLU:23 C:TYR:24 {'kind': {'peptide_bond'}}
C:GLU:23 C:HIS:112 {'kind': {'ionic'}}
C:TYR:24 C:GLY:25 {'kind': {'peptide_bond'}}
C:GLY:25 C:ALA:26 {'kind': {'peptide_bond'}}
C:ALA:26 C:GLU:27 {'kind': {'peptide_bond'}}
C:GLU:27 C:ALA:28 {'kind': {'peptide_bond'}}
C:GLU:27 C:ARG:31 {'kind': {'ionic'}}
C:GLU:27 C:HIS:112 {'kind': {'ionic'}}
C:ALA:28 C:LEU:29 {'kind': {'peptide_bond'}}
C:LEU:29 C:GLU:30 {'kind': {'peptide_bond'}}
C:GLU:30 C:ARG:31 {'kind': {'peptide_bond', 'ionic'}}
C:GLU:30 C:HIS:50 {'kind': {'ionic'}}
C:ARG:31 C:MET:32 {'kind': {'peptide_bond'}}
C:MET:32 C:PHE:33 {'kind': {'peptide_bond'}}
C:PHE:33 C:LEU:34 {'kind': {'peptide_bond'}}
C:PHE:33 C:PHE:43 {'kind': {'aromatic'}}
C:LEU:34 C:SER:35 {'kind': {'peptide_bond'}}
C:SER:35 C:PHE:36 {'kind': {'peptide_bond'}}
C:PHE:36 C:PRO:37 {'kind': {'peptide_bond'}}
C:PHE:36 C:HIS:103 {'kind': {'aromatic'}}
C:PRO:37 C:THR:38 {'kind': {'peptide_bond'}}
C:THR:38 C:THR:39 {'kind': {'peptide_bond'}}
C:THR:39 C:LYS:40 {'kind': {'peptide_bond'}}
C:LYS:40 C:THR:41 {'kind': {'peptide_bond'}}
C:THR:41 C:TYR:42 {'kind': {'peptide_bond'}}
C:TYR:42 C:PHE:43 {'kind': {'peptide_bond'}}
C:PHE:43 C:PRO:44 {'kind': {'peptide_bond'}}
C:PHE:43 C:HIS:58 {'kind': {'aromatic'}}
C:PHE:43 C:PHE:46 {'kind': {'aromatic'}}
C:PRO:44 C:HIS:45 {'kind': {'peptide_bond'}}
C:HIS:45 C:PHE:46 {'kind': {'aromatic', 'peptide_bond'}}
C:PHE:46 C:ASP:47 {'kind': {'peptide_bond'}}
C:PHE:46 C:HIS:58 {'kind': {'aromatic'}}
C:ASP:47 C:LEU:48 {'kind': {'peptide_bond'}}
C:ASP:47 C:SER:49 {'kind': {'hbond'}}
C:LEU:48 C:SER:49 {'kind': {'peptide_bond'}}
C:SER:49 C:HIS:50 {'kind': {'peptide_bond'}}
C:HIS:50 C:GLY:51 {'kind': {'peptide_bond'}}
C:GLY:51 C:SER:52 {'kind': {'peptide_bond'}}
C:SER:52 C:ALA:53 {'kind': {'peptide_bond'}}
C:ALA:53 C:GLN:54 {'kind': {'peptide_bond'}}
C:GLN:54 C:VAL:55 {'kind': {'peptide_bond'}}
C:VAL:55 C:LYS:56 {'kind': {'peptide_bond'}}
C:LYS:56 C:GLY:57 {'kind': {'peptide_bond'}}
C:GLY:57 C:HIS:58 {'kind': {'peptide_bond'}}
C:HIS:58 C:GLY:59 {'kind': {'peptide_bond'}}
C:GLY:59 C:LYS:60 {'kind': {'peptide_bond'}}
C:LYS:60 C:LYS:61 {'kind': {'peptide_bond'}}
C:LYS:60 C:ASP:64 {'kind': {'ionic', 'hbond'}}
C:LYS:61 C:VAL:62 {'kind': {'peptide_bond'}}
C:LYS:61 C:ASP:64 {'kind': {'ionic'}}
C:VAL:62 C:ALA:63 {'kind': {'peptide_bond'}}
C:ALA:63 C:ASP:64 {'kind': {'peptide_bond'}}
C:ASP:64 C:ALA:65 {'kind': {'peptide_bond'}}
C:ALA:65 C:LEU:66 {'kind': {'peptide_bond'}}
C:LEU:66 C:THR:67 {'kind': {'peptide_bond'}}
C:THR:67 C:ASN:68 {'kind': {'peptide_bond'}}
C:ASN:68 C:ALA:69 {'kind': {'peptide_bond'}}
C:ALA:69 C:VAL:70 {'kind': {'peptide_bond'}}
C:VAL:70 C:ALA:71 {'kind': {'peptide_bond'}}
C:ALA:71 C:HIS:72 {'kind': {'peptide_bond'}}
C:HIS:72 C:VAL:73 {'kind': {'peptide_bond'}}
C:HIS:72 C:ASP:75 {'kind': {'ionic'}}
C:VAL:73 C:ASP:74 {'kind': {'peptide_bond'}}
C:ASP:74 C:ASP:75 {'kind': {'peptide_bond'}}
C:ASP:75 C:MET:76 {'kind': {'peptide_bond'}}
C:MET:76 C:PRO:77 {'kind': {'peptide_bond'}}
C:PRO:77 C:ASN:78 {'kind': {'peptide_bond'}}
C:ASN:78 C:ALA:79 {'kind': {'peptide_bond'}}
C:ALA:79 C:LEU:80 {'kind': {'peptide_bond'}}
C:LEU:80 C:SER:81 {'kind': {'peptide_bond'}}
C:SER:81 C:ALA:82 {'kind': {'peptide_bond'}}
C:SER:81 C:LYS:139 {'kind': {'hbond'}}
C:ALA:82 C:LEU:83 {'kind': {'peptide_bond'}}
C:LEU:83 C:SER:84 {'kind': {'peptide_bond'}}
C:SER:84 C:ASP:85 {'kind': {'peptide_bond'}}
C:ASP:85 C:LEU:86 {'kind': {'peptide_bond'}}
C:ASP:85 C:LYS:139 {'kind': {'ionic', 'hbond'}}
C:ASP:85 C:HIS:89 {'kind': {'ionic'}}
C:LEU:86 C:HIS:87 {'kind': {'peptide_bond'}}
C:HIS:87 C:ALA:88 {'kind': {'peptide_bond'}}
C:HIS:87 C:PHE:98 {'kind': {'aromatic'}}
C:HIS:87 C:TYR:140 {'kind': {'aromatic'}}
C:ALA:88 C:HIS:89 {'kind': {'peptide_bond'}}
C:HIS:89 C:LYS:90 {'kind': {'peptide_bond'}}
C:LYS:90 C:LEU:91 {'kind': {'peptide_bond'}}
C:LEU:91 C:ARG:92 {'kind': {'peptide_bond'}}
C:ARG:92 C:VAL:93 {'kind': {'peptide_bond'}}
C:VAL:93 C:ASP:94 {'kind': {'peptide_bond'}}
C:ASP:94 C:PRO:95 {'kind': {'peptide_bond'}}
C:PRO:95 C:VAL:96 {'kind': {'peptide_bond'}}
C:VAL:96 C:ASN:97 {'kind': {'peptide_bond'}}
C:ASN:97 C:PHE:98 {'kind': {'peptide_bond'}}
C:PHE:98 C:LYS:99 {'kind': {'peptide_bond'}}
C:PHE:98 C:TYR:140 {'kind': {'aromatic'}}
C:LYS:99 C:LEU:100 {'kind': {'peptide_bond'}}
C:LEU:100 C:LEU:101 {'kind': {'peptide_bond'}}
C:LEU:101 C:SER:102 {'kind': {'peptide_bond'}}
C:SER:102 C:HIS:103 {'kind': {'peptide_bond'}}
C:HIS:103 C:CYS:104 {'kind': {'peptide_bond'}}
C:CYS:104 C:LEU:105 {'kind': {'peptide_bond'}}
C:LEU:105 C:LEU:106 {'kind': {'peptide_bond'}}
C:LEU:106 C:VAL:107 {'kind': {'peptide_bond'}}
C:VAL:107 C:THR:108 {'kind': {'peptide_bond'}}
C:THR:108 C:LEU:109 {'kind': {'peptide_bond'}}
C:LEU:109 C:ALA:110 {'kind': {'peptide_bond'}}
C:ALA:110 C:ALA:111 {'kind': {'peptide_bond'}}
C:ALA:111 C:HIS:112 {'kind': {'peptide_bond'}}
C:HIS:112 C:LEU:113 {'kind': {'peptide_bond'}}
C:LEU:113 C:PRO:114 {'kind': {'peptide_bond'}}
C:PRO:114 C:ALA:115 {'kind': {'peptide_bond'}}
C:ALA:115 C:GLU:116 {'kind': {'peptide_bond'}}
C:GLU:116 C:PHE:117 {'kind': {'peptide_bond'}}
C:PHE:117 C:THR:118 {'kind': {'peptide_bond'}}
C:PHE:117 D:HIS:116 {'kind': {'aromatic'}}
C:THR:118 C:PRO:119 {'kind': {'peptide_bond'}}
C:PRO:119 C:ALA:120 {'kind': {'peptide_bond'}}
C:ALA:120 C:VAL:121 {'kind': {'peptide_bond'}}
C:VAL:121 C:HIS:122 {'kind': {'peptide_bond'}}
C:HIS:122 C:ALA:123 {'kind': {'peptide_bond'}}
C:HIS:122 C:ASP:126 {'kind': {'ionic'}}
C:ALA:123 C:SER:124 {'kind': {'peptide_bond'}}
C:SER:124 C:LEU:125 {'kind': {'peptide_bond'}}
C:LEU:125 C:ASP:126 {'kind': {'peptide_bond'}}
C:ASP:126 C:LYS:127 {'kind': {'peptide_bond', 'ionic'}}
C:LYS:127 C:PHE:128 {'kind': {'peptide_bond'}}
C:PHE:128 C:LEU:129 {'kind': {'peptide_bond'}}
C:LEU:129 C:ALA:130 {'kind': {'peptide_bond'}}
C:ALA:130 C:SER:131 {'kind': {'peptide_bond'}}
C:SER:131 C:VAL:132 {'kind': {'peptide_bond'}}
C:VAL:132 C:SER:133 {'kind': {'peptide_bond'}}
C:SER:133 C:THR:134 {'kind': {'peptide_bond'}}
C:THR:134 C:VAL:135 {'kind': {'peptide_bond'}}
C:VAL:135 C:LEU:136 {'kind': {'peptide_bond'}}
C:LEU:136 C:THR:137 {'kind': {'peptide_bond'}}
C:THR:137 C:SER:138 {'kind': {'peptide_bond'}}
C:SER:138 C:LYS:139 {'kind': {'peptide_bond'}}
C:LYS:139 C:TYR:140 {'kind': {'peptide_bond'}}
C:TYR:140 C:ARG:141 {'kind': {'peptide_bond'}}
D:VAL:1 D:HIS:2 {'kind': {'peptide_bond'}}
D:HIS:2 D:LEU:3 {'kind': {'peptide_bond'}}
D:HIS:2 D:GLU:7 {'kind': {'ionic'}}
D:LEU:3 D:THR:4 {'kind': {'peptide_bond'}}
D:THR:4 D:PRO:5 {'kind': {'peptide_bond'}}
D:PRO:5 D:GLU:6 {'kind': {'peptide_bond'}}
D:GLU:6 D:GLU:7 {'kind': {'peptide_bond'}}
D:GLU:7 D:LYS:8 {'kind': {'peptide_bond', 'ionic'}}
D:GLU:7 D:LYS:132 {'kind': {'ionic'}}
D:LYS:8 D:SER:9 {'kind': {'peptide_bond'}}
D:LYS:8 D:ASP:79 {'kind': {'ionic'}}
D:SER:9 D:ALA:10 {'kind': {'peptide_bond'}}
D:ALA:10 D:VAL:11 {'kind': {'peptide_bond'}}
D:VAL:11 D:THR:12 {'kind': {'peptide_bond'}}
D:THR:12 D:ALA:13 {'kind': {'peptide_bond'}}
D:ALA:13 D:LEU:14 {'kind': {'peptide_bond'}}
D:LEU:14 D:TRP:15 {'kind': {'peptide_bond'}}
D:TRP:15 D:GLY:16 {'kind': {'peptide_bond'}}
D:GLY:16 D:LYS:17 {'kind': {'peptide_bond'}}
D:LYS:17 D:VAL:18 {'kind': {'peptide_bond'}}
D:LYS:17 D:GLU:121 {'kind': {'ionic'}}
D:VAL:18 D:ASN:19 {'kind': {'peptide_bond'}}
D:ASN:19 D:VAL:20 {'kind': {'peptide_bond'}}
D:VAL:20 D:ASP:21 {'kind': {'peptide_bond'}}
D:ASP:21 D:GLU:22 {'kind': {'peptide_bond'}}
D:ASP:21 D:LYS:65 {'kind': {'ionic', 'hbond'}}
D:GLU:22 D:VAL:23 {'kind': {'peptide_bond'}}
D:GLU:22 D:HIS:117 {'kind': {'ionic'}}
D:VAL:23 D:GLY:24 {'kind': {'peptide_bond'}}
D:GLY:24 D:GLY:25 {'kind': {'peptide_bond'}}
D:GLY:25 D:GLU:26 {'kind': {'peptide_bond'}}
D:GLU:26 D:ALA:27 {'kind': {'peptide_bond'}}
D:GLU:26 D:HIS:117 {'kind': {'ionic'}}
D:GLU:26 D:HIS:116 {'kind': {'ionic'}}
D:GLU:26 D:ARG:30 {'kind': {'ionic'}}
D:ALA:27 D:LEU:28 {'kind': {'peptide_bond'}}
D:LEU:28 D:GLY:29 {'kind': {'peptide_bond'}}
D:GLY:29 D:ARG:30 {'kind': {'peptide_bond'}}
D:ARG:30 D:LEU:31 {'kind': {'peptide_bond'}}
D:LEU:31 D:LEU:32 {'kind': {'peptide_bond'}}
D:LEU:32 D:VAL:33 {'kind': {'peptide_bond'}}
D:VAL:33 D:VAL:34 {'kind': {'peptide_bond'}}
D:VAL:34 D:TYR:35 {'kind': {'peptide_bond'}}
D:TYR:35 D:PRO:36 {'kind': {'peptide_bond'}}
D:PRO:36 D:TRP:37 {'kind': {'peptide_bond'}}
D:TRP:37 D:THR:38 {'kind': {'peptide_bond'}}
D:THR:38 D:GLN:39 {'kind': {'peptide_bond'}}
D:GLN:39 D:ARG:40 {'kind': {'peptide_bond'}}
D:ARG:40 D:PHE:41 {'kind': {'peptide_bond'}}
D:ARG:40 D:GLU:43 {'kind': {'ionic'}}
D:PHE:41 D:PHE:42 {'kind': {'aromatic', 'peptide_bond'}}
D:PHE:42 D:GLU:43 {'kind': {'peptide_bond'}}
D:PHE:42 D:HIS:63 {'kind': {'aromatic'}}
D:PHE:42 D:PHE:45 {'kind': {'aromatic'}}
D:GLU:43 D:SER:44 {'kind': {'peptide_bond'}}
D:SER:44 D:PHE:45 {'kind': {'peptide_bond'}}
D:PHE:45 D:GLY:46 {'kind': {'peptide_bond'}}
D:PHE:45 D:HIS:63 {'kind': {'aromatic'}}
D:GLY:46 D:ASP:47 {'kind': {'peptide_bond'}}
D:ASP:47 D:LEU:48 {'kind': {'peptide_bond'}}
D:ASP:47 D:SER:49 {'kind': {'hbond'}}
D:LEU:48 D:SER:49 {'kind': {'peptide_bond'}}
D:SER:49 D:THR:50 {'kind': {'peptide_bond'}}
D:THR:50 D:PRO:51 {'kind': {'peptide_bond'}}
D:PRO:51 D:ASP:52 {'kind': {'peptide_bond'}}
D:ASP:52 D:ALA:53 {'kind': {'peptide_bond'}}
D:ALA:53 D:VAL:54 {'kind': {'peptide_bond'}}
D:VAL:54 D:MET:55 {'kind': {'peptide_bond'}}
D:MET:55 D:GLY:56 {'kind': {'peptide_bond'}}
D:GLY:56 D:ASN:57 {'kind': {'peptide_bond'}}
D:ASN:57 D:PRO:58 {'kind': {'peptide_bond'}}
D:PRO:58 D:LYS:59 {'kind': {'peptide_bond'}}
D:LYS:59 D:VAL:60 {'kind': {'peptide_bond'}}
D:VAL:60 D:LYS:61 {'kind': {'peptide_bond'}}
D:LYS:61 D:ALA:62 {'kind': {'peptide_bond'}}
D:ALA:62 D:HIS:63 {'kind': {'peptide_bond'}}
D:HIS:63 D:GLY:64 {'kind': {'peptide_bond'}}
D:GLY:64 D:LYS:65 {'kind': {'peptide_bond'}}
D:LYS:65 D:LYS:66 {'kind': {'peptide_bond'}}
D:LYS:66 D:VAL:67 {'kind': {'peptide_bond'}}
D:VAL:67 D:LEU:68 {'kind': {'peptide_bond'}}
D:LEU:68 D:GLY:69 {'kind': {'peptide_bond'}}
D:GLY:69 D:ALA:70 {'kind': {'peptide_bond'}}
D:ALA:70 D:PHE:71 {'kind': {'peptide_bond'}}
D:PHE:71 D:SER:72 {'kind': {'peptide_bond'}}
D:SER:72 D:ASP:73 {'kind': {'peptide_bond'}}
D:ASP:73 D:GLY:74 {'kind': {'peptide_bond'}}
D:ASP:73 D:HIS:77 {'kind': {'ionic'}}
D:GLY:74 D:LEU:75 {'kind': {'peptide_bond'}}
D:LEU:75 D:ALA:76 {'kind': {'peptide_bond'}}
D:ALA:76 D:HIS:77 {'kind': {'peptide_bond'}}
D:HIS:77 D:LEU:78 {'kind': {'peptide_bond'}}
D:LEU:78 D:ASP:79 {'kind': {'peptide_bond'}}
D:ASP:79 D:ASN:80 {'kind': {'peptide_bond'}}
D:ASN:80 D:LEU:81 {'kind': {'peptide_bond'}}
D:LEU:81 D:LYS:82 {'kind': {'peptide_bond'}}
D:LYS:82 D:GLY:83 {'kind': {'peptide_bond'}}
D:GLY:83 D:THR:84 {'kind': {'peptide_bond'}}
D:THR:84 D:PHE:85 {'kind': {'peptide_bond'}}
D:PHE:85 D:ALA:86 {'kind': {'peptide_bond'}}
D:ALA:86 D:THR:87 {'kind': {'peptide_bond'}}
D:THR:87 D:LEU:88 {'kind': {'peptide_bond'}}
D:LEU:88 D:SER:89 {'kind': {'peptide_bond'}}
D:SER:89 D:GLU:90 {'kind': {'peptide_bond'}}
D:GLU:90 D:LEU:91 {'kind': {'peptide_bond'}}
D:GLU:90 D:LYS:144 {'kind': {'ionic'}}
D:LEU:91 D:HIS:92 {'kind': {'peptide_bond'}}
D:HIS:92 D:CYS:93 {'kind': {'peptide_bond'}}
D:HIS:92 D:PHE:103 {'kind': {'aromatic'}}
D:HIS:92 D:TYR:145 {'kind': {'aromatic'}}
D:CYS:93 D:ASP:94 {'kind': {'peptide_bond'}}
D:ASP:94 D:LYS:95 {'kind': {'peptide_bond', 'ionic'}}
D:ASP:94 D:HIS:97 {'kind': {'ionic'}}
D:ASP:94 D:HIS:146 {'kind': {'ionic'}}
D:LYS:95 D:LEU:96 {'kind': {'peptide_bond'}}
D:LEU:96 D:HIS:97 {'kind': {'peptide_bond'}}
D:HIS:97 D:VAL:98 {'kind': {'peptide_bond'}}
D:VAL:98 D:ASP:99 {'kind': {'peptide_bond'}}
D:ASP:99 D:PRO:100 {'kind': {'peptide_bond'}}
D:PRO:100 D:GLU:101 {'kind': {'peptide_bond'}}
D:GLU:101 D:ASN:102 {'kind': {'peptide_bond'}}
D:GLU:101 D:ARG:104 {'kind': {'ionic'}}
D:ASN:102 D:PHE:103 {'kind': {'peptide_bond'}}
D:PHE:103 D:ARG:104 {'kind': {'peptide_bond'}}
D:PHE:103 D:TYR:145 {'kind': {'aromatic'}}
D:ARG:104 D:LEU:105 {'kind': {'peptide_bond'}}
D:LEU:105 D:LEU:106 {'kind': {'peptide_bond'}}
D:LEU:106 D:GLY:107 {'kind': {'peptide_bond'}}
D:GLY:107 D:ASN:108 {'kind': {'peptide_bond'}}
D:ASN:108 D:VAL:109 {'kind': {'peptide_bond'}}
D:VAL:109 D:LEU:110 {'kind': {'peptide_bond'}}
D:LEU:110 D:VAL:111 {'kind': {'peptide_bond'}}
D:VAL:111 D:CYS:112 {'kind': {'peptide_bond'}}
D:CYS:112 D:VAL:113 {'kind': {'peptide_bond'}}
D:VAL:113 D:LEU:114 {'kind': {'peptide_bond'}}
D:LEU:114 D:ALA:115 {'kind': {'peptide_bond'}}
D:ALA:115 D:HIS:116 {'kind': {'peptide_bond'}}
D:HIS:116 D:HIS:117 {'kind': {'aromatic', 'peptide_bond'}}
D:HIS:117 D:PHE:118 {'kind': {'peptide_bond'}}
D:PHE:118 D:GLY:119 {'kind': {'peptide_bond'}}
D:GLY:119 D:LYS:120 {'kind': {'peptide_bond'}}
D:LYS:120 D:GLU:121 {'kind': {'peptide_bond', 'ionic'}}
D:GLU:121 D:PHE:122 {'kind': {'peptide_bond'}}
D:PHE:122 D:THR:123 {'kind': {'peptide_bond'}}
D:PHE:122 D:TYR:130 {'kind': {'aromatic'}}
D:THR:123 D:PRO:124 {'kind': {'peptide_bond'}}
D:PRO:124 D:PRO:125 {'kind': {'peptide_bond'}}
D:PRO:125 D:VAL:126 {'kind': {'peptide_bond'}}
D:VAL:126 D:GLN:127 {'kind': {'peptide_bond'}}
D:GLN:127 D:ALA:128 {'kind': {'peptide_bond'}}
D:ALA:128 D:ALA:129 {'kind': {'peptide_bond'}}
D:ALA:129 D:TYR:130 {'kind': {'peptide_bond'}}
D:TYR:130 D:GLN:131 {'kind': {'peptide_bond'}}
D:GLN:131 D:LYS:132 {'kind': {'peptide_bond'}}
D:LYS:132 D:VAL:133 {'kind': {'peptide_bond'}}
D:VAL:133 D:VAL:134 {'kind': {'peptide_bond'}}
D:VAL:134 D:ALA:135 {'kind': {'peptide_bond'}}
D:ALA:135 D:GLY:136 {'kind': {'peptide_bond'}}
D:GLY:136 D:VAL:137 {'kind': {'peptide_bond'}}
D:VAL:137 D:ALA:138 {'kind': {'peptide_bond'}}
D:ALA:138 D:ASN:139 {'kind': {'peptide_bond'}}
D:ASN:139 D:ALA:140 {'kind': {'peptide_bond'}}
D:ALA:140 D:LEU:141 {'kind': {'peptide_bond'}}
D:LEU:141 D:ALA:142 {'kind': {'peptide_bond'}}
D:ALA:142 D:HIS:143 {'kind': {'peptide_bond'}}
D:HIS:143 D:LYS:144 {'kind': {'peptide_bond'}}
D:LYS:144 D:TYR:145 {'kind': {'peptide_bond'}}
D:TYR:145 D:HIS:146 {'kind': {'peptide_bond'}}
plt.rcParams["figure.figsize"] = (10, 10)
/Users/arianjamasb/opt/anaconda3/envs/graphein-wip/lib/python3.8/site-packages/mpl_chord_diagram/ RuntimeWarning:

invalid value encountered in true_divide

ss_graph = gp.compute_secondary_structure_graph(g, remove_self_loops=True, return_weighted_graph=True)
for u, v, d in ss_graph.edges(data=True):
    print(u, v, d)
Name: 4hhb
Type: Graph
Number of nodes: 80
Number of edges: 86
Average degree:   2.1500
H1 H7 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 1, 'hbond': 2}
H1 G2 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1}
H1 T7 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H1 T1 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T1 H2 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'peptide_bond': 1, 'ionic': 1}
T1 H6 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
H2 H6 {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
H2 T3 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
T2 S1 {'weight': 2, 'kind': {'aromatic', 'peptide_bond'}, 'aromatic': 1, 'peptide_bond': 1}
S1 H3 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
S2 T3 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H3 T4 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T4 G2 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'peptide_bond': 1, 'ionic': 1}
G2 H4 {'weight': 2, 'kind': {'peptide_bond', 'hbond'}, 'peptide_bond': 1, 'hbond': 1}
H4 T5 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T5 H5 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H5 T8 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'hbond': 2, 'ionic': 1}
H5 I1 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'peptide_bond': 1, 'ionic': 1}
I1 H6 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
T6 H6 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H6 H7 {'weight': 1, 'kind': {'hbond'}, 'hbond': 1}
H7 S3 {'weight': 1, 'kind': {'hbond'}, 'hbond': 1}
H7 T8 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H8 H14 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H8 T9 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T9 G6 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H9 H11 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H9 H13 {'weight': 3, 'kind': {'ionic'}, 'ionic': 3}
H9 S3 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
S3 G3 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G4 H11 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
S4 H10 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H11 T10 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'ionic': 1, 'peptide_bond': 1}
T10 G5 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G5 H12 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H12 I2 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H12 T12 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
I2 H13 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
T11 H13 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H13 G6 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G6 S5 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
S5 H14 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
H14 T12 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H15 H21 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'hbond': 2, 'ionic': 1}
H15 G9 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1}
H15 T18 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H15 G7 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G7 H16 {'weight': 3, 'kind': {'aromatic', 'peptide_bond', 'ionic'}, 'peptide_bond': 1, 'ionic': 1, 'aromatic': 1}
G7 H20 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
H16 H20 {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
H16 T14 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
T13 S6 {'weight': 2, 'kind': {'aromatic', 'peptide_bond'}, 'aromatic': 1, 'peptide_bond': 1}
S6 H17 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
S7 T14 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H17 T15 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T15 G9 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'peptide_bond': 1, 'ionic': 1}
G9 H18 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H18 T16 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T16 H19 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H19 T19 {'weight': 3, 'kind': {'ionic', 'hbond'}, 'hbond': 2, 'ionic': 1}
H19 I3 {'weight': 2, 'kind': {'peptide_bond', 'ionic'}, 'ionic': 1, 'peptide_bond': 1}
I3 H20 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
T17 H20 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H21 T19 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H22 H28 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H22 T23 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H22 T20 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T20 G12 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H23 H25 {'weight': 2, 'kind': {'ionic', 'hbond'}, 'ionic': 1, 'hbond': 1}
H23 H27 {'weight': 3, 'kind': {'ionic'}, 'ionic': 3}
H23 S8 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
S8 G10 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G10 G11 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
G11 H25 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
S9 H24 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H24 T21 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H25 T22 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H26 I4 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H26 T25 {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
I4 H27 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
I4 S10 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
T24 H27 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
H27 G12 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
G12 S11 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}
S11 H28 {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
H28 T25 {'weight': 1, 'kind': {'peptide_bond'}, 'peptide_bond': 1}

Chain Graph#

Chain graphs represent the quaternary structure of a protein complex; nodes represent individual chains and edges are the interactions between them. Again, we can compute either a multigraph or a weighted graphs.


g = gp.construct_graph(config=config, pdb_code='2y69')
chain_graph = gp.compute_chain_graph(g, remove_self_loops=False, return_weighted_graph=False)

mat = nx.adjacency_matrix(chain_graph)
a = gp.visualisation.chord_diagram(mat, names=list(chain_graph.nodes), use_gradient=True)

for i, (u, v, d) in enumerate(chain_graph.edges(data=True)):
    print(u, v, d)
    if i == 15:
INFO:graphein.protein.edges.distance:Found 1285 hbond interactions.
INFO:graphein.protein.edges.distance:Found 231 hbond interactions.
INFO:graphein.protein.edges.distance:Found 44 disulfide interactions.
INFO:graphein.protein.edges.distance:Found 30676 ionic interactions.
INFO:graphein.protein.edges.distance:Found: 610 aromatic-aromatic interactions
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'ionic', 'hbond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'ionic'}}
A A {'kind': {'peptide_bond', 'ionic'}}
A A {'kind': {'peptide_bond'}}
A A {'kind': {'peptide_bond'}}

Weighted Graph#

chain_graph = gp.compute_chain_graph(g, remove_self_loops=False, return_weighted_graph=True)

mat = nx.adjacency_matrix(chain_graph)
a = gp.visualisation.chord_diagram(mat, names=list(chain_graph.nodes), use_gradient=True)

for u, v, d in chain_graph.edges(data=True):
    print(u,v, d)
A A {'weight': 587, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 512, 'ionic': 18, 'hbond': 11, 'aromatic': 46}
A L {'weight': 8, 'kind': {'aromatic', 'ionic'}, 'ionic': 4, 'aromatic': 4}
A J {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
A B {'weight': 17, 'kind': {'ionic', 'aromatic', 'hbond'}, 'hbond': 5, 'ionic': 10, 'aromatic': 2}
A C {'weight': 8, 'kind': {'aromatic', 'ionic'}, 'ionic': 5, 'aromatic': 3}
A T {'weight': 2, 'kind': {'aromatic', 'hbond'}, 'hbond': 1, 'aromatic': 1}
A G {'weight': 1, 'kind': {'hbond'}, 'hbond': 1}
A D {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
A M {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
A F {'weight': 3, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 1, 'aromatic': 1, 'hbond': 1}
B B {'weight': 257, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 226, 'aromatic': 5, 'ionic': 21, 'hbond': 5}
B D {'weight': 3, 'kind': {'aromatic', 'ionic'}, 'aromatic': 1, 'ionic': 2}
B I {'weight': 7, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1, 'aromatic': 4}
B E {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
B H {'weight': 3, 'kind': {'ionic', 'hbond'}, 'hbond': 1, 'ionic': 2}
C C {'weight': 318, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 258, 'aromatic': 42, 'ionic': 15, 'hbond': 3}
C J {'weight': 4, 'kind': {'aromatic', 'ionic'}, 'ionic': 3, 'aromatic': 1}
C F {'weight': 3, 'kind': {'ionic'}, 'ionic': 3}
C T {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
C H {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
C G {'weight': 7, 'kind': {'aromatic', 'ionic'}, 'ionic': 6, 'aromatic': 1}
D D {'weight': 184, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 143, 'ionic': 31, 'hbond': 6, 'aromatic': 4}
D M {'weight': 4, 'kind': {'aromatic', 'hbond'}, 'hbond': 1, 'aromatic': 3}
D E {'weight': 9, 'kind': {'ionic', 'hbond'}, 'ionic': 6, 'hbond': 3}
D K {'weight': 5, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 3, 'hbond': 1, 'aromatic': 1}
D I {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1}
E E {'weight': 129, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 103, 'ionic': 22, 'aromatic': 2, 'hbond': 2}
E I {'weight': 4, 'kind': {'ionic'}, 'ionic': 4}
E F {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
F F {'weight': 108, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 92, 'ionic': 6, 'hbond': 9, 'aromatic': 1}
F T {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
G G {'weight': 92, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 81, 'ionic': 7, 'aromatic': 3, 'hbond': 1}
G N {'weight': 2, 'kind': {'aromatic', 'hbond'}, 'hbond': 1, 'aromatic': 1}
G S {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
G H {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
H H {'weight': 103, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'disulfide', 'hbond'}, 'peptide_bond': 74, 'hbond': 8, 'ionic': 13, 'disulfide': 2, 'aromatic': 6}
I I {'weight': 94, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 70, 'aromatic': 9, 'ionic': 13, 'hbond': 2}
J J {'weight': 64, 'kind': {'aromatic', 'peptide_bond', 'ionic'}, 'peptide_bond': 56, 'ionic': 6, 'aromatic': 2}
J L {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
K K {'weight': 57, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 48, 'hbond': 1, 'ionic': 6, 'aromatic': 2}
L L {'weight': 52, 'kind': {'peptide_bond', 'ionic', 'aromatic'}, 'aromatic': 3, 'peptide_bond': 45, 'ionic': 4}
L M {'weight': 3, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 1, 'aromatic': 1, 'hbond': 1}
M M {'weight': 46, 'kind': {'aromatic', 'peptide_bond', 'ionic'}, 'peptide_bond': 42, 'ionic': 2, 'aromatic': 2}
N N {'weight': 584, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 512, 'ionic': 18, 'hbond': 8, 'aromatic': 46}
N Y {'weight': 6, 'kind': {'aromatic', 'ionic'}, 'ionic': 3, 'aromatic': 3}
N W {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
N O {'weight': 18, 'kind': {'ionic', 'aromatic', 'hbond'}, 'hbond': 6, 'ionic': 10, 'aromatic': 2}
N P {'weight': 8, 'kind': {'aromatic', 'ionic'}, 'ionic': 5, 'aromatic': 3}
N T {'weight': 2, 'kind': {'ionic', 'hbond'}, 'ionic': 1, 'hbond': 1}
N Q {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1}
N Z {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
N S {'weight': 3, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 1, 'aromatic': 1, 'hbond': 1}
O O {'weight': 256, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 225, 'aromatic': 5, 'ionic': 21, 'hbond': 5}
O Q {'weight': 3, 'kind': {'aromatic', 'ionic'}, 'aromatic': 1, 'ionic': 2}
O V {'weight': 8, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 3, 'hbond': 1, 'aromatic': 4}
O R {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
O U {'weight': 3, 'kind': {'ionic', 'hbond'}, 'hbond': 1, 'ionic': 2}
P P {'weight': 319, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 258, 'aromatic': 43, 'ionic': 15, 'hbond': 3}
P S {'weight': 4, 'kind': {'ionic'}, 'ionic': 4}
P W {'weight': 4, 'kind': {'aromatic', 'ionic'}, 'ionic': 3, 'aromatic': 1}
P U {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
P T {'weight': 7, 'kind': {'aromatic', 'ionic'}, 'ionic': 6, 'aromatic': 1}
Q Q {'weight': 179, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 143, 'hbond': 4, 'aromatic': 4, 'ionic': 28}
Q S {'weight': 2, 'kind': {'ionic'}, 'ionic': 2}
Q R {'weight': 10, 'kind': {'ionic', 'hbond'}, 'ionic': 7, 'hbond': 3}
Q X {'weight': 6, 'kind': {'aromatic', 'ionic', 'hbond'}, 'ionic': 4, 'hbond': 1, 'aromatic': 1}
Q Z {'weight': 3, 'kind': {'aromatic'}, 'aromatic': 3}
Q V {'weight': 3, 'kind': {'ionic', 'hbond'}, 'ionic': 2, 'hbond': 1}
R R {'weight': 128, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 103, 'ionic': 21, 'aromatic': 2, 'hbond': 2}
R V {'weight': 5, 'kind': {'ionic', 'hbond'}, 'ionic': 4, 'hbond': 1}
R S {'weight': 3, 'kind': {'ionic'}, 'ionic': 3}
S S {'weight': 107, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 92, 'ionic': 6, 'hbond': 8, 'aromatic': 1}
T T {'weight': 93, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 81, 'ionic': 7, 'aromatic': 4, 'hbond': 1}
T U {'weight': 1, 'kind': {'ionic'}, 'ionic': 1}
U U {'weight': 100, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'disulfide', 'hbond'}, 'peptide_bond': 74, 'hbond': 6, 'ionic': 12, 'disulfide': 2, 'aromatic': 6}
V V {'weight': 93, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 70, 'aromatic': 8, 'ionic': 13, 'hbond': 2}
W W {'weight': 64, 'kind': {'aromatic', 'peptide_bond', 'ionic'}, 'peptide_bond': 56, 'ionic': 6, 'aromatic': 2}
W Y {'weight': 1, 'kind': {'aromatic'}, 'aromatic': 1}
X X {'weight': 56, 'kind': {'peptide_bond', 'ionic', 'aromatic', 'hbond'}, 'peptide_bond': 48, 'hbond': 1, 'ionic': 5, 'aromatic': 2}
Y Y {'weight': 52, 'kind': {'peptide_bond', 'ionic', 'aromatic'}, 'aromatic': 3, 'peptide_bond': 45, 'ionic': 4}
Y Z {'weight': 2, 'kind': {'aromatic', 'ionic'}, 'ionic': 1, 'aromatic': 1}
Z Z {'weight': 46, 'kind': {'aromatic', 'peptide_bond', 'ionic'}, 'peptide_bond': 41, 'ionic': 3, 'aromatic': 2}