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In protein complexes, the residues on the contact surface and the area of the contact surface can be calculated through the inter-chain distance, using the BioPython library and the SASA (Solvent Accessible Surface Area, Solvent Accessible Surface Area) library. SASA calculation is mainly based on whether water molecules pass through. The radius of water molecules is 1.4 A and the diameter is 2.8 A. Therefore, the distance of 2.8 A is used to determine whether the chains are connected.
related functions:
- Get the chain list of protein complex, i.e.
get_chain_ids() - Obtain the residue-atom dictionary. Note that the atom name may be different from the name of the PDB, that is
get_atom_list() - Get the all-atom list, that is
get_all_atoms() - Determine whether the atoms are connected, that is,
is_contact() - Get all the contact surfaces and calculate the residue dimensions atomically, that is
get_contacts() - Print the display command of ChimeraX, that is
get_chimerax_cmd() - End-to-end calculated contact residues, i.e.
cal_chain_interface_residue() - Calculate the SASA area, i.e.
cal_sasa() - Obtain the substructure of the complex multi-chain, i.e.
get_sub_structure() - End-to-end calculated contact area, that is,
cal_chain_interface_area()
Taking PDB 8j18 as an example, calculate the contact residues and areas between chain A and chain R:
The source code is as follows:
#!/usr/bin/env python
# -- coding: utf-8 --
"""
Copyright (c) 2022. All rights reserved.
Created by C. L. Wang on 2023/12/8
"""
import os
from Bio.PDB import NeighborSearch
from Bio.PDB import PDBParser, Selection
from Bio.PDB.Chain import Chain
from Bio.PDB.Model import Model
from Bio.PDB.Structure import Structure
from root_dir import DATA_DIR
class MainComplexChainDist(object):
"""
复合物，多链距离计算
"""
def __init__(self):
pass
@staticmethod
def get_chain_ids(structure):
chain_ids = []
for chain in structure.get_chains():
chain_ids.append(chain.id)
return chain_ids
@staticmethod
def get_atom_list(structure, chains):
"""
获取 atom list 列表
注意: 输出的 atom 名字与 PDB 文件中的 atom 名字略有差异，例如
8jtl 第1个，PRO: CG 对应 OG1，CD 对应 CG2
8jtl 第2个，VAL: CG1 对应 CD1，CG2 对应 CD2
"""
output = dict()
for chain in structure:
if chain.id in chains:
for residue in chain.get_residues():
het_flag, res_seq, i_code = residue.get_id()
the_id = (chain.id + "_" + str(res_seq) + "_" + i_code).strip()
for atom in residue.get_unpacked_list():
if het_flag == ' ':
if the_id in output:
output[the_id].append(atom)
else:
output[the_id] = [atom]
return output
# Filter out all the atoms from the chain,residue map given by residue_map
@staticmethod
def get_all_atoms(residue_map):
all_atoms_out = []
for residue in residue_map:
for atom in residue_map[residue]:
all_atoms_out.append(atom)
# Set the b-factor to zero for coloring by contacts
atom.set_bfactor(0.0)
return all_atoms_out
@staticmethod
def is_contact(res_1, other_atoms, cutoff):
for atom in res_1:
ns = NeighborSearch(other_atoms)
center = atom.get_coord()
neighbors = ns.search(center, cutoff) # 5.0 for distance in angstrom
residue_list = Selection.unfold_entities(neighbors, 'R') # R for residues
if len(residue_list) > 0:
return True
return False
@classmethod
def get_contacts(cls, struc, all_atoms, verbose, cutoff):
progress = 0
contacts = []
for residue in struc:
progress += 1
# if len(verbose) > 0:
# print(verbose, progress, "out of", len(struc))
atom_list = struc[residue]
outcome = cls.is_contact(atom_list, all_atoms, cutoff)
if outcome:
contacts.append(residue)
return contacts
@staticmethod
def get_chimerax_cmd(contacts, chain_id, pdb_id="2"):
"""
计算命令
"""
tmp_list = []
for item in contacts:
req_id = int(item.split("_")[1])
tmp_list.append(req_id)
contacts_gap = []
prev, post = -1, -1
for i in tmp_list:
if prev == -1:
prev = post = i
continue
if i - post == 1:
post = i
else:
contacts_gap.append(f"#{
pdb_id}/{
chain_id}:{
prev}-{
post}")
prev = post = i
cmd = "select " + " ".join(contacts_gap)
return cmd
@classmethod
def cal_chain_interface_residue(cls, structure, chain1, chain2, cutoff=7.5):
"""
计算复合物结构的链内距离
"""
chain_ids = cls.get_chain_ids(structure)
# ['A', 'B', 'G', 'R', 'S']
print(f"[Info] chain_ids: {
chain_ids}")
assert chain1 in chain_ids and chain2 in chain_ids
# C 表示 chain，即将 structure 展开 chain 的形式
# 同时支持 A, R, C, M, S
structure_c = Selection.unfold_entities(structure, target_level="C")
atom_dict1 = cls.get_atom_list(structure_c, chains=[chain1])
atom_dict2 = cls.get_atom_list(structure_c, chains=[chain2])
print(f"[Info] res_num: {
len(atom_dict1.keys())}")
all_atoms_1 = cls.get_all_atoms(atom_dict1)
all_atoms_2 = cls.get_all_atoms(atom_dict2)
cutoff = cutoff
contacts_1 = cls.get_contacts(atom_dict1, all_atoms_2, "First molecule, residue ", cutoff)
contacts_2 = cls.get_contacts(atom_dict2, all_atoms_1, "Second molecule, residue ", cutoff)
print(f"[Info] contacts_1: {
len(contacts_1)}")
print(f"[Info] contacts_2: {
len(contacts_2)}")
return contacts_1, contacts_2
@staticmethod
def cal_sasa(structure):
"""
计算单体的表面积
"""
import freesasa
structure = freesasa.structureFromBioPDB(structure)
result = freesasa.calc(structure)
# classArea = freesasa.classifyResults(result, structure)
return result.totalArea()
@staticmethod
def get_sub_structure(structure, chain_list):
"""
获取 PDB 结构的子结构
"""
new_structure = Structure(0)
new_model = Model(0)
# 遍历模型中的所有链
for chain in structure[0]:
# 获取链的ID
tmp_chain_id = chain.get_id()
if tmp_chain_id not in chain_list:
continue
# 创建一个新的结构对象，只包含当前链
new_chain = Chain(tmp_chain_id)
new_chain.child_list = chain.child_list
new_model.add(new_chain)
new_structure.add(new_model)
return new_structure
@classmethod
def cal_chain_interface_area(cls, structure, chain1, chain2):
sub_all_structure = cls.get_sub_structure(structure, [chain1, chain2])
sub1_structure = cls.get_sub_structure(structure, [chain1])
sub2_structure = cls.get_sub_structure(structure, [chain2])
v1_area = cls.cal_sasa(sub_all_structure)
v2_area = cls.cal_sasa(sub1_structure) + cls.cal_sasa(sub2_structure)
inter_area = max(int((v2_area - v1_area) // 2), 0)
return inter_area
def process(self, input_path, chain1, chain2):
"""
核心逻辑
"""
print(f"[Info] input_path: {
input_path}")
print(f"[Info] chain1: {
chain1}, chain2: {
chain2}")
chain1 = chain1.upper()
chain2 = chain2.upper()
parser = PDBParser(QUIET=True)
structure = parser.get_structure("def", input_path)
contacts_1, contacts_2 = self.cal_chain_interface_residue(structure, chain1, chain2, cutoff=7.5)
cmd1 = self.get_chimerax_cmd(contacts_1, chain1)
cmd2 = self.get_chimerax_cmd(contacts_2, chain2)
print(f"[Info] chimerax: {
cmd1}")
print(f"[Info] chimerax: {
cmd2}")
inter_area = self.cal_chain_interface_area(structure, chain1, chain2)
print(f"[Info] inter_area: {
inter_area}")
def main():
ccd = MainComplexChainDist()
# input_path = os.path.join(DATA_DIR, "templates", "8p3l.pdb")
# ccd.process(input_path, "A", "D") # 2562
# ccd.process(input_path, "A", "J") # 490
input_path = os.path.join(DATA_DIR, "templates", "8j18.pdb")
# ccd.process(input_path, "R", "S") # 0
ccd.process(input_path, "A", "R") # 1114
if __name__ == '__main__':
main()