How to calculate distance matrix between two chain in a single PDB file?

[Edward Wijaya]

Hi,

Is there a way I can calculate distance matrix between residue in just two wanted chains (e.g chain A and B ) from a single PDB file. But this code calculate all against all (even A against A and B agains B).

library(bio3d)
pdb <- read.pdb("5hie")

# I only want to calculate distance of residue for Chain A and B of 5hie.pdb

ca_ind <- atom.select(pdb, chain=c("A","B"))
dm(pdb, inds=ca_ind) 

At the end of the day, I have list of residue from each chain which I want to calculate the distance in Armstrong:
First 3 column is residue, residue number, chain name from 5hie.

  SER   602   A   LYS   601   B
  SER   465   A   ASP   663   B
  ASN   660   A   ILE   543   B
  SER   602   A   VAL   600   B
  VAL   600   A   VAL   600   B
  ASP   663   A   ILE   463   B
  ASN   660   A   TYR   538   B
  GLY   615   A   GLY   615   B
  GLY   615   A   ARG   662   B
  SER   602   A   THR   599   B
  ILE   463   A   GLN   664   B
  ILE   543   A   ASN   660   B
  ARG   603   A   GLN   493   B
  GLY   464   A   GLN   664   B
  GLN   664   A   ILE   463   B
  ARG   603   A   LYS   601   B
  ARG   662   A   GLY   615   B
  TYR   472   A   ARG   671   B
  ARG   462   A   GLN   664   B
  GLN   664   A   GLY   464   B
  LYS   601   A   VAL   600   B
  GLY   464   A   ASP   663   B
  LYS   601   A   LYS   601   B
  ARG   603   A   VAL   600   B
  VAL   600   A   LYS   601   B
  LYS   601   A   THR   599   B
  TYR   538   A   ASN   660   B
  THR   599   A   ARG   603   B
  THR   599   A   SER   602   B
  ASP   663   A   SER   465   B
  ILE   463   A   ASP   663   B
  VAL   600   A   SER   602   B
  GLN   664   A   ARG   462   B
  PHE   667   A   ARG   462   B
  LYS   601   A   ARG   603   B
  ASP   663   A   GLY   464   B
  ARG   462   A   PHE   667   B
  ARG   462   A   ASP   663   B
  ARG   603   A   ALA   598   B
  ASP   663   A   ARG   462   B
  THR   599   A   LYS   601   B
  ALA   598   A   ARG   603   B
  ARG   662   A   SER   614   B
  ARG   603   A   THR   599   B
  VAL   600   A   ARG   603   B
  LYS   601   A   SER   602   B
  GLY   615   A   SER   614   B

How can I go about it?

EW

[Xinqiu Yao]

Hi,

‌

The data you want is a subset of the full distance matrix, which you can easily extract using the information from the PDB. For example,

# get the number of residues for chain A
n <- sum(trim(pdb, chain='A')$calpha)

# get the full matrix
dmat <- dm(pdb, inds=ca_ind)

# the matrix between A and B
dAB <- dmat[1:n, (n+1):ncol(dmat)]

‌

[Edward Wijaya]

Hi,
Thanks so much for your answer. From dAB how can I get the original residue number (as in PDB file) of each chain?

For example given this:

SER 602 A LYS 601 B

I would like to check the distance betwen SER (residue 602 of chain A) and LYS (residue 601 of chain B ).

[Xinqiu Yao]

One way is to label your full matrix with residue id and number (and possibly chain ID), and then you can easily locate residues you are interested in. For example,

‌

pdbca <- trim(pdb, "calpha")
labs <- paste(pdbca$atom$resid, pdbca$atom$resno, pdbca$atom$chain, sep="_")
rownames(dmat) <- labs
colnames(dmat) <- labs

dmat["SER_602_A", "LYS_601_B"]

‌

[Edward Wijaya]

Xinqiu, thank you so much. This is very very helpful!
EW

[Edward Wijaya]

Resolved