Suppose, I have a protein (say, 16PK).

and, I want to calculate

  1. the distance between one of its alpha-carbons and the nearest beta-sheet.
  2. the distance between two strands in a beta-sheet (i, j).

How should I proceed to achieve this?


The documentation for the PDB module in biopython, which you have tagged, is very clear about how distances are measured between two given Cα atoms.

To find out the secondary structure and interactions between strands of a sheet, you may want to look at the header of the PDB. This is the stuff before the ATOM/HETATM entries. SHEET entries are what you are after. Please read the PDB format specifications for secondary structure. Biopython PDB does not parse headers well, but reading the file and finding the SHEET entry and positionally splicing out the strings of interest from the entry is beyond straightforward.

Example take from the above link:

         1         2         3         4         5         6         7         8
SHEET    1   A 5 THR A 107  ARG A 110  0
SHEET    2   A 5 ILE A  96  THR A  99 -1  N  LYS A  98   O  THR A 107
SHEET    3   A 5 ARG A  87  SER A  91 -1  N  LEU A  89   O  TYR A  97
SHEET    4   A 5 TRP A  71  ASP A  75 -1  N  ALA A  74   O  ILE A  88
SHEET    5   A 5 GLY A  52  PHE A  56 -1  N  PHE A  56   O  TRP A  71
SHEET    1   B 5 THR B 107  ARG B 110  0
SHEET    2   B 5 ILE B  96  THR B  99 -1  N  LYS B  98   O  THR B 107
SHEET    3   B 5 ARG B  87  SER B  91 -1  N  LEU B  89   O  TYR B  97
SHEET    4   B 5 TRP B  71  ASP B  75 -1  N  ALA B  74   O  ILE B  88
SHEET    5   B 5 GLY B  52  ILE B  55 -1  N  ASP B  54   O  GLU B  73
  • $\begingroup$ what does it mean by i and j in case of beta-sheets? $\endgroup$
    – user366312
    Oct 19 at 18:53
  • $\begingroup$ It likely depends on the context of the paper or textbook... But in the PDB format snippet above sheet A is composed of 5 strands, so the mean distance between the closest Cα atoms in strand i and those in j varies depending on their adjacency... $\endgroup$ Oct 20 at 9:35

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