How can I find the the helixID and length of each helix in a PDB file please
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5.6 years ago
ishackm ▴ 110

Hi everyone,

I would like to find the helix ID and the length of each helix in the following PDB file:

https://files.rcsb.org/view/5O5Z.pdb

I can't seem to find it all.

Many Thanks,

Ish

gene protein • 3.3k views
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5.6 years ago
natasha.sernova ★ 4.0k

Your PDB file has HELIX and SHEET records describing where secondary structure exists.

I found 23 HELICES in subunitA (their corresponding lengths are the last number in the strings - 26,3,13,11,etc) and 24 HELICES in subunit B (their lengths are 24,3,13,11,16, etc).

HELIX    1 AA1 LYS A    2  ILE A   27  1                                  26    
HELIX    2 AA2 PRO A   28  VAL A   30  5                                   3    
HELIX    3 AA3 ASP A   48  GLY A   60  1                                  13    
HELIX    4 AA4 GLY A   60  ASN A   70  1                                  11    
HELIX    5 AA5 SER A   77  GLY A   92  1                                  16    
HELIX    6 AA6 SER A  101  GLY A  112  1                                  12    
HELIX    7 AA7 GLY A  120  GLY A  130  1                                  11    
HELIX    8 AA8 PRO A  145  GLU A  150  1                                   6    
HELIX    9 AA9 HIS A  171  ALA A  175  5                                   5    
HELIX   10 AB1 TYR A  213  VAL A  217  5                                   5    
HELIX   11 AB2 ARG A  220  GLY A  226  1                                   7    
HELIX   12 AB3 GLY A  226  ARG A  232  1                                   7    
HELIX   13 AB4 GLY A  241  LEU A  245  5                                   5    
HELIX   14 AB5 THR A  254  TYR A  272  1                                  19    
HELIX   15 AB6 ASN A  285  LEU A  296  1                                  12    
HELIX   16 AB7 PRO A  297  PHE A  299  5                                   3    
HELIX   17 AB8 GLU A  306  GLY A  317  1                                  12    
HELIX   18 AB9 ASP A  318  GLU A  327  1                                  10    
HELIX   19 AC1 HIS A  329  GLY A  345  1                                  17    
HELIX   20 AC2 GLY A  384  GLY A  399  1                                  16    
HELIX   21 AC3 GLY A  403  GLY A  422  1                                  20    
HELIX   22 AC4 ARG A  426  VAL A  436  5                                  11    
HELIX   23 AC5 ASN A  439  PHE A  453  1                                  15    

HELIX   24 AC6 SER B    4  ILE B   27  1                                  24    
HELIX   25 AC7 PRO B   28  VAL B   30  5                                   3    
HELIX   26 AC8 ASP B   48  GLY B   60  1                                  13    
HELIX   27 AC9 GLY B   60  ASN B   70  1                                  11    
HELIX   28 AD1 SER B   77  GLY B   92  1                                  16    
HELIX   29 AD2 SER B  101  GLY B  112  1                                  12    
HELIX   30 AD3 GLY B  120  GLY B  130  1                                  11    
HELIX   31 AD4 PRO B  145  GLU B  150  1                                   6    
HELIX   32 AD5 HIS B  171  ALA B  175  5                                   5    
HELIX   33 AD6 TYR B  213  VAL B  217  5                                   5    
HELIX   34 AD7 ARG B  220  GLY B  226  1                                   7    
HELIX   35 AD8 GLY B  226  ARG B  232  1                                   7    
HELIX   36 AD9 GLY B  241  LEU B  245  5                                   5    
HELIX   37 AE1 THR B  254  TYR B  272  1                                  19    
HELIX   38 AE2 ASN B  285  LEU B  296  1                                  12    
HELIX   39 AE3 PRO B  297  PHE B  299  5                                   3    
HELIX   40 AE4 ASN B  305  GLY B  317  1                                  13    
HELIX   41 AE5 ASP B  318  GLU B  327  1                                  10    
HELIX   42 AE6 HIS B  329  GLY B  345  1                                  17    
HELIX   43 AE7 GLY B  384  GLY B  399  1                                  16    
HELIX   44 AE8 GLY B  403  GLY B  422  1                                  20    
HELIX   45 AE9 ILE B  427  ALA B  433  1                                   7    
HELIX   46 AF1 LEU B  434  VAL B  436  5                                   3    
HELIX   47 AF2 ASN B  439  LYS B  451  1                                  13

I hope I didn't forget how to treat pdb-files.

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Hi Natasha,

Can you post a screenshot of it, please?

I am very new to this

thanks,

Ish

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I did.

Let's consider this line:

HELIX 47 AF2 ASN B 439 LYS B 451 1 13

This is helix 47 of subunit B starting from asparagine 439 going to lysine 451. Its length is 13 amino acids.

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Thank you very much, the documentation is very confusing to me. Thank you also for the explanation for the different lines.

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See also this link.

https://proteinstructures.com/Structure/Structure/proteinstructure-databases2.html

There is some useful information inside.

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f=open('5ogb.pdb') lines=f.readlines()

print lines[337] print lines[338]

print "helixID= AA2"

How can I modify the code so it can print the following please? :

the helix id of each helix and the length, in a list

sheetID, number of strands and the total number of residues, also a list.

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