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The following are the first 14 atoms from the protein 1CRN:

ATOM      1  N   THR A   1      17.047  14.099   3.625  1.00 13.79           N  
ATOM      2  CA  THR A   1      16.967  12.784   4.338  1.00 10.80           C  
ATOM      3  C   THR A   1      15.685  12.755   5.133  1.00  9.19           C  
ATOM      4  O   THR A   1      15.268  13.825   5.594  1.00  9.85           O  
ATOM      5  CB  THR A   1      18.170  12.703   5.337  1.00 13.02           C  
ATOM      6  OG1 THR A   1      19.334  12.829   4.463  1.00 15.06           O  
ATOM      7  CG2 THR A   1      18.150  11.546   6.304  1.00 14.23           C  

ATOM      8  N   THR A   2      15.115  11.555   5.265  1.00  7.81           N  
ATOM      9  CA  THR A   2      13.856  11.469   6.066  1.00  8.31           C  
ATOM     10  C   THR A   2      14.164  10.785   7.379  1.00  5.80           C  
ATOM     11  O   THR A   2      14.993   9.862   7.443  1.00  6.94           O  
ATOM     12  CB  THR A   2      12.732  10.711   5.261  1.00 10.32           C  
ATOM     13  OG1 THR A   2      13.308   9.439   4.926  1.00 12.81           O  
ATOM     14  CG2 THR A   2      12.484  11.442   3.895  1.00 11.90           C  

These fourteen atoms are members of two THR residues.

Can the information regarding atomic bonds be interpreted only from these fourteen lines?

For example,

  • the first atom, N, has three bonds attached to CA.
  • the second atom, CA, has four bonds; three are attached to N, and one is to C.
  • the third atom, C, has four bonds; one is attached to CA, one to oxygen, and two are empty.
  • the fourth atom, O, has two bonds; one is attached to the third carbon, and one is to the fifth atom beta-carbon.
  • the fifth atom, beta-carbon, has four bonds; one is attached to the fourth atom, two are attached to the first branch (OG1), and one is attached to the second branch (CG2).

Or do I have to use my background knowledge of amino acids to find bonds?

Note: I am not talking about hydrogen bonds. I am talking about atomic bonds only in the atoms in the residue.

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2 Answers 2

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The official list of bonds in each residue in the PDB is in the Chemical Component Dictionary.

You could also use interatomic distances to infer connectivity, but that's less reliable.

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You can use topology files to extract bond information. Here is an example at CHARMM36

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