<p>The official list of bonds in each residue in the PDB is in the <a href="https://www.wwpdb.org/data/ccd" rel="nofollow noreferrer">Chemical Component Dictionary</a>.</p>
<p>You could also use interatomic distances to infer connectivity, but that's less reliable.</p>

CC BY-SA 4.0
2022-11-24T18:46:32.797Z
2022-11-24T18:46:32.797Z
marcin
<p>You can use topology files to extract bond information.
Here is an example at <a href="https://charmm-gui.org/?doc=open_toppar&amp;filename=top_all36_prot.rtf" rel="nofollow noreferrer">CHARMM36</a></p>

CC BY-SA 4.0
2022-11-23T10:56:16.683Z
2022-11-23T10:56:16.683Z
SuleymanSelim
<p>The following are the first 14 atoms from the protein <strong>1CRN</strong>:</p>
<pre><code>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  
</code></pre>
<p>These fourteen atoms are members of two <strong>THR</strong> residues.</p>
<p>Can the information regarding atomic bonds be interpreted only from these fourteen lines?</p>
<p>For example,</p>
<ul>
<li>the first atom, N, has three bonds attached to CA.</li>
<li>the second atom, CA, has four bonds; three are attached to N, and one is to C.</li>
<li>the third atom, C, has four bonds; one is attached to CA, one to oxygen, and two are empty.</li>
<li>the fourth atom, O, has two bonds; one is attached to the third carbon, and one is to the fifth atom beta-carbon.</li>
<li>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).</li>
</ul>
<p>Or do I have to use my background knowledge of amino acids to find bonds?</p>
<p><strong>Note:</strong> I am not talking about hydrogen bonds. I am talking about atomic bonds only in the atoms in the residue.</p>

<proteins>
Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?
# Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?

(Asked by: username_0 on 2022-11-22)

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.

**Tags:** proteins

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## 2 answers

### Answer by username_1 on 2022-11-24. Score: 2

The official list of bonds in each residue in the PDB is in the [Chemical Component Dictionary](https://www.wwpdb.org/data/ccd).

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


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### Answer by username_2 on 2022-11-23. Score: 1

You can use topology files to extract bond information.
Here is an example at [CHARMM36](https://charmm-gui.org/?doc=open_toppar&filename=top_all36_prot.rtf)


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