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Can I infer it from the atom name alone? Or do I need to look at the structure of the residue it is in?

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  • $\begingroup$ Can you add background to your research, why you need to know, and explain what PDB is? $\endgroup$
    – AliceD
    Commented Apr 11 at 10:51
  • $\begingroup$ PDB is a file format that was used with the Protein Data Bank to record information on the position and relations of atoms in a molecule. $\endgroup$
    – mgkrebbs
    Commented Apr 11 at 16:51

1 Answer 1

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Looking at the ATOM records for an Ala residue, as an example:

ATOM 132 N ALA A 33 0.179 -33.349 1.978 1.00 18.93 N

ATOM 133 CA ALA A 33 0.316 -32.425 0.863 1.00 21.72 C

ATOM 134 C ALA A 33 -0.617 -32.824 -0.275 1.00 24.91 C

ATOM 135 O ALA A 33 -0.538 -33.915 -0.831 1.00 23.04 O

ATOM 136 CB ALA A 33 1.764 -32.365 0.428 1.00 15.90 C

I've bolded the name field. The carbonyl carbon is designated C and the carbonyl oxygen is designated O. See here for a note on nomenclature:

Atoms names follow the recommendations of described in Pure & Appl. Chem., 70, 117-142, 199

And from that IUPAC publication:

In the peptide backbone, the nitrogen is denoted by N, its attached hydrogen by H, and the carbonyl carbon and oxygen by C and 0, respectively (ref. 20).

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