Subject: Re: CCL:atom names in PDB files

From: Konrad Hinsen <[email-masked]>
Date: Thu, 19 Jul 2001 13:58:09 +0200

> ATOM      1  N   GLN A   1      63.870 -23.035  -4.001  1.00  2.09
> MCP1 N  
> ATOM      2  CA  GLN A   1      65.000 -22.112  -3.695  1.00  1.89
> MCP1 C  
> ATOM      3  C   GLN A   1      64.534 -20.647  -3.880  1.00  1.67
> MCP1 C  
> 
> my question is there are 2 Nitrogens, 5 carbons etc.,..in Glutamine
> residue. how would i know which corresponds to what?

Each atom has a unique name, for example, the "CA" is the alpha
carbon, and "C" is the carbon in the peptide group. Check the PDB
specification for details.

However, some programs use their own naming rules instead of those
defined by the PDB, including widespread codes such as CHARMM and
XPlor. And for hydrogens, the chaos is almost perfect. Moreover, not
all programs respect the rules for atom name justification (right
justification for the element symbol, left justification for the
unique identification part). Alpha-carbons thus are frequently
labelled as calcium atoms.
-- 
-------------------------------------------------------------------------------
Konrad Hinsen                            | E-Mail: [email-masked]
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24
Rue Charles Sadron                       | Fax:  +33-2.38.63.15.17
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais
-------------------------------------------------------------------------------

---

From: Rick Venable <[email-masked]>
Date: Thu, 19 Jul 2001 13:29:19 -0400

> labelled as calcium atoms.

CHARMM follows the same alpha-amino acid atom name conventions as PDB
wrt. heavy atoms for the most part; the exceptions are few (C terminal O
atoms, CD vs. CD1 for ILE).  The only other major issue for CHARMM is
for the HIS residue; CHARMM has 3 separate residues (HSD, HSE, HSC)
depending on the protonation state.

PDB2 format includes the element symbol, so that CA should be recognized
as a carbon atom, if the newer format is used.

Hydrogen naming is systematic in most cases, just different; it's so
difficult to deal with the 1:1 correspondence of H atom names that it's
usually not worth the effort.

If you want to see real chaos, try looking at the heavy atom labels that
come from data extracted from the Cambridge small molecule database,
e.g. for saccharides.

=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   [email-masked]
ALT email:  [email-masked]
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=