Atom Nomenclature for TDD

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for TDD

Atom Name (V3) Atom Name (V2)
N N
CA CA
CB CB
CG1 CG1
CG2 CG2
CG3 CG3
C C
O O
OXT OXT
H H
H2 H2
HA HA
HG11 HG11
HG12 HG12
HG13 HG13
HG21 HG21
HG22 HG22
HG23 HG23
HG31 HG31
HG32 HG32
HG33 HG33
HXT HXT