Atom Nomenclature for HQA

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 HQA

Atom Name (V3) Atom Name (V2)
OXT OXT
C C
O O
CA CA
N N
C03 C03
C04 C04
C05 C05
N06 N06
C07 C07
C08 C08
O09 O09
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
HOXT HOXT
HA HA
HN HN
HNA HNA
H03 H03
H03A H03A
H05 H05
HO09 HO09
H10 H10
H11 H11
H12 H12
H14 H14