Atom Nomenclature for ABS

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 ABS

Atom Name (V3) Atom Name (V2)
P P
OP1 O1P
OP2 O2P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C1' C1*
N9 N9
C4 C4
N3 N3
C2 C2
N1 N1
C6 C6
N6 N6
CA CA
OA OA
CB CB
CS6 CS6
CS1 CS1
CS5 CS5
CS2 CS2
CS4 CS4
CS3 CS3
C5 C5
N7 N7
C8 C8
C2' C2*
C3' C3*
O3' O3*
OP3 O3P
HOP2 2HOP
H5' 1H5*
H5'' 2H5*
H4' H4*
H1' H1*
H2 H2
H6 H6
HA HA
HOA HOA
HB1 HB1
HB2 HB2
HS1 HS1
HS5 HS5
HS2 HS2
HS4 HS4
HS3 HS3
H8 H8
H2' 1H2*
H2'' 2H2*
H3' H3*
HO3' H3T
HOP3 3HOP