Atom Nomenclature for 95V

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 95V

Atom Name (V3) Atom Name (V2)
C5 C1
C7 C2
C10 C3
C3 C4
C2 C5
C15 C6
C16 C7
C17 C8
C18 C9
C19 C10
C20 C11
C22 C12
C24 C13
C25 C14
N21 N1
N4 N2
N6 N3
N8 N4
O11 O1
O13 O2
O14 O3
S1 S1
S23 S2
S9 S3
BR12 BR1
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11