Atom Nomenclature for FA6

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 FA6

Atom Name (V3) Atom Name (V2)
O2 O2
C7 C7
O1 O1
C1 C1
O3 O3
C2 C2
C3 C3
N1 N1
O6 O6
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
H1 H1
H3 H3
H2C1 1H2C
H2C2 2H2C
H6 H6
H4C H4C
H4 H4
H5C H5C
H5 H5
H6C1 1H6C
H6C2 2H6C