Atom Nomenclature for HI6

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 HI6

Atom Name (V3) Atom Name (V2)
O3 O3
C14 C14
N4 N4
C11 C11
C10 C10
C9 C9
N3 N3
C13 C13
C12 C12
C8 C8
O2 O2
C7 C7
N2 N2
C2 C2
C1 C1
N1 N1
O1 O1
C3 C3
C4 C4
C5 C5
C6 C6
HN41 1HN4
HN42 2HN4
H10 H10
H9 H9
H13 H13
H12 H12
H81 1H8
H82 2H8
H71 1H7
H72 2H7
H1 H1
HO1 HO1
H3 H3
H4 H4
H5 H5
H6 H6