Atom Nomenclature for T4J

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 T4J

Atom Name (V3) Atom Name (V2)
N1 N1
C4 C1
C5 C2
C6 C3
C7 C4
C8 C5
C10 C6
N N2
C C7
O O1
C1 C8
C11 C9
C12 C10
C2 C11
C3 C12
C9 C13
O1 O2
S S1
H4 H1
H5 H2
H6 H3
H9 H4
H10 H5
H2 H6
H H7
H15 H8
H1 H9
H11 H10
H12 H11
H13 H12
H14 H13
H3 H14
H7 H15
H8 H16