Atom Nomenclature for T4V

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 T4V

Atom Name (V3) Atom Name (V2)
N1 N1
C4 C1
C5 C2
C6 C3
C7 C4
C8 C5
C10 C6
C13 C7
C15 C8
N N2
C C9
O O1
C1 C10
C11 C11
C12 C12
C14 C13
C16 C14
C2 C15
C3 C16
C9 C17
H6 H2
H7 H3
H8 H4
H9 H5
H10 H6
H11 H7
H14 H8
H16 H9
H15 H10
H H11
H20 H12
H1 H13
H12 H14
H13 H15
H18 H16
H17 H17
H3 H18
H2 H19
H5 H20
H4 H21