Atom Nomenclature for VEK

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 VEK

Atom Name (V3) Atom Name (V2)
C01 C01
C02 C02
C03 C03
C04 C04
C05 C05
N06 N06
C07 C07
C08 C08
N09 N09
C10 C10
C11 C11
BR BR
C13 C13
N14 N14
C15 C15
N16 N16
C17 C17
C18 C18
C19 C19
N20 N20
C21 C21
N22 N22
C23 C23
N24 N24
C25 C25
C26 C26
C27 C27
N28 N28
O29 O29
H01 H01
H01A H01A
H01B H01B
H03 H03
H05 H05
H05A H05A
H07 H07
H07A H07A
H08 H08
H08A H08A
H13 H13
H19 H19
H21 H21
H23 H23
H23A H23A
H23B H23B
HN24 HN24
H26 H26
H26A H26A
H27 H27
H27A H27A