Atom Nomenclature for D95

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 D95

Atom Name (V3) Atom Name (V2)
CAA C1
CAB C2
CAC C3
CAD C4
CAE C5
CAF C6
CAG C7
CAI C8
CAJ C9
CAK C10
CAL C11
CAM C12
CAN C13
CAR C14
CAT C15
CAV C16
CAW C17
CAX C18
CBA C19
OAH O1
OAO O2
OAP O3
OAQ O4
OAS O5
OAU O6
OAY O7
OAZ O8
HAA H1
HAB H2
HAC H3
HAD H4
HAF H5
HAE H6
HAG H7
HAH H8
HAI H9
HAJ H10
HAK H11
HAL H12
HAM H13
HAN H14
HAO H15
HAQ H16
HAP H17
HAR H18
HAT H19
HAS H20
HAV H21
HAW H22
HAY H23
HAX H24
HBB H25
HBA H26
HBC H27
H1 H28