Atom Nomenclature for AZP

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 AZP

Atom Name (V3) Atom Name (V2)
N N
CAI CAI
OAH OAH
CAG CAG
CAE CAE
CAD CAD
CAC CAC
CAB CAB
CAA CAA
CAF CAF
OAL OAL
CA CA
CB CB
CG CG
CD1 CD1
CD2 CD2
C C
O O
NAS NAS
CAT CAT
CAV CAV
CAW CAW
CBF CBF
CBG CBG
CBH CBH
CBI CBI
CBJ CBJ
CAU CAU
OAY OAY
NAX NAX
NAZ NAZ
CBA CBA
CBB CBB
CBC CBC
NBE NBE
OBD OBD
CBK CBK
OBL OBL
CBM CBM
CBO CBO
OBN OBN
CBP CBP
OBQ OBQ
OBR OBR
CBS CBS
CBT CBT
HN HN
HAG1 1HAG
HAG2 2HAG
HAD HAD
HAC HAC
HAB HAB
HAA HAA
HAF HAF
HA HA
HB1 1HB
HB2 2HB
HG HG
HD11 1HD1
HD12 2HD1
HD13 3HD1
HD21 1HD2
HD22 2HD2
HD23 3HD2
HAS HAS
HAT HAT
HAV1 1HAV
HAV2 2HAV
HBF HBF
HBG HBG
HBH HBH
HBI HBI
HBJ HBJ
HAX HAX
HBA1 1HBA
HBA2 2HBA
HBB1 1HBB
HBB2 2HBB
HBE1 1HBE
HBE2 2HBE
HBM1 1HBM
HBM2 2HBM
HBO HBO
HBN HBN
HBS1 1HBS
HBS2 2HBS
HBT1 1HBT
HBT2 2HBT
HBT3 3HBT