Atom Nomenclature for COH

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 COH

Atom Name (V3) Atom Name (V2)
CO CO
CHA CHA
CHB CHB
CHC CHC
CHD CHD
NA N A
C1A C1A
C2A C2A
C3A C3A
C4A C4A
CMA CMA
CAA CAA
CBA CBA
CGA CGA
O1A O1A
O2A O2A
NB N B
C1B C1B
C2B C2B
C3B C3B
C4B C4B
CMB CMB
CAB CAB
CBB CBB
NC N C
C1C C1C
C2C C2C
C3C C3C
C4C C4C
CMC CMC
CAC CAC
CBC CBC
ND N D
C1D C1D
C2D C2D
C3D C3D
C4D C4D
CMD CMD
CAD CAD
CBD CBD
CGD CGD
O1D O1D
O2D O2D
HHA HHA
HHB HHB
HHC HHC
HHD HHD
HMA1 1HMA
HMA2 2HMA
HMA3 3HMA
HAA1 1HAA
HAA2 2HAA
HBA1 1HBA
HBA2 2HBA
H2A H2A
HMB1 1HMB
HMB2 2HMB
HMB3 3HMB
HAB HAB
HBB1 1HBB
HBB2 2HBB
HMC1 1HMC
HMC2 2HMC
HMC3 3HMC
HAC HAC
HBC1 1HBC
HBC2 2HBC
HMD1 1HMD
HMD2 2HMD
HMD3 3HMD
HAD1 1HAD
HAD2 2HAD
HBD1 1HBD
HBD2 2HBD
H2D H2D