Atom Nomenclature for HE5

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 HE5

Atom Name (V3) Atom Name (V2)
O1A O1A
CGA CGA
O2A O2A
C40 C40
CBA CBA
CAA CAA
C2A C2A
C1A C1A
CHA CHA
C3A C3A
CMA CMA
C4A C4A
NA NA
CHB CHB
C1B C1B
C2B C2B
C3B C3B
CAB CAB
NB NB
ZN ZN
ND ND
C4D C4D
C4B C4B
CHC CHC
C1C C1C
C2C C2C
C3C C3C
CAC CAC
NC NC
C4C C4C
CHD CHD
C1D C1D
C2D C2D
CMD CMD
C3D C3D
CAD CAD
CBD CBD
CGD CGD
O1D O1D
O2D O2D
C41 C41
H401 1H40
H402 2H40
H403 3H40
HBA1 1HBA
HBA2 2HBA
HAA1 1HAA
HAA2 2HAA
HHA HHA
HMA1 1HMA
HMA2 2HMA
HMA3 3HMA
HHB HHB
H2B1 1H2B
H2B2 2H2B
H3B H3B
HAB1 1HAB
HAB2 2HAB
HAB3 3HAB
HHC HHC
H2C H2C
HAC1 1HAC
HAC2 2HAC
HAC3 3HAC
HHD HHD
HMD1 1HMD
HMD2 2HMD
HMD3 3HMD
HAD1 1HAD
HAD2 2HAD
HBD1 1HBD
HBD2 2HBD
H411 1H41
H412 2H41
H413 3H41