Atom Nomenclature for FAF

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 FAF

Atom Name (V3) Atom Name (V2)
CX CX
OX OX
CAX CAX
NL NL
CAL CAL
CBL CBL
CGL CGL
CDL CDL
CDM CDM
C C
O O
N N
CA CA
CB CB
CG CG
CD1 CD1
CD2 CD2
CE1 CE1
CE2 CE2
CZ CZ
CW CW
OW OW
HAX1 1HAX
HAX2 2HAX
HAX3 3HAX
HL HL
HAL HAL
HBL1 1HBL
HBL2 2HBL
HGL HGL
HDL1 1HDL
HDL2 2HDL
HDL3 3HDL
HDM1 1HDM
HDM2 2HDM
HDM3 3HDM
HN HN
HA HA
HB1 HB1
HB2 HB2
HD1 HD1
HD2 HD2
HE1 HE1
HE2 HE2
HZ HZ
HW HW