Atom Nomenclature for LL4

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 LL4

Atom Name (V3) Atom Name (V2)
CAV CAV
CAU CAU
CAW CAW
CAT CAT
CAS CAS
CAQ CAQ
OAR OAR
NAN NAN
CAO CAO
CAP CAP
CAM CAM
CAL CAL
CAK CAK
CAH CAH
NAG NAG
OAI OAI
NAJ NAJ
CAF CAF
CAE CAE
CAD CAD
CAC CAC
CAB CAB
SAA SAA
HAV HAV
HAVA HAVA
HAVB HAVB
HAU HAU
HAW HAW
HAWA HAWA
HAWB HAWB
HAT HAT
HATA HATA
HAS HAS
HASA HASA
HAO HAO
HAOA HAOA
HAP HAP
HAPA HAPA
HAM HAM
HAMA HAMA
HAL HAL
HALA HALA
HAK HAK
HAD HAD
HAC HAC
HAB HAB