Atom Nomenclature for SMK

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 SMK

Atom Name (V3) Atom Name (V2)
CAA CAA
CB CB
CA CA
N N
C C
O O
NAY NAY
CBI CBI
CBB CBB
OAF OAF
NBK NBK
CBF CBF
CAS CAS
CAQ CAQ
NAB NAB
CAT CAT
CAU CAU
CBG CBG
CAV CAV
CAW CAW
CBJ CBJ
CBA CBA
OAE OAE
NAX NAX
CBH CBH
CBC CBC
CAM CAM
CAI CAI
CAG CAG
CAJ CAJ
CAN CAN
CBD CBD
CAO CAO
CAK CAK
CAH CAH
CAL CAL
CAP CAP
HAA HAA
HAAA HAAA
HAAB HAAB
HB HB
HBA HBA
HA HA
HN HN
HNA HNA
HNAY HNAY
HBI HBI
HBF HBF
HAS HAS
HASA HASA
HAQ HAQ
HAQA HAQA
HNAB HNAB
HNAA HNAA
HAT HAT
HATA HATA
HAU HAU
HAUA HAUA
HBG HBG
HAV HAV
HAVA HAVA
HAW HAW
HAWA HAWA
HBJ HBJ
HNAX HNAX
HBH HBH
HAM HAM
HAI HAI
HAG HAG
HAJ HAJ
HAN HAN
HAO HAO
HAK HAK
HAH HAH
HAL HAL
HAP HAP