Atom Nomenclature for WAY

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 WAY

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
CF2 CF2
CH CH
CF1 CF1
C6 C6
C10 C10
O11 O11
N12 N12
O13 O13
CE CE
N20 N20
S21 S21
CD CD
CK CK
CM CM
N25 N25
CJ CJ
C27 C27
CI CI
C35 C35
CC1 CC1
CB1 CB1
C38 C38
CB2 CB2
CC2 CC2
O45 O45
CA CA
O50 O50
O51 O51
HF2 HF2
HH HH
HF1 HF1
H14 H14
H15 H15
HE1 HE1
HE2 HE2
HE3 HE3
HD1 HD1
HD2 HD2
HK HK
HL HL
HJ HJ
HI HI
HC1 HC1
HB1 HB1
HB2 HB2
HC2 HC2
HA1 HA1
HA2 HA2
HA3 HA3