Atom Nomenclature for BLN

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 BLN

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C5 C5
C6 C6
O1 O1
O2 O2
N1 N1
N N
CA CA
CB CB
CG CG
CD1 CD1
CD2 CD2
C C
O O
CB' CB'
N' N'
OG OG
CD CD
C1' C1'
C2' C2'
C3' C3'
C4' C4'
C5' C5'
C6' C6'
C' C'
N40 N40
CA' CA'
HC21 1HC2
HC22 2HC2
HC31 1HC3
HC32 2HC3
HC51 1HC5
HC52 2HC5
HC61 1HC6
HC62 2HC6
HN HN
HCA HCA
HCB1 1HCB
HCB2 2HCB
HCG HCG
HD11 1HD1
HD12 2HD1
HD13 3HD1
HD21 1HD2
HD22 2HD2
HD23 3HD2
HB'1 1HB'
HB'2 2HB'
HN' HN'
HCD1 1HCD
HCD2 2HCD
H2'C CH2'
H3'C CH3'
H4'C CH4'
H5'C CH5'
H6'C CH6'
HA'C CHA'