Atom Nomenclature for SWE

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 SWE

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
O2 O2
O3 O3
O4 O4
O5 O5
O6 O6
O1 O1
C1' C7
O1' O7
C2' C8
O2' O8
C3' C9
O3' O9
C4' C10
O4' O10
C5' C11
C6' C12
O6' O11
H1 H1
H2 H2
H3 H4
H4 H6
H5 H8
H6 H10
H6A H9
HO2 H3
HO3 H5
HO4 H7
HO6 H11
H1'A H13
H1' H12
HO1' H14
H3' H15
HO3' H16
H4' H17
HO4' H18
H5' H19
H6' H20
H6'A H21
HO6' H22