Atom Nomenclature for 86M

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 86M

Atom Name (V3) Atom Name (V2)
C10 C1
C11 C2
C12 C3
C13 C4
C14 C5
C15 C6
C1 C7
O1 O1
C2 C8
C3 C9
C4 C10
C5 C11
C6 C12
O2 O2
C7 C13
C8 C14
C9 C15
N1 N1
N2 N2
N3 N3
C10A H1
C11A H2
C12A H3
C13A H4
C15A H5
HC1A H6
HC1C H7
HC1B H8
HC3A H9
HC5B H10
HC7B H13
HC7A H14
HC9A H15
O3 O3