Atom Nomenclature for PY1

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 PY1

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
N3 N3
N4 N4
C5 C5
C8 C8
C10 C10
N12 N12
C13 C13
C14 C14
C15 C15
C16 C16
C21 C21
C22 C22
N23 N23
C24 C24
C25 C25
C28 C28
C29 C29
C30 C30
C31 C31
HN4 HN4
H5 H5
H13 H13
H14 H14
H15 H15
H16 H16
H24 H24
H25 H25
H28 H28
H29 H29
H30 H30
H31 H31