Atom Nomenclature for INT

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 INT

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
O1 O1
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
N1 N1
C10 C10
C11 C11
O2 O2
C12 C12
CG1 CG1
CG2 CG2
N2 N2
C19 C19
O4 O4
C18 C18
C20 C20
N4 N4
C31 C31
O8 O8
O9 O9
CA CA
C C
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
H1 H1
H21 1H2
H22 2H2
HO1 HO1
H31 1H3
H32 2H3
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
HN1 HN1
H10 H10
H12 H12
HG11 1HG1
HG12 2HG1
HG13 3HG1
HG21 1HG2
HG22 2HG2
HG23 3HG2
HN2 HN2
H18 H18
H201 1H20
H202 2H20
H203 3H20
HN4 HN4
HA1 1HA
HA2 2HA
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17