Atom Nomenclature for EAL

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 EAL

Atom Name (V3) Atom Name (V2)
O4 O4
O5 O5
N2 N2
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
H4 H4
H5 H5
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H8C1 1H8C
H8C2 2H8C
O1 O1
C1 C1
C2 C2
C10 C10
HA HA
H101 1H10
H102 2H10
H103 3H10
N1 N1
C3 C3
C4 C4
O2 O2
O3 O3
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
H1 H1
H2 H2
HB HB
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21