Atom Nomenclature for LEE

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 LEE

Atom Name (V3) Atom Name (V2)
N N1
CA C1
C C2
O O1
CB C3
CG C4
CD C5
OE1 O2
OXT O3
N1 N3
CA1 C6
CB1 C7
SG S1
C1 C8
C2 C9
C3 C10
C4 C11
C5 C12
C6 C13
C7 C14
O1 O5
N2 N4
CA2 C15
C8 C16
O2 O6
OXT1 O7
H H1
H2 H2
HA H3
HB2 H4
HB3 H5
HG2 H6
HG3 H7
HXT H10
H1 H11
HA1 H13
HB21 H14
HB31 H15
H11 H16
H12 H17
H21 H18
H22 H19
H31 H20
H32 H21
H41 H22
H42 H23
H51 H24
H52 H25
H61 H26
H62 H27
H63 H28
H3 H30
HA2 H32
HA3 H33
HXT1 H34