Atom Nomenclature for U66

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 U66

Atom Name (V3) Atom Name (V2)
C C
C1 C1
C2 C2
C3 C3
N N
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
O O
C12 C12
O13 O13
C14 C14
C15 C15
N16 N16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
N25 N25
C26 C26
C27 C27
N28 N28
C29 C29
C30 C30
NZ NZ
H31 1H3
H41 1H4
H51 1H5
H61 1H6
H91 1H9
H92 2H9
H101 1H10
H111 1H11
H121 1H12
H141 1H14
H142 2H14
H151 1H15
H161 1H16
H117 17H1
H181 1H18
H182 2H18
H191 1H19
H192 2H19
H201 1H20
H202 2H20
H231 1H23
H232 2H23
H241 1H24
H261 1H26
H262 2H26
H291 1H29
H301 1H30