Atom Nomenclature for R84

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 R84

Atom Name (V3) Atom Name (V2)
C1 C1
O2 O2
C3 C3
C4 C4
C5 C5
O6 O6
C7 C7
C8 C8
C9 C9
C10 C10
N11 N11
C12 C12
O13 O13
C14 C14
C15 C15
C16 C16
O17 O17
O18 O18
S19 S19
O20 O20
O21 O21
N22 N22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
N30 N30
C31 C31
C32 C32
C33 C33
C34 C34
O35 O35
C36 C36
O37 O37
C38 C38
C39 C39
C40 C40
O41 O41
O42 O42
C43 C43
C44 C44
H11C H11C
H12C H12C
H13C H13C
H4 H4
H71C H71C
H72C H72C
H73C H73C
H9 H9
H11 H11
H141 H141
H142 H142
H151 H151
H152 H152
H18 H18
H22 H22
H231 H231
H232 H232
H25 H25
H26 H26
H27 H27
H28 H28
H311 H311
H312 H312
H441 H441
H442 H442
H321 H321
H322 H322
H33 H33
H341 H341
H342 H342
H431 H431
H432 H432
H381 H381
H382 H382
H391 H391
H392 H392
H42 H42