Atom Nomenclature for CTT

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 CTT

Atom Name (V3) Atom Name (V2)
C2B C2
C3B C3
C4B C6
C5B C4
C6B C5
C1B C1
O1B O1
O2B O2
O3B O3
O4B O6
O5B O4
O6B O5
C2C C8
C3C C9
C4C C12
C5C C10
C6C C11
C1C C7
O2C O7
O3C O8
O4C O11
O5C O9
O6C O10
C2D C14
C3D C15
C4D C18
C5D C16
C6D C17
C1D C13
O2D O12
O3D O13
O4D O16
O5D O14
O6D O15
C2E C20
C3E C21
C4E C22
C5E C23
C6E C24
C1E C19
O2E O17
O3E O18
O4E O19
O5E O20
O6E O21
H2B H3
H3B H5
H4B H11
H5B H7
H6B H9
H6BA H8
H1B H2
HO1B H1
HO2B H4
HO3B H6
HO6B H10
H2C H13
H3C H15
H4C H21
H5C H17
H6C H19
H6CA H18
H1C H12
HO2C H14
HO3C H16
HO6C H20
H2D H23
H3D H25
H4D H31
H5D H27
H6D H29
H6DA H28
H1D H22
HO2D H24
HO3D H26
HO6D H30
H2E H33
H3E H35
H4E H37
H5E H39
H6E H41
H6EA H40
H1E H32
HO2E H34
HO3E H36
HO4E H38
HO6E H42