Atom Nomenclature for EVB

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 EVB

Atom Name (V3) Atom Name (V2)
C11 C1
C12 C2
C13 C3
C14 C4
C15 C5
C17 C6
C18 C7
C19 C8
C20 C9
C21 C10
C22 C11
C23 C12
C1 C13
C2 C14
C3 C15
C4 C16
C5 C17
C6 C18
C7 C19
C8 C20
C9 C21
C10 C22
C16 C23
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
C41 C41
C42 C42
C43 C43
C44 C44
C45 C45
C46 C46
C47 C47
C48 C48
C49 C49
C50 C50
C51 C51
C52 C52
C53 C53
C54 C54
C55 C55
O1 O1
O2 O2
O3 O3
O4 O4
O5 O5
O6 O6
O7 O7
O8 O8
S64 S1
S65 S2
S66 S3
S67 S4
S68 S5
S69 S6
S70 S7
S71 S8
C72 C56
O9 O9
O10 O10
O11 O11
O12 O12
O13 O13
O14 O14
O15 O15
O16 O16
O17 O17
O18 O18
O19 O19
O20 O20
O21 O21
O22 O22
O23 O23
O24 O24
O25 O25
O26 O26
O27 O27
O28 O28
O29 O29
O30 O30
O31 O31
O32 O32
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H6 H6
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29
H30 H30
H31 H31
H32 H32
H33 H33
H34 H34
H35 H35
H36 H36
H37 H37
H38 H38
H39 H39
H40 H40
H41 H41
H42 H42
H43 H43
H44 H44
H45 H45
H46 H46
H47 H47
H48 H48