Appendix 4: Standard Residue Names and Abbreviations

Note that there will be a change to what are considered standard groups due to the adoption of the new PDB Het Group Dictionary. Only the twenty common amino acids and five nucleic acids plus inosine will be treated as "standard" with all others being treated as modified residues to be described by MODRES records.

No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U, I).

Amino Acids

RESIDUE                     ABBREVIATION                SYNONYM
-----------------------------------------------------------------------------
Alanine                     ALA                         A
Arginine                    ARG                         R
Asparagine                  ASN                         N
Aspartic acid               ASP                         D
ASP/ASN ambiguous           ASX                         B
Cysteine                    CYS                         C
Glutamine                   GLN                         Q
Glutamic acid               GLU                         E
GLU/GLN ambiguous           GLX                         Z
Glycine                     GLY                         G
Histidine                   HIS                         H
Isoleucine                  ILE                         I
Leucine                     LEU                         L
Lysine                      LYS                         K
Methionine                  MET                         M
Phenylalanine               PHE                         F
Proline                     PRO                         P
Serine                      SER                         S
Threonine                   THR                         T
Tryptophan                  TRP                         W
Tyrosine                    TYR                         Y
Unknown                     UNK
Valine                      VAL                         V

Nucleic Acids

RESIDUE                                  ABBREVIATION
-----------------------------------------------------------------------
Adenosine                                  A
Modified adenosine                        +A
Cytidine                                   C
Modified cytidine                         +C
Guanosine                                  G
Modified guanosine                        +G
Inosine                                    I
Modified inosine                          +I
Thymidine                                  T
Modified thymidine                        +T
Uridine                                    U
Modified uridine                          +U
Unknown                                  UNK

Remarks 103 and 104 are included when an entry contains inosine.


Appendix 5: Formulas and Molecular Weights for Standard Residues

These weights and formulas correspond to the unpolymerized state of the component. The atoms of one water molecule are eliminated for each two components joined.

Amino Acids

NAME                    CODE           FORMULA                 MOL. WT.
-----------------------------------------------------------------------------
Alanine                 ALA            C3 H7 N1 O2             89.09
Arginine                ARG            C6 H14 N4 O2            174.20
Asparagine              ASN            C4 H8 N2 O3             132.12
Aspartic acid           ASP            C4 H7 N1 O4             133.10
ASP/ASN ambiguous       ASX            C4 H71/2 N11/2 O31/2    132.61
Cysteine                CYS            C3 H7 N1 O2 S1          121.15
Glutamine               GLN            C5 H10 N2 O3            146.15
Glutamic acid           GLU            C5 H9 N1 O4             147.13
GLU/GLN ambiguous       GLX            C5 H91/2 N11/2 O31/2    146.64
Glycine                 GLY            C2 H5 N1 O2             75.07
Histidine               HIS            C6 H9 N3 O2             155.16
Isoleucine              ILE            C6 H13 N1 O2            131.17
Leucine                 LEU            C6 H13 N1 O2            131.17
Lysine                  LYS            C6 H14 N2 O2            146.19
Methionine              MET            C5 H11 N1 O2 S1         149.21
Phenylalanine           PHE            C9 H11 N1 O2            165.19
Proline                 PRO            C5 H9 N1 O2             115.13
Serine                  SER            C3 H7 N1 O3             105.09
Threonine               THR            C4 H9 N1 O3             119.12
Tryptophan              TRP            C11 H12 N2 O2           204.23
Tyrosine                TYR            C9 H11 N1 O3            181.19
Valine                  VAL            C5 H11 N1 O2            117.15
Undetermined            UNK            C5 H6 N1 O3             128.16