# Version: August 13, 1993 # # LIBRARY OF RESIDUE TYPES # # MODELLER 1.1, Copyright Andrej Sali # # # Several residue naming schemes exist: # # (1) Three-letter Brookhaven Protein Data Bank, extended. # (2) Single-letter Brookhaven Protein Data Bank, extended. # (3) Four letter CHARMM, extended. # # # This file gives: # # (1) The residue names in those three sets. # (2) Equivalences between the three sets. # # Each residue type may have several PDB-3 names, but only one PDB-1 # name and one CHARMM name. The naming schemes are case sensitive. If # a certain existing CHARMM residue type does not have an equivalent # in the PDB-1/3 lists, its name is invented, or the name of a similar # residue is used. In contrast, if an existing PDB residue type does # not occur in the CHARMM list, its name is kept undefined (####) # so that the lack of the CHARMM topology entry is properly flagged. # This means that a certain residue's name may appear several times # within the same scheme (for example, CHARMM charged and neutral # species are not distinguished in the PDB list). # # Each residue type can be ATOM, DEFATM, or HETATM. The first two # correspond to PDB ATOM records, and the last to HETAM. # # The first 21 residue types are hard-coded, and their order should not be # changed. For certain applications (e.g. alignment) only these residue types # are supported. Other residues will be treated as equivalent to that named # in the 'STD' column, or if blank, as the default residue type defined on # the DEFATM line. # # To add a new residue type, simply add a new line to the end of this file. # Note that multiple names can be listed in the PDB-3 column, because PDB # can use different names for the same residue type (e.g. water can be HOH, # WAT, etc.). The PDB-1 code must be a single character. It does not have to # be unique, but if it is not unique you cannot use it in the alignment file. # Any character is fine (it does not have to be a letter). If you run out of # characters you can re-define the existing ones that you do not need. The # CHARMM field gives the four-character CHARMM residue name, as specified # in the RESI record of the topology library. # # # TYPE PDB-3 PDB-1 STD CHARMM DESCRIPTION #------------------------------------------------------------------------------- ATOM | ALA | A | | ALA | alanine ATOM | CYS CSH | C | | CYS | cysteine ATOM | ASP | D | | ASP | aspartic acid, +1 ATOM | GLU | E | | GLU | glutamic acid, +1 ATOM | PHE | F | | PHE | phenylalanine DEFATM | GLY | G | | GLY | glycine ATOM | HIS | H | | HIS | histidine, neutral, proton on ND1 (HSD originally) ATOM | ILE | I | | ILE | isoleucine ATOM | LYS | K | | LYS | lysine, +1 ATOM | LEU | L | | LEU | leucine ATOM | MET | M | | MET | methionine ATOM | ASN | N | | ASN | asparagine ATOM | PRO PR0 PRZ | P | | PRO | proline ATOM | GLN | Q | | GLN | glutamine ATOM | ARG | R | | ARG | arginine, +1 ATOM | SER | S | | SER | serine ATOM | THR | T | | THR | threonine ATOM | VAL | V | | VAL | valine ATOM | TRP | W | | TRP | tryptophan ATOM | TYR | Y | | TYR | tyrosine ATOM | GAP | - | | GAP | an alignment gap ATOM | ASX | B | N | ASX | ASP/ASN ambiguous ATOM | GLX | Z | Q | GLX | GLU/GLN ambiguous ATOM | UNK MSE | X | A | UNK | unknown residue type HETATM | PCA PGA | p | | #### | pyrrolidine carboxylic acid (pyroglutamate) ATOM | HSE | 6 | | HSE | histidine, neutral, proton on NE2 ATOM | HSP | 7 | | HSP | histidine, +1 (proton on NE2 and ND1) HETATM | HOH H2O OH2 MOH WAT | w | | TIP3 | water HETATM | CA CAL | 3 | | CAL | calcium ion, +2 HETATM | ZN ZN2 | z | | ZN2 | zinc, +2 HETATM | HEM | h | | HEME | heme ligand HETATM | OXY O2 | o | | O2 | O2 ligand for heme HETATM | CMO CO | b | | CO | CO ligand for heme HETATM | CYS CSS CYX | C | | CSS | cystine HETATM | BRK | / | - | BRK | chain break HETATM | HIS | H | H | HIS | histidine for TOPH19 HETATM | HIS | H | H | HSC | doubly protonated HIS for TOPH19 HETATM | BLK | . | | BLK | BLOCK, place holder HETATM | GDP | x | | GDP | GDP HETATM | GTP | y | | GTP | GTP HETATM | ATP | @ | | ATP | ATP HETATM | MG | $ | | MG | magnesium ion ATOM | A ADE | a | | ADE | Adenine (RNA) ATOM | C CYT | c | | CYT | Cytosine (RNA) ATOM | G GUA | g | | GUA | Guanine (RNA) ATOM | T THY | s | | THY | Thymine (RNA) ATOM | U URA | u | | URA | Uracil (RNA) ATOM | DA | e | | DADE | Adenine (DNA) ATOM | DC | j | | DCYT | Cytosine (DNA) ATOM | DG | l | | DGUA | Guanine (DNA) ATOM | DT | t | | DTHY | Thymine (DNA) ATOM | DU | v | | DURA | Uracil (DNA) HETATM | K | % | | K | potassium ion HETATM | ADE | # | | ADE | HETATM | CYT | # | | CYT | HETATM | ADP | & | | ADP | adenosine diphosphate, jjp1/adm jr. HETATM | DEO | d | | DEOT | DEOXYRIBOSE, Wilma Olsen's dihedral model HETATM | DMP | m | | DMPA | Dimethylphosphate HETATM | DUM | # | | DUM | DUMMY ATOM HETATM | GUA | # | | GUA | HETATM | MP_ | 0 | | MP_0 | Methylphosphate, neutral HETATM | MP_ | 1 | | MP_1 | Methylphosphate, anionic HETATM | MP_ | 2 | | MP_2 | Methylphosphate, dianionic HETATM | NAD | n | | NAD | oxidized nicotinamide adeine dinucleotide, jjp1/adm jr. HETATM | NAD | 4 | | NADH | reduced nicotinamide adenine dinucleotide, jjp1/adm jr. HETATM | NCA NIC | k | | NIC | oxidized nicotinamide, jjp1/adm jr. HETATM | NIC | 5 | | NICH | reduced nicotinamide, jjp1/adm jr. HETATM | PPI | f | | PPI1 | Inorganic phosphate, jjp1/adm jr. HETATM | RIB | r | | RIBT | RIBOSE, Wilma Olsen's dihedral model HETATM | NA SOD | i | | SOD | Sodium Ion HETATM | THY | # | | THY | HETATM | URA | # | | URA | HETATM | PEN | # | | PEN | Penicillamine for TOPH19 HETATM | FRM | # | | FORM | for TOPH19 HETATM | AMN | # | | AMN | for TOPH19 HETATM | CBX | # | | CBX | for TOPH19 HETATM | ETH | # | | ETH | for TOPH19 HETATM | OHH | # | | OH2 | TIPS3P water model for TOPH19 HETATM | COH | # | | COH | for TOPH19 HETATM | ST2 | # | | ST2 | for TOPH19 HETATM | NAG | 1 | | NAG | N-ACETYL-D-GLUCOSAMINE HETATM | MAN | 2 | | MAN | ALPHA-D-MANNOSE HETATM | MN | 4 | | MN | manganese ion, +2 HETATM | MYR | 5 | | MYR | MYRISTATE HETATM | IGL | q | | IGLN | iso-glutamin HETATM | 156 | i | | 0156 | 0156 HETATM | ABU | g | | #### | amino-butyric acid HETATM | ACD | d | | #### | acidic unknown HETATM | ALB | l | | #### | beta-alanine HETATM | ALI | a | | #### | aliphatic unknown HETATM | ARO | r | | #### | aromatic unknown HETATM | BAS | b | | #### | basic unknown HETATM | HYP | # | | #### | hydroxyproline HETATM | SAR | s | | #### | sarcosine HETATM | FOR | f | | #### | formyl HETATM | MSE | X | M | UNK | selenomethionine HETATM | MEX | C | | #### | cysteine bridged with beta-mercaptoethanol HETATM | SO4 | # | | SO4 | sulphate ion -2 HETATM | ABU | # | | #### | similar to Cys, but SG->CG