This file contains a variety of parameters used in protein modeling. Each parameter is identified by a four-letter keyword and the data for that parameter is terminated with the keyword END. Several data types involve two-dimensional matrices of values for one amino acid type against another amino acid type. The order in which the amino acids appear in the matrix is defined by the keyword ORDEr followed by a list of the 4-letter codes for the amino acids in the appropriate order. The list is terminated with an asterisk (*).
AMINo acid names
This is a list of the residue names which would be recognized as amino acids and displayed in the Sequence Viewer. Any other residue names in a mainly-protein MSF would be regard as solvent or ligand.
name code substitute
name: four letter residue name
code: single character code used in the Sequence Viewer
substitute: for none standard amino acids many parameters have not being derived but parameters for a similar standard amino acid will be substituted if the four-letter name of the similar standard amino acid is entered.
SOLVent
This keyword is followed by a list of four-letter residue names which will be recognized as water. This information is used in the protein specific display utility Molecule Colors on the Protein Utilities palette.
CLASS
This is followed by definitions of the classifications used in coloring sequences:
NAMEclassification
group_type color name_1 name_2 ... name_n
classification: the name of the classification (e.g. Hydrophobicity) This name will appear in the Molecule Colors dialog box for you to select coloring by that classification.
group_type: the name for the type of a group of amino acids color: the color that will be applied to a the group of amino acids
name_1, name_2, ...name_n: the four-letter names for the amino acids which belong to this group
EQUIvalent torsions
lookup
In modeling side chain conformations may be copied between equivalent residues in homologous structures. If the residues are not of identical amino acid type then copying side chain torsions is only reasonable where the side chains have some structural similarity. The following table gives the maximum number of torsions that are copied between pairwise combinations of amino acid types.
PARAM name
Parameters which have one value for each amino acid type are defined. Currently only the ACCESS parameter, the maximum solvent accessible area, is defined here.
ROTAmer rotamer_type
name n_rotamer
sec_str frequency tor_1 tor_2 ... tor_nrotamer_type: the name of the author of the rotamer library name: four character residue name n_rotamer: the number of rotamers for that residue type - the rotamers are list on the following lines
sec_str: if the rotamer is specific for one secondary structure type then H (helix) or E (extended) are indicated
frequency: the observed percentage frequency of that rotamer tor_1, tor_2 ...
tor_n: the ideal torsion values for the rotamer. These are not necessary for all the torsions in the sidechain.
FOLD
n_res sec_str_code name
phi_1 psi_1
phi_2 psi_2
...
phi_n psi_n
The standard backbone folds are defined here and are used to fold a chain in a standard structure in the Apply Conformation utility in the Model Backbone application.
n_res: number of residues in the fold. A negative value implies that the fold can be extended indefinitely.
sec_str_code: A numerical code for the secondary structure type used within QUANTA. The values are:
possible beta strand with appropriate conformation but without correct hydrogen bonding |
|
possible alpha helix with appropriate conformation but without correct hydrogen bonding |
|
name: the name of the fold which will be used in the interface dialog box
phi_n, psi_n: The main chain phi and psi angles, in degrees, for n_res residues. A value of -999.9 implies that there is no defined value for this torsion.