Before the individual options are described, some general remarks about the principle of this module are needed.
WHAT IF can NOT keep track of accessibilities when chnages are made to the SOUP. So, after making mutations, insertions, deletions, etc. you have to issue the INIACC command to initialize all accessibility related parameters, and recalculate the accessibilities with SETACC. Don't worry, the accessibility module in WHAT IF in WHAT IF is the fastest in the world...
Also, some remarks are needed on the accessibility calculation algorithm. There is much confusion in the literature about nomenclature. In WHAT IF the following definitions are being used: The contact surface, or molecular surface, is the area at the Van der Waals surface that can be touched by a water molecule (or any probe, you define that with the WATRAD parameter in the PARAMS menu). The accessible surface area is defined by all positions where the center of that water molecule (or probe) can be found. Re-entrant surfaces are neglected by WHAT IF. Nevertheless, the WHAT IF results always come out within a few procent of the, much fancier but much slower, Connolly program values.
At any one time, WHAT IF can only work with one kind of surface: either the contact (molecular) surface, or the accessible surface. The WHAT IF relational database (see chapter on SCAN3D) holds the accessible surfaces and the contact surfaces for the water probe with radius = 1.4 Angstrom.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
Second a list of residue types will be given. For each of the 20 amino acid types its frequency in the given range, and the average of the observed accessibilities for residues of this type in the given range will be shown.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
The accessibility calculations are done with respect to an environment. You will be prompted for this environment. All molecules that you don't add to this environment are for the accessibility calculations regarded as being absent. Any second calculation of accessibilities will use the same molecules as environment, unless you use the INIENV command in-between. The molecule that holds the residues for which you want to calculate the surface is always part of its own environment.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
You will be prompted for a residue range. The above mentioned calculation will be performed one by one for every residue in the given range. The values obtained are a good approximation for the accessibility in the unfolded state of the protein.
If the normal accessibilities were calculated prior to execution of this option (with the SETACC command) the relative accessibilities are also calculated. Relative accessibilities are the percentage of the accessibility in the unfolded state, still available in the folded protein.
For every residue WHAT IF will show you the same table as given by the LISTA option, but underneath the accessibility and the unfolded state (or vacuum) accessibility the totals are given. Also two extra columns at the right side are added, one for the atomic unfolded state accessibility, and one for percentage.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
ANASRF will first cause WHAT IF to calculate the sum of the buried and and of the accessible surface area for the four backbone atoms (N, Ca, C, O). The same numbers are also calculated for the four atom types (C, N, O, S) that can occur in side chains. For the side chains all atoms of a certain type are added up, so for example Ser-O-gamma and Asp-O-delta2 both are added to the bin for O.
If you are in the business of protein design, and are generating large quantities of potential models, you might want to get an impression about the quality of these models. WHAT IF provides many protein structure quality control tools, e.g. RNGQUA in the QUALTY menu, or EVACHI in the CHIANG menu. The option ANASRF will list the summed accessibilities for this range, and list next to it the average accessibility for that residue type in the June 1991 version of the PDB.
Thereafter a per residue the following information will be shown:
Residue number Residue type PDB unique identifier Molecular surface area Frequency of this residue type in the database Average accessibility of this residue in database Standard deviation in this averaged accessibility Score (whatever that means) for this residue.At the end the total score will be given, and the total score per residue. The so-called sigma score is a very rough estimator for the total quality of the residues in the inspected range.
You might want to experiment a bit with known molecules to see what this sigma score means.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
Proceed as follows:
First calculate the accessibility of the protein, using everything in the environment that is part of the complex, but not the waters. If a few waters are explicitly part of the active site, put them in a separate water group (see WATER menu), and add only that group to the environment.
After that, type DIFACC. This will cause WHAT IF to calculate the accessibilities again, but this time, you add the ligand, or the other molecule to the environment.
Afterwards, you get all kinds of statistics (see SHOACC and ANASRF for an explanation) that are based on the accessibility differences.
Warning. Both before and during the ACCDIF option, you should include ALL residues in the calculation, because the statistics are based on ALL residues.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
All accessibility related options use united heavy atoms, and thus neglect all the protons.
1 2 3 5 8 13 21 34 55 89 144 233 377 610 987The ACPREC+10-th Fibonacci number from this range is the number of dots used. ACPREC can only range from 0 till 4 (is 89 to 610 dots)
WARNING. You should not change WATRAD between calculating the accessible surface and displaying it. After changing WATRAD, the accessible surface, Vanderdot surface, and/or contact surface have to be re-calculated.
1) Dots are put at the Van der Waals radius (VDD-options) or at the sum of the Van der Waals radius and the radius of a water molecule (default =1.4 Angstrom) (for ACC-options).
2) Every dot gets the value 1.
3) Every dot that falls within another sphere gets the value 0.
4) The sum of the values of all dots, divided by the total number, and multiplied with the surface area of the sphere is used as the VDD-value, or the ACC-value.
The dots are placed using a Fibonacci algorithm, which ensures that they are placed on the surface as homogeneously as possible. Since WHAT IF uses 233 dots per surface as the default, and for its databases, the expected precision is roughly 5 percent. Much larger errors however, are introduced by the choice of Van der Waals radii... You can see and change WHAT IF's Van der Waals radii that using the SETVDW menu.
The accessible surface is not to be compared with the well known Connolly surface since reentrant surfaces are not calculated. The WHAT IF molecular surface and the Connolly surface however, agree very well.