SURFNET Operating Manual

6. Clefts and cavities

SURFNET can compute all the clefts and cavities in a given protein structure. This is particularly useful for extracting and examining the cleft corresponding to the protein's binding site (usually the largest of the clefts).

The clefts and cavities are defined as all gap regions in the protein structure. These are computed by fitting spheres between all pairs of atoms in the protein, reducing the size of each one until all clashes with other atoms are avoided, as described in Appendix C.

The plot below shows the gap-regions in the aspartic protease endothiapepsin from the PDB file 3er5. The surface of the protein is shown in yellow while all its clefts and cavities are depicted in lilac. The plot was produced using the solid rendering of InsightII.

The surfnet.par file used in generating the above plot is shown below, with the section keywords in bold.

For a detailed explanation of all the parameters involved, see Editing the surfnet.par file.

Parameters for SURFNET              (surfnet.par)
----------------------
 
TITLE
Endothiapepsin: Clefts and cavities
 
INPUT FILE
/data/pdb/3er5.pdb

Output files listed below. The information entered for each is as follows.
The numbers in square brackets refer to the notes at the end of the file.
The program names indicate which programs need to be rerun when any of the
parameters are changed.

            <----SURFNET----><-SURFACE-><----------SURFPLOT------------>
                                        Foregrnd  Backgrnd        
                   Atom range            colour    colour     Line 
          File     1st   Last  Contour   /shade    /shade     width  SOLID
Filename  type[1] atom   atom  level[2]  (0-10)[3] (0-10)[3]   [4]  /WIRE

OUTPUT FILES
protein      S      1    2390   100.0       1         1        0.1
gaps         G      0       0   100.0       9         9        0.1

Program parameters
------------------

SURFNET
  0.0   0.0   0.0  <- Origin of grid box (to use: set atom range below to 0 0)
-1000 10000     <- Atom range defining grid bounds (0 0 to use origin above)
6.0 6.0 6.0     <- Additional boundary round atom-range/origin (Angstroms)
0.80      <- Grid separation
1.0       <- Minimum radius for gap spheres (in Angstroms)
4.0       <- Maximum radius for gap spheres (in Angstroms)
I         <- (C)CP4, (I)nsightII, (Q)uanta, (S)ybyl contour files, or (N)one
Y         <- Calculate gap volume - (Y/N)?
1.0       <- Scaling factor

Two output files are defined under the OUTPUT FILES keyword above. One .srf file will be generated for each: protein.srf and gaps.srf.

The output format has been defined as InsightII (I in line 7 of the SURFNET parameters) so the program will also write out two files in InsightII grid format: protein.grd and gaps.grd.

The plot below shows just the gap regions (lilac) with the protein removed. The largest one (in the middle of the picture) corresponds to the protein's binding site where the inhibitor binds and can be separately extracted and displayed (see Extracting and comparing gap regions).