SURFNET Operating Manual

5. Gaps between molecules

The gap regions or crevices between two molecules can give an indication of how closely the molecules fit against one another. Large gap regions can show where alternative sidechains might give a better fit; conversely, an absence of gap regions can show where the molecules fit tightly together.

SURFNET computes all the gap regions between two molecules by fitting spheres between all pairs of atoms and reducing the spheres until all clashes with other atoms are avoided, as described in Appendix C.

The plot below shows a protein-inhibitor complex and the gap regions between the two. The protein is the aspartic protease endothiapepsin (yellow) and its inhibitor is pepstatin (red), taken from the structure in the PDB file 3er5. The gap regions between the two surfaces are shown in blue. 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
Gap regions between endothiapepsin and its inhibitor, pepstatin
 
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
inhibitor    S   2391    2482   100.0       8         8        0.1
gaps         G      1       2   100.0       5         5        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

Here three output files are defined under the OUTPUT FILES keyword. One .srf file will be generated for each: protein.srf, inhibitor.srf and gaps.srf. The gap regions in gaps.srf will be the regions between the atoms of file 1 (the protein) and file 2 (the inhibitor).

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

The plot below shows just the inhibitor (red) and the gap regions (blue) surrounding it. The gaps around the right-hand end are especially large as, in the crystal structure, this end sticks out into the solvent and away from the protein.