The above example shows the gap regions between the aspartic protease endothiapepsin and the inhibitor H-189 from PDB code 3er5.
The inhibitor is represented by the bonds and the green wire-cage contours which represent its van der Waals surface.
The gaps between the inhibitor and protein are shown by the red solid surfaces; water atoms are shown in blue.
The inhibitor is viewed from the side of the protein (not shown), meaning that its visible parts, which are not obscured by the gap regions, are those that are directly in contact with the protein.
(Illustration obtained from a PostScript file generated by SURFPLOT).