The Van der Waals surface is that formed by those parts of each atomic sphere which lies outside of all other atomic spheres. A contour surface is a general suface which seperates 3D space into regions of greater than and less than a value associated with the surface. Note that molecular, accessible and VdW surfaces are all subclasses of contour surfaces. The tesselation more commomly used, and which I make use of herein, is the triangular tesselation. A surface is termed closed if each triangle edge is shared with exactly one other triangle.
Exceptions occur for weak ligands such as sugars and for ions.
Electrostatic complementarity between surfaces of protein and small ligand is rigorously enforced, although exceptions may occur within large protein-protein surfaces. NET charge ANTI-complementarity is almost universal between proteins and small ligands. Examples of each pattern will be presented. The correlation of such patterns with protein function, and methods to make such observations automatic and quantifiable will constitute the bulk of this paper. Each example will utilize progressively greater quantification and automation of comparison procedures.