From Protein Structure to Function with Bioinformatics.pdf

168 N.J. Burgoyne and R.M. Jacksonequal to the van der Waals’ radius of the representative atom. The van der Waalssurface is the outermost surface of the atoms. It is infrequently used to describe theprotein surface as the majority of the free space between atoms in the protein issmaller than the solvent atoms (see Fig. 7.1). However, it is the basis of a common3D graphical representation of the molecule in the form of the Corey-Pauling-Koltun (CPK) model, also called the space-filling molecular model.7.1.2 Molecular Surface (Solvent Excluded Surface)A more useful description is the molecular surface, also called the Connolly surface(Connolly 1984). This is the surface made by the contact point of a solvent molecule(commonly water) modelled as a sphere of radius 1.4 Å rolling over the van derWaal’s surface. The molecular surface is similar to the van der Waals contact surfacebut the spaces inaccessible to solvent are covered with a surface known as re-entrant(see Fig. 7.1). As a consequence the molecular surface represents a continuous functionalsurface of the molecule, the surface that is available to interact with.7.1.3 The Solvent Accessible SurfaceThe Solvent Accessible Surface (SAS) is the most commonly used surface representationin structural biology, and was first defined by Lee and Richards (1971).Like the molecular surface it is a functional surface of a protein with respect to theFig. 7.1 Surface definitions: van der Waals surface; molecular surface; solvent accessible surface