As the surface actually models that region of space that a probe sphere cannot penetrate, many distracting features are removed from the proteins appearance. Molviewer-ogl allows the construction of partial molecular surfaces. The surface has been generated as if all aminoacid atoms were present in the calculation. On this scale the binding site is an obvious feature and we can see the complementarity between the shape of the surface and the bound sugar. Here we see the molecular surface around the binding site colour coded according to electrostatic potential.
Colouring is red for negative and blue for positive.
A slightly closer look at the binding site of neuraminidase. Now the surface is coloured according to distance to the nearest atom of the bound sialic acid. Red indicates a close contact. Note how the rear of the binding pocket is white, indicating no significant contacts between the sialic acid and the protein in this region. Protein Schematics Useful ways of simplifying the complexity of protein structures are to use backbone schematics to show the fold of the polypeptide chain.