A new method for characterising protein-protein complexes is presented wherein the interface is modelled as a separating surface. This surface is defined by a set of points located halfway on the shortest distance vectors between surface points of the two molecular partners. The surface is generated using a grid-based algorithm. The distance to the nearest atom is stored on the grid points and an isosurface is generated forming the separating surface. Size and shape of the surface characterises the complex interface. Distances, forces, and other physicochemical properties can be mapped onto the surface and are used to study the intermolecular interactions. This is demonstrated with the systems lysozym-antibody, p53-DNA and trypsin-BPTI.