A protein-protein interface (PPI) is defined by a pair of regions of two interacting protein molecules that are linked by non-covalent bonds. Recognition of conserved 3D patterns of physico-chemical interactions may suggest their importance for the function as well as for the stability and formation of the protein-protein complex. It may assist in discovery of new drug leads that target these interactions. We present a novel method, MAPPIS, for multiple structural alignment of PPIs which allows recognition of a set of common physico-chemical properties and their interactions without the need to assume similarity of sequential patterns or backbone patterns. We show its application to several biological examples, such as alignment of interfaces of G proteins with their effectors and regulators, as well as previously created clusters of interfaces.