This paper provides a detailed experimental study of an interface model developed in the companion article F. Cazals and F. Proust, Revisiting the description of Protein-Protein interfaces. Part I: algorithms. Our experimental study is concerned with the usual database of protein-protein complexes, split into five families (Proteases, Immune system, Enzyme Complexes, Signal transduction, Misc.) Our findings, which bear some contradictions with usual statements are the following: (i)Connectivity properties incur important variations across families. These properties are sensitive to water molecules and their variations upon consideration of structural water quantify the filling of packing defects by water molecules. (ii)The model of interfaces as a hydrophilic rim and a hydrophobic core is not general. (iii)At the interface scale, curvature properties correlate with the interface surface area, while locally, the absolute mean curvature follows a bimodal distribution. (iv)About 10% of interfaces consists of several connected components, and this multi-patch structure is independent from structural water. Almost all interfaces feature holes of significant size filled by structural water. Stable crystallographic water molecules play a prominent in reconnecting disconnected interfaces. (v)The chemical composition of interfaces in terms or pairwise contacts features a constant ratio of undetermined interactions, with subtle inter-families variations of determined interactions. Overall, these conclusions shed some light on which structural parameters are most relevant to describe protein-protein interactions.
