Glossary

The elements of the data bank DIP

The Motivation for creating the data bank was to obtain representative pairs of complementary surfaces (interfaces) from protein structures. Direct contact in this context means that atomic vdW surfaces are closer than a given cut-off distance.
The basic elements of our dictionary of interfaces of proteins are molecular surface patches of protein substructures. Due the fact that the exterior and the interior surfaces do not show any genuine "starting point", and a particular substructure has more than one neighbor, a meaningful dissection of this continuous molecular surface area had to be introduced. This procedure corresponds to a widespread approach to disintegrate multiple problems into a number of pair-problems. Therefore we selected an unambiguous, reversible procedure to divide the protein structure, as well as the interface between protein and solvent, into patches. After the dissection of the molecular surface the patches were stored in a data bank, which enables fast similarity screening.

secondary structural element (SSE) unit of secondary structure according to the algorithm of DSSP (Kabsch & Sander, 1983); only three types are used: alpha-helix, extended structure and coils

non-protein elements ligands, substrates (hetero-atoms), explicit inner solvent, virtual outer solvent (described as continuum and considered as one large structure)

cut-off allowed maximum distance between vdW spheres of an atomic contact (max. 2.8Å)

neighboring atoms (atoms in contact) two atoms (from different SSEs) within a distance smaller than the sum of their vdW radii and the cut-off value

atomic surface area surface area defined according to Connolly (1983); (surface around the protein which is not accessible for a solvent molecule)

inner Connolly surface surface enclosing cavities within proteins (larger than one water molecule)

molecular surface patch (MSP) set of atoms of a given secondary structure which are in contact with atoms of another structure (secondary structural element, solvent, ligands)

external MSP all atoms of one secondary structure which are in contact with the Connolly surface of the protein

interface (internal) pair of MSPs from different structural elements in direct contact

secondary structural element (SSE)	unit of secondary structure according to the algorithm of DSSP (Kabsch & Sander, 1983); only three types are used: alpha-helix, extended structure and coils
non-protein elements	ligands, substrates (hetero-atoms), explicit inner solvent, virtual outer solvent (described as continuum and considered as one large structure)
cut-off	allowed maximum distance between vdW spheres of an atomic contact (max. 2.8Å)
neighboring atoms (atoms in contact)	two atoms (from different SSEs) within a distance smaller than the sum of their vdW radii and the cut-off value
atomic surface area	surface area defined according to Connolly (1983); (surface around the protein which is not accessible for a solvent molecule)
inner Connolly surface	surface enclosing cavities within proteins (larger than one water molecule)
molecular surface patch (MSP)	set of atoms of a given secondary structure which are in contact with atoms of another structure (secondary structural element, solvent, ligands)
external MSP	all atoms of one secondary structure which are in contact with the Connolly surface of the protein
interface (internal)	pair of MSPs from different structural elements in direct contact