Table 1.

Distance criteria (in Å) and atom types for each interaction

Type of interaction	Atom types	Minimum distance	Maximum distance
Aromatic stacking	Two aromatic atoms	1.5	3.5
Disulfide bridge	Two cysteines	1.4	2.3
Hydrogen bond	An acceptor and a donor atom	2.0	3.0
Hydrophobic	Two hydrophobic atoms	2.0	3.8
Repulsive	Two atoms with the same charge	2.0	6.0
Salt bridges	Two atoms with opposite charge	2.0	6.0