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Table 1 Interaction classification scheme.

From: Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

Interaction type Type atom i Type atom j Distance Criteria Angle criteria
van der Waals Any any d(a i , a j ) < vdw(a i )+vdw(a j )+0.5Å -
van der Waals clash Any any d(a i , a j )< vdw(a i )+vdw(a j ) -
hydrogen bond* hydrogen bond donor hydrogen bond acceptor d(a i , a j ) < 3.9Å d(a h , a acc ) < 2.5Å θ(a don , a h , a acc ) > 90° θ(a don , a acc , a acc-antecedent ) > 90° θ(a h , a acc , a acc-antecedent ) > 90°
water-mediated hydrogen bond* hydrogen bond donor or acceptor hydrogen bond donor or acceptor d(a i , a j ) < 3.9Å d(a h , a acc ) < 2.5Å θ(a don , a h , a acc ) > 90° θ(a don , a acc , a acc-antecedent ) > 90° θ (a h , a acc , a acc-antecedent ) > 90°
amino-aromatic hydrogen bond* hydrogen bond donor amino-aromatic hydrogen bond acceptor d(a i , a j ) < 3.9Å d(a h , a acc ) < 2.5Å θ(a don ,a acc ,N aromatic-plane ) < 20° θ(a don ,a h ,N aromatic-plane ) < 20°
hydrophobic contact hydrophobic hydrophobic d(a i , a j ) < 5.0Å -
Ionic cationic anionic d(a i , a j ) < 6.0Å -
Aromatic aromatic aromatic d(a i , a j ) < 6.0Å -
π-cation cationic aromatic d(a i , a j ) < 6.0Å -
Disulphide sulphur residue: cys sulphur residue: cys d(a i , a j ) < 2.08Å -
aromatic-sulphur sulphur aromatic d(a i , a j ) < 5.3Å -
Covalent any any d(a i , a j ) < cov(a i ) + cov(a j ) -
Proximal any any d(a i , a j ) < 6.05Å -
  1. Interactions between atom i and atom j are classified based on the atom types of i and j, the distance between them (d) and angle criteria ).
  2. * indicates that the interaction is defined by HBPLUS. The following conventions have been used: d(a i , a j ) = Euclidean distance between atoms ai and aj; vdw(a) = van der Waals radius of atom a; cov(a) = covalent radius of atom a; θ(a 1 , a 2 , a 3 ) = angle at a 2 between a 1 -a 2 and a 2 -a 3 ; a h = donated hydrogen atom; a don = hydrogen bond donor atom; a acc = hydrogen bond acceptor atom; a acc-antecednt = atom antecedent to the hydrogen bond acceptor atom and N aromatic-plane = Normal to aromatic plane. In all cases i and j are exchangeable.