Table 1 Interaction classification scheme.
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 )+0.5Ã… | - |
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 ) < 5.0Ã… | - |
Ionic | cationic | anionic | d(a i , a j ) < 6.0Ã… | - |
Aromatic | aromatic | aromatic | d(a i , a j ) < 6.0Ã… | - |
Ï€-cation | cationic | aromatic | d(a i , a j ) < 6.0Ã… | - |
Disulphide | sulphur residue: cys | sulphur residue: cys | d(a i , a j ) < 2.08Ã… | - |
aromatic-sulphur | sulphur | aromatic | d(a i , a j ) < 5.3Ã… | - |
Covalent | any | any | d(a i , a j ) < cov(a i ) + cov(a j ) | - |
Proximal | any | any | d(a i , a j ) < 6.05Ã… | - |