Getcontacts

Interaction analysis for protein structures and dynamics

The following table defines criteria for interactions that are recognized by GetContacts. All numerical values can be changed from the command-line if needed.

Interaction type Illustration Geometric criteria Chemical criteria
Hydrogen bond
  • hbbb - backbone to backbone
  • hbsb - side-chain to backbone
  • hbss - side-chain to side-chain
  • lbs - ligand to side-chain
  • lbb - ligand to backbone
|AD| < 3.5Å
∠AHD < 70°

A (acceptor) and D (donor) are any atom except hydrogen, carbon or sulphur

Ligands supported

Salt bridge (sb) |AC| < 4.0Å

A (anion): ASP/OD1+OD2, GLU/OE1+OE2
C (cation): LYS/NZ, ARG/NH1+NH2

Ligands not supported

Pi-cation (pc) |AC| < 6.0Å
∠CAn < 60°

A (aromatic): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)
C (cation): LYS/NZ, ARG/NH1+NH2

Ligands not supported

Pi-stacking (ps) |A1A2| < 7.0Å
∠(n1, n2) < 30°
∠(n1, A1A2) < 45°
∠(n2, A1A2) < 45°

A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)

Ligands not supported

T-stacking (ts) |A1A2| < 5.0Å
60° < ∠(n1, n2) < 90°
∠(n1, A1A2) < 45°
∠(n2, A1A2) < 45°

A1, A2 (aromatic rings): center(PHE/CG+CE1+CE2), center(TRP/CD2+CZ2+CZ3), center(TYR/CG+CE1+CE2)

Ligands not supported

Hydrophobic (hp) |AB| < Rvdw(A) + Rvdw(B) + 0.5

A, B: ALA+CYS+PHE+GLY+ILE+LEU+MET+PRO+VAL+TRP and element C or S

Ligands supported

van der Waals (vdw) |AB| < Rvdw(A) + Rvdw(B) + 0.5

A and B are any non-hydrogen atoms

Ligands supported