3decision detects contacts between a ligand and its receptor (protein residues or water molecules) and types each one from the atoms involved and the geometry. Interactions between two ligands, or between receptor residues, are not detected.
The types are shown as dashed lines in the 3D viewer (see Interactions) and used by Interaction Search.
An interactant is an atom, or group of atoms, involved in an interaction. Interactants are typed from their connectivity, hybridization and partial charge. One interactant can have several types.
| Type | Description |
|---|---|
| Anion | Negatively charged atom. |
| Apolar | Atom with a negligible partial charge. |
| Aromatic | Non-nitrogen atom in an aromatic system. |
| Aromatic N | Nitrogen atom in an aromatic system. |
| Carbonyl carbon | Carbon of a carbonyl group. |
| Carbonyl oxygen | Oxygen of a carbonyl group. |
| Cation | Positively charged atom. |
| Function - amide | Carbon or nitrogen atom of an amide group. |
| H-bond acceptor | Atom that can accept a hydrogen bond. |
| H-bond donor | Atom that can donate a hydrogen bond. |
| Hydrophobic | Hydrophobic atom. |
| Metals | Metal atom. |
| Neg ionisable | Atom that can be negatively ionized. |
| Polar | Atom with a significant partial charge. |
| Pos ionisable | Atom that can be positively ionized. |
| Uncharacterized | Atom whose interaction capabilities are not characterized. |
| Water | Oxygen of a water molecule. |
| Weak H-bond acceptor | Atom that can accept a weak hydrogen bond. |
| Weak H-bond donor | Atom that can donate a weak hydrogen bond. |
| X-bond acceptor | Atom that can accept a halogen bond. |
| X-bond donor | Atom that can donate a halogen bond. |
Interaction types are grouped. In Interaction Search, each group also has an Any type, for example Any Polar, which matches every type of the group.
| Type | Description |
|---|---|
| Hydrophobic | Between hydrophobic interactants. |
| Type | Description |
|---|---|
| Amide interaction | Involves a planar amide group. |
| Halogen Bond | Between a halogen and an atom with a lone pair. |
| H-Bond | Between an H-bond donor and an H-bond acceptor. |
| Polar interaction | Between polar interactants, one with a positive and one with a negative partial charge. |
| Weak polar | Between a weak polar interactant and the side of an aromatic ring. |
| Water Mediated Interaction | Polar interaction between a water molecule and the receptor, for water molecules that also contact the ligand. |
| Type | Description |
|---|---|
| Ionic | Between an anion and a cation. |
| Potential Ionic | Between a negatively and a positively ionisable interactant. |
The classic π–π stacking geometries:
| Type | Description |
|---|---|
| Aromatic Sandwich | The two rings are parallel and stacked exactly on top of each other. |
| Aromatic T-shape | The side of one ring points at the center of the other; the rings are perpendicular. |
| Parallel-displaced Aromatic | The rings are parallel but shifted, so they are not stacked. |
Contacts outside those strict geometries:
| Type | Description |
|---|---|
| Aromatic Edge-to-face | The edge of one ring faces the other ring, but not perpendicular enough for a T-shape. |
| Aromatic Face-to-face | The faces of the two rings are in contact. |
| Aromatic Side-by-side | The sides of the two rings are in contact. |
| Screw Aromatic | Like a sandwich, but one ring is rotated around its axis. |
| Atom-Aromatic Face | A non-aromatic atom is in contact with the face of an aromatic ring. |
Contacts that are unfavorable or uncertain:
| Type | Description |
|---|---|
| Apolar contact with aromatic side | An apolar atom close to the side of an aromatic ring, in a geometry that would suit a polar contact. |
| Hydrophobic Polar Contact | A hydrophobic interactant in contact with a polar one. |
| Ionic Repulsion | Short-range contact between two atoms with the same charge. |
| Potential Ionic Repulsion | Short-range contact between a charged atom and an atom that may carry the same charge, depending on pH or environment. |
| Light Clash | The atoms are slightly too close, which is slightly unfavorable. |
| Critical Clash | The atoms are much too close: a real clash. |
| Potential Covalent Bond | The distance fits a covalent bond. Only the distance is checked, not chemistry. |
| Type | Description |
|---|---|
| Uncharacterized | Involves at least one uncharacterized interactant. |
| Uncharacterized Aromatic | Aromatic-aromatic contact with an undefined geometry. |