contact_report
Lists contacting residue pairs between two selections, reporting distances and interaction types to show what holds a ligand in a pocket or forms an interface.
Instructions
Lists the residues in contact across two selections, with distances and types.
This is the numeric counterpart to ligand_view and interface_view: instead of drawing the interactions, it reports them — which residue pairs touch, how close they get, and whether the contact is a salt bridge, hydrogen bond, hydrophobic packing or pi-stacking. Use it to answer "what holds this ligand in the pocket" or "which residues form this interface".
Classification uses heavy-atom distance criteria, since crystal structures usually have no hydrogens: salt bridge <= 4.0 A between formally charged sidechain tips, hydrogen bond <= 3.5 A between N/O pairs, hydrophobic <= 4.5 A between C/S pairs, pi-stacking <= 5.5 A between aromatic ring centroids (classified parallel or T-shaped by interplanar angle). A reported hydrogen bond is therefore a donor-acceptor pair with plausible geometry, not one verified against a hydrogen position.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cutoff | No | Maximum heavy-atom separation to count as a contact, in Angstrom. 4.0 captures the interactions above; raise toward 5.0 for a looser survey. | |
| max_pairs | No | How many residue pairs to list, closest first. The count of any omitted pairs is always reported. | |
| selection1 | Yes | One side, e.g. "1hsg and resn MK1" (a ligand). | |
| selection2 | Yes | The other side, e.g. "1hsg and polymer". | |
| include_water | No | Include waters, for water-mediated contacts. Off by default, as ordered waters otherwise dominate the list. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |