antibody_antigen_contacts
Read-only
Type the ANTIBODY-ANTIGEN INTERFACE of a deposited complex: which residue of each antibody chain touches which residue of the antigen, how close, and what kind of interaction each pair makes - ionic, polar, weak polar, hydrophobic, aromatic, carbonyl, or a disulfide.
Tool call template
Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.
{
"id": 1,
"jsonrpc": "2.0",
"method": "tools/call",
"params": {
"arguments": {
"text": "<text>"
},
"name": "antibody_antigen_contacts"
}
}Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| text | Yes | the coordinate file's contents - a PDB flat file or a PDBx/mmCIF; the format is read from the bytes, not from a name. | |
| model | No | which model of an ensemble to type, 1-based: conformers touch in different places, so one is typed rather than all. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| antibodyChain | No | type only this chain against the antigen. Left out, every chain carrying a variable domain is typed. | |
| antigenChains | No | comma-separated chain ids to treat as the antigen. Left out, every protein chain with no variable domain is the antigen. | |
| interactingCutoff | No | atom pairs further apart than this (Å) are not reported at all; Arpeggio's own default is 5. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| byType | Yes | atom pairs carrying each type over the whole interface, distance bands included | |
| contacts | Yes | one row per residue pair: the antibody residue (chain, author number, name, and its scheme position where it sits in a variable domain), the antigen residue, the closest atom distance, the atom-pair count, and the interaction types | |
| residues | Yes | how many residues each side contributes, per antibody chain | |
| antigenChains | Yes | the chain ids treated as the antigen | |
| antibodyChains | Yes | the chains typed, each with its variable-domain chain types |