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ent_iface_res_ent_iface_res_id_e3f93cbf

Read-only

Retrieve PISA-calculated interface residue contacts for a PDB entry, including interaction types, distances, and atom/residue details, with optional filtering by assembly and interface.

Instructions

Returns all interface residue contacts calculated by PISA (Proteins, Interfaces, Structures and Assemblies) for a specified PDB entry ID. The results include interaction types (e.g., salt bridges and hydrogen bonds), interatomic distances, and details of the participating atoms and residues from both interacting chains. Results can optionally be filtered by assembly_id and interface_id.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
assembly_idNoNumerical assembly id code
interface_idNoIndex of interface, one based.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

A3.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds real value beyond them by naming the data source (PISA) and the shape of the payload: interaction types such as salt bridges and hydrogen bonds, interatomic distances, and atoms/residues from both interacting chains. It does not mention result size, pagination, or ordering.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three sentences, front-loaded with the core action and followed by return content and filtering options; nothing is padded. Minor repetition between the opening clause and the filter sentence keeps it just short of ideal.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With no output schema, the description does carry the burden of describing return values, and it does so at a useful level (interaction types, distances, participating residues). It stops short of covering result volume or ordering, but for a three-parameter read-only tool it is nearly sufficient.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%: pdb_id (4-character code), assembly_id (numerical), and interface_id (one-based index) are all documented in the schema itself. The description only restates that the latter two act as filters and adds no format or semantics beyond the schema, matching the baseline 3.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource ('Returns all interface residue contacts calculated by PISA') scoped to a PDB entry ID. However, it does not differentiate itself from the near-duplicate sibling iface_res_ent_interfaces_id_entity_id_49a0e419, so an agent cannot tell the two apart from text alone.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It notes that results can 'optionally be filtered by assembly_id and interface_id', which implies a use case, but there is no guidance on when to choose this tool over the similar interface-residue sibling, nor any prerequisites or exclusions. Usage must be inferred entirely.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.