Contact mapper (chemical)
Types every contact between a chosen partner (a chain or a ligand) and the rest of a structure — hydrogen bond, salt bridge, aromatic stacking, hydrophobic — using Arpeggio's implementation of the CREDO interaction rules. Use alongside Contact mapper (geometric) when the chemistry of an interface, not just its geometry, is the question.
Contact mapper (chemical)
What it does
Takes one structure and one partner — a chain or a ligand — and reports every contact between that partner and the rest of the structure, each labelled with what kind of interaction it is: hydrogen bond, salt bridge (ionic), aromatic ring stacking, hydrophobic contact, halogen bond, and several finer categories from the CREDO interaction rules.
This is the companion to Contact mapper (geometric), which answers "which residues are close" using distance alone. This tool answers the next question: why they're close, and whether that closeness means anything chemically. Run both when both questions matter — they're deliberately two separate tools rather than one with a mode switch, since "how close" and "what kind" are genuinely different questions with different answers.
How the typing is done
The engine is Arpeggio, which perceives bonds and atom types (via Open Babel), works out which residues form rings and amide groups, adds hydrogens if the structure doesn't already have them, and then classifies every close atom pair against the CREDO rule set — the same interaction taxonomy used in drug-discovery interaction fingerprinting more broadly.
Choosing a partner
Same two ways to name a partner as the geometric mapper:
- Chain — every contact between one chain and everything else
- Ligand — every contact between a bound ligand (by its 3-letter code) and everything else
Reading the output
The table lists every contact, closest first, with the interaction type(s) it was classified as — a single contact can carry more than one label (a hydrogen bond that's also flagged polar, for instance). The summary counts how many contacts of each type were found, so "how many hydrogen bonds does this interface have" is a number, not a manual count through a table.
Input
One structure, saved as mmCIF. This tool cannot currently read PDB files — if the only saved copy is a PDB, run Format conversion first to get an mmCIF version.
Important limitations
mmCIF only, for now. Not a design choice worth working around — the underlying tool's own chemistry-lookup step requires it.
A static calculation on one conformation, the same caveat every structure-based tool here carries — a contact that would form with a small side-chain rotation won't appear, because that rotation isn't in the file.
Hydrogens are added automatically when a structure doesn't have them, at the pH set (default 7.4). Where hydrogens are added rather than resolved experimentally, hydrogen-bond geometry is a reasonable estimate, not a measurement.