Non-Covalent Interactions
Detect, filter, validate, and communicate non-covalent contacts in structures and trajectories.
The Viewer detects non-covalent contacts and connects them to the 3D scene. Use the right-side Interactions tool for display and scope, then open the interaction table when you need a filterable record of donors, acceptors, types, and distances.
Supported interaction types
| Interaction | Default maximum distance | Typical interpretation |
|---|---|---|
| H-Bonds | 3.5 Å, or 4.1 Å when sulfur is involved | Directional donor–acceptor contact |
| Weak H-Bonds | 3.5 Å | Weaker donor–acceptor geometry |
| Hydrophobic | 4.0 Å | Nonpolar contact |
| Pi-Pi | 5.5 Å | Aromatic stacking |
| Cation-Pi | 6.0 Å | Cation–aromatic contact |
| Ionic / Salt Bridge | 5.0 Å | Oppositely charged groups |
| Halogen Bonds | 4.0 Å | Directional halogen contact |
| Metal Coord. | 3.0 Å | Metal coordination contact |
These thresholds define candidate contacts. Treat the visualization as analysis support, not as a substitute for reviewing geometry, protonation, chemistry, and the quality of the source data.
Choose the interaction scope
| Scope | Use it for |
|---|---|
| Protein–ligand | Binding-site review and pose analysis |
| Protein–protein | Chain interfaces and intraprotein contacts |
| All | Broad exploration when you do not yet know which partners matter |
Start with the narrowest scope that answers the question. A smaller, intentional interaction set is easier to validate and communicate than every possible contact.
Display interactions in 3D
For a quick static-structure review, interaction toggles may also appear in Display. Use the full Interactions tool when you need scope and appearance controls.
Use the Interactions Table
Open Applications → Ligand Interaction → Interactions Table when a ligand is detected.
- Filter rows by interaction type or molecular partner.
- Read the donor, acceptor, and distance fields.
- Select a row to connect the tabular record with the 3D contact.
- Keep the active ligand and scope consistent with the 2D and 3D ligand views.
Validate an interaction
Before presenting a contact as a conclusion:
- Confirm the active structure, ligand, and frame.
- Verify the donor and acceptor identities in the table.
- Inspect the contact from more than one camera angle.
- Check whether hidden waters, ions, or alternate partners change the interpretation.
- Record the relevant frame when working with a trajectory.
- Save the validated scene or capture it in a story.
For trajectories, available interaction analysis can update by frame. Pause before citing a contact, and always record the frame number or analyzed range.
Reduce visual noise
- Show only interaction types relevant to the current claim.
- Hide distant chains and nonessential solvent in the hierarchy.
- Keep the ligand in an atom-detailed representation.
- Use a restrained protein color so interaction lines remain legible.
- Separate independent conclusions into different scenes or story frames.