Contacts

The Contacts analysis tracks how many feature pairs are in contact at each frame and can also summarize their occupancies in a heatmap. It is very useful for following interfaces, binding events, packing changes, and domain interactions.

Adding the plot

1. Open Path Analyzer.
2. Choose Contacts in Observable.
3. Choose a Path.
4. Define Group A and Group B.
5. Set the contact Cutoff.
6. Click Add Contact Series or Add Contact Map.

Inputs

• Two atom-containing selections are required.
• The cutoff is given in A.
• The root selections you choose determine the map axes, so residue, ligand, chain, or domain selections are often easier to interpret than one large atom cloud.

Views

• Contact series: show the total number of contacts per frame.
• Contact map: show the occupancy of each feature pair across the full path.

Key equations

If \(F_A\) and \(F_B\) are the selected feature sets and \(r_c\) is the cutoff, the contact series follows

\[ C(t)=\sum_{u\in F_A}\sum_{v\in F_B}\mathbf{1}\!\left[d^{\min}_{uv}(t)<r_c\right] \]

where \(\mathbf{1}[\cdot]\) is the indicator function and \(d^{\min}_{uv}(t)\) is the minimum inter-atomic distance between features \(u\) and \(v\) at frame \(t\).

The contact map summarizes the occupancy of each feature pair:

\[ O_{uv}=\frac{1}{T}\sum_{t=1}^{T}\mathbf{1}\!\left[d^{\min}_{uv}(t)<r_c\right] \]

Tip

• Use the series to spot when an interface forms or breaks.
• Use the map to see which specific feature pairs are responsible.
• If you need the full binary time history of each contact pair, use Contact persistence.