A contact count can tell you that a molecular interface has changed—but not which interactions are responsible. Two frames might contain the same number of contacts while involving entirely different atom pairs. That makes it difficult to distinguish a stable interaction from one that repeatedly appears and disappears along a path.
Contact persistence addresses this identity problem by tracking contact pairs across the path, rather than pooling them into a single count. In SAMSON’s Path Analyzer, the result can be viewed as a timeline heatmap or as a distribution of contact occupancies.
From a changing structure to a contact history
For each pair formed between Group A and Group B, the analysis records a binary state at every frame: the pair is present when its minimum distance is below the selected cutoff, and absent otherwise. In other words, each row of the timeline follows one specific pair through the path.
This pair-by-pair view helps answer practical questions: Does a particular interaction persist throughout the motion? Does it break and reform? Are contacts concentrated in one part of the path, or scattered across it? These are questions a total contact count alone cannot answer.
Read the two views together
- Contact timeline: Each row represents a contact pair, and each frame shows whether that pair is present. A row that remains active across much of the path indicates a long-lived contact. A patchy row indicates an intermittent one. The timeline keeps only pairs that occur at least once.
- Persistence distribution: Each pair’s occupancy is the fraction of frames in which it is present. An occupancy near 1 means the pair is present in nearly all frames; a low value means it occurs in relatively few. This fraction describes how often the contact appears, not whether it was continuously present: the timeline is needed to see when appearances occurred.
That distinction is useful when comparing interactions. Two pairs can have the same occupancy even if one stays present for a continuous stretch and the other switches on and off. The distribution summarizes frequency; the timeline preserves the pattern along the path.
A practical setup
- Open Path Analyzer and choose Contact persistence as the observable.
- Select the path you want to examine.
- Define two atom-containing selections as Group A and Group B. These groups determine which cross-group pairs are tested; the analysis does not treat them as one pooled atom list.
- Choose a contact cutoff in Å. The cutoff determines the distance rule used to classify each pair as present or absent.
- Add a contact timeline, a persistence distribution, or both.
Group choice is part of the scientific question. For a crowded interface, atom-level rows may be difficult to scan; residue-level or domain-level groups can make labels more readable. The cutoff matters too: because presence is determined by comparing distance with that value, changing it can change which pairs qualify. When interpreting results, keep the selections and cutoff in mind, and use the same settings when making a direct comparison.
Use the count and the identities for different questions
Contact persistence complements the broader Contacts analysis. A contact-count series answers “how many contacts exist?” Contact persistence answers “which contact pairs exist, and how consistently?” Looking at both can separate a change in the overall number of contacts from a change in the identities of the interacting pairs.
This is especially useful when examining interfaces, proximity patterns such as hydrogen-bond-like contacts, or gating motions: the timeline can reveal whether an interaction is sustained, intermittent, or limited to part of the path.
Learn more in the Contact Persistence documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.