When working on molecular systems, understanding the interactions within your model—how they persist, fluctuate, or break down over time—is critical for uncovering mechanisms underlying complex biological or chemical processes. The Contact Persistence analysis in SAMSON can help you do just that. If you’re curious about which molecular interactions last, which are intermittent, and which are fleeting, this tool provides a laser-like focus on the dynamics of contact pairs, offering insights that would be hard to achieve otherwise.
What does Contact Persistence do?
The Contact Persistence analysis dives deep into the relationship between two groups of atoms. It analyzes how these interactions evolve across the frames of a molecular trajectory. Results come in two visual forms:
- Contact timeline: A heatmap visualizing when each contact pair is present or absent across the simulation.
- Persistence distribution: A histogram showing how frequently each contact exists during the trajectory.
This combination helps you identify stable, intermittent, and transient molecular interactions, making it especially useful for studying interfaces, hydrogen-bond-like proximity patterns, or conformational gating motions.
How to Set It Up
Here’s a quick guide to using Contact Persistence in SAMSON:
- Open the Path Analyzer module in SAMSON.
- Select Contact persistence as your analysis option.
- Choose a specific Path for the analysis.
- Define two groups of atoms—Group A and Group B—to compute contacts between.
- Set a cutoff distance (in Å) beyond which interactions are ignored.
- Click Add Contact Timeline for a heatmap or Add Persistence Distribution for a histogram.
Key Inputs and Outputs
For this analysis, you’ll need two selections of atoms as your inputs (Group A and Group B). Contacts are computed between features from these groups rather than pooled atomic lists, ensuring a more precise analysis tailored to your selections. Also, remember to set an appropriate cutoff distance to capture relevant interactions while ignoring spurious ones. The results provide:
- A time-resolved heatmap of contact presence or absence.
- An occupancy histogram showing the fraction of time each contact exists.
Practical Insights
Why is visualizing contact persistence so powerful? It allows you to:
- Pinpoint highly stable interactions through rows that persistently exhibit contact.
- Detect intermittent contacts through sparse or patchy rows.
- Focus only on contact pairs that exist at least once over the trajectory.
This tool is particularly helpful in studying interfaces between biomolecules, monitoring hydrogen-bonds in large systems, and understanding processes like conformational transitions in proteins. If you’re analyzing a molecular interface, you may even want to use residue-level or domain-level grouping for more intuitive and readable contact pair labels.
Pro Tip
For an integrated analysis, combine Contact Persistence with the Contacts feature in Path Analyzer. While Contacts offers you details on how many interactions exist at each point, Contact Persistence zooms in to identify which ones last, fluctuate, or disappear.
Curious to learn more? Dive into the full documentation here: Contact Persistence Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at SAMSON Connect.