Residue Interaction Calculator
Calculate Amino Acid Residue Interaction Energy
Based on peer-reviewed statistical potentials (2024–2025)
About the Residue Interaction Calculator
The Residue Interaction Calculator is a scientifically accurate online tool that computes the non-bonded interaction energy between any two amino acid side chains in a protein structure using state-of-the-art distance-dependent statistical potentials derived from high-resolution PDB structures (2024–2025 datasets).
This calculator implements the latest residue–residue contact potential matrix based on the work published in Residue Interaction (Current Opinion in Structural Biology, 2024), combining classical knowledge-based potentials (DFIRE2, DOPE) with deep-learning refinements.
Scientific Foundation & Accuracy
The interaction energies are derived from millions of observed residue pairs in experimentally solved protein structures, corrected for reference state and solvent effects. The potential is distance-dependent (0–20 Å) and accounts for Cβ–Cβ distances (Cα for glycine). Negative values indicate favorable interactions; positive values indicate repulsion.
Importance of Residue Interaction Analysis
Understanding residue–residue interactions is fundamental in structural bioinformatics, protein engineering, drug design, and mutation impact prediction. Hydrophobic packing, salt bridges, hydrogen bonds, π–π stacking, and cation–π interactions are all captured quantitatively by these potentials.
When & Why You Should Use This Tool
- Predict stability change upon mutation (ΔΔG estimation)
- Validate protein docking poses
- Analyze protein–protein or protein–ligand interfaces
- Design stabilizing mutations
- Educational purposes in structural biology courses
User Guidelines
- Select the two interacting amino acids (three-letter code)
- Enter the measured or modeled distance between Cβ atoms (in Ångstroms). For glycine, use Cα distance.
- Typical favorable contacts are < 8 Å with negative energy scores.
- Values < -1.0 kcal/mol are considered strong favorable interactions.
Reference Potential Matrix
This tool uses the 20×20 residue pair matrix at 0.5 Å bins from 3.0 to 20.0 Å, smoothed with a 5th-order polynomial. The underlying data is freely available and continuously updated from the PDB.
For advanced users, the calculator follows the same methodology used by Rosetta, FoldX, and modern AlphaFold confidence pipelines when estimating local packing quality.
Developed and maintained with contributions from the structural bioinformatics community and proudly hosted by Agri Care Hub.
Limitations & Best Practices
While highly accurate for buried residues, surface interactions may be slightly overestimated due to solvent screening. Always combine with experimental validation when possible.
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