Protein Contact Map Calculator
Enter or Paste Your Protein Sequence & Parameters
About the Protein Contact Map Calculator
The Protein Contact Map Calculator is a free, accurate, and user-friendly online tool that instantly generates a 2D contact map from any protein amino acid sequence. A protein contact map is a fundamental representation in structural bioinformatics that shows which residues in a protein are close in 3D space, even if they are far apart in the primary sequence. This calculator strictly follows established scientific principles used in CASP, AlphaFold, Rosetta, and thousands of peer-reviewed studies.
What is a Protein Contact Map?
A protein contact map is a symmetric N × N matrix (where N is the number of residues) in which a black dot at position (i,j) indicates that residue i and residue j are in spatial proximity (typically ≤ chosen distance cutoff). Contact maps are distance-based and do not require experimental 3D structures — they can be predicted or calculated from known structures.
Importance of Protein Contact Maps
Protein contact maps are essential in:
- Predicting protein 3D structure from sequence (AlphaFold2, trRosetta, DMPfold)
- Protein folding studies and misfolding diseases (Alzheimer’s, Parkinson’s)
- Comparing native vs. decoy structures
- Identifying domains, secondary structure packing, and tertiary contacts
- Validating NMR and Cryo-EM models
Scientific Basis & Formulas Used
This Protein Contact Map Calculator uses the universally accepted definition:
Two residues i and j (with |i-j| ≥ min_sep) are in contact if the Euclidean distance between their representative atoms ≤ cutoff distance (Å).
- Cα–Cα distance ≤ 8 Å → most common for backbone contacts
- Cβ–Cβ distance ≤ 8 Å → preferred for side-chain packing (Gly uses Cα)
All calculations follow the standards published in:
- Duarte et al., “Optimal contact definition for reconstruction of contact maps”, BMC Bioinformatics (2010)
- Vassura et al., “Reconstruction of 3D structures from protein contact maps”, IEEE/ACM TCBB (2008)
- Marks et al., “Protein 3D structure computed from evolutionary sequence variation”, PLoS ONE (2011)
When and Why You Should Use This Tool
Use the Protein Contact Map Calculator when you:
- Want to visualize predicted contacts from AlphaFold2, ESMFold, RoseTTAFold, etc.
- Need to compare predicted vs experimental contact maps
- Study long-range tertiary contacts in intrinsically disordered regions
- Teach structural bioinformatics or protein folding courses
- Perform quick validation of modeled structures
User Guidelines
- Paste or type your protein sequence using single-letter amino acid codes.
- Choose the desired distance cutoff (8 Å is standard).
- Select Cα or Cβ representation (Cβ is generally more informative).
- Set minimum sequence separation (≥6 is standard to remove local contacts).
- Click “Generate Contact Map” – the symmetric map appears instantly.
- Black dots = contacts; the lower triangle is shown for clarity.
Interpretation of the Contact Map
- Diagonal is always empty (a residue is not in contact with itself)
- Parallel lines offset from diagonal = α-helices
- Anti-parallel lines = β-sheets
- Off-diagonal clusters = tertiary contacts and domain packing
This free Protein Contact Map Calculator is proudly provided by Agri Care Hub to support researchers, students, and educators worldwide. For in-depth reading, visit the Protein Contact Map - Wikipedia page.
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