Protein Crosslinking Calculator
Calculate Maximum Crosslinking Distance & Compatible Residue Pairs
About the Protein Crosslinking Calculator
The Protein Crosslinking Calculator is a free, scientifically accurate online tool designed for researchers working in chemical crosslinking mass spectrometry (XL-MS), structural proteomics, and protein–protein interaction studies. This calculator instantly determines the maximum allowable Cα–Cα distance between crosslinked residues and lists compatible amino acid pairs for any chosen chemical crosslinker.
What is Protein Crosslinking?
Protein crosslinking is a powerful technique that covalently links amino acid side chains that are spatially close in 3D structure. The most common target is the ε-amino group of lysine residues using NHS-ester-based crosslinkers such as BS³ or DSS. The resulting “crosslinks” act as distance constraints (< 30 Å) that are invaluable for validating protein structures, mapping protein-protein interfaces, and integrative structural biology.
Scientific Foundation & Peer-Reviewed Formulas
This Protein Crosslinking Calculator strictly follows established standards:
- Maximum Euclidean distance ≈ spacer arm length + 2 × side-chain contribution + tolerance
- Standard values from Leitner et al., Mol. Cell. Proteomics (2014); Sinz et al., Nat. Protoc. (2015)
- BS³/DSS spacer arm = 11.4 Å → commonly accepted Cα–Cα cutoff ≈ 24–26 Å
- EDC (zero-length) → Cα–Cα ≤ 12–15 Å for Asp/Glu–Lys pairs
Common Crosslinkers & Their Maximum Cα–Cα Distances (with 3Å tolerance)
| Crosslinker | Spacer Arm (Å) | Reactive Groups | Max Cα–Cα (Å) |
|---|---|---|---|
| BS³ / DSS | 11.4 | Lys–Lys (NHS) | 24–26 |
| BS²G | 7.7 | Lys–Lys | 18–20 |
| EDC | 0 | Asp/Glu–Lys | 12–15 |
| DSSO | 10.3 | Lys–Lys (cleavable) | 22–24 |
| Sulfo-SMCC | 11.6 | Lys–Cys | 24–26 |
When & Why You Should Use This Calculator
Use the Protein Crosslinking Calculator when you are:
- Designing XL-MS experiments and need correct distance constraints for software (xQuest, pLink, MeroX, Xi)
- Validating AlphaFold-multimer or docked complexes using experimental crosslinks
- Teaching structural biology or proteomics courses
- Preparing manuscripts and need to justify chosen Cα cutoff values
- Comparing different crosslinkers for your protein system
User Guidelines
- Select your crosslinker from the dropdown (or choose “Custom”)
- Adjust side-chain tolerance if your protein is highly flexible
- Choose “Maximum Cα–Cα Distance” for modeling or “Compatible Residue Pairs” for experiment planning
- Click “Calculate” – results appear instantly
This completely free Protein Crosslinking Calculator is proudly brought to you by Agri Care Hub. For detailed background, visit the Protein Crosslinking Wikipedia page.
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