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PreprintCC BYChemRxiv

Contact organization separates biological from crystal protein interfaces matched on area and disjoint in sequence

  • Olga Lavinda1,2
  1. 1Department of Chemistry and Biochemistry
  2. 2Stern College for Women, Yeshiva University
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Abstract

Interface area can dominate discrimination between physiological protein interfaces and crystal contacts. We tested whether local contact organization remains informative after area matching and sequence-cluster separation. In 2,000 balanced BioMany/XtalMany interfaces, sequence cluster aware cross validation gave ROC AUC 0.904 for area and 0.937 after adding five normalized contact descriptors (difference 0.033; bootstrap 95% interval 0.015–0.058). We then fixed 40 biological and 40 crystal homomeric interfaces from the Duarte–Capitani collection, matched pairwise on area within 800–2000 Å2 and sharing no 30%-identity cluster with development. Area reached AUC 0.523; the frozen contact score reached 0.849 (dependency-component bootstrap 95% interval 0.751–0.927) and average precision 0.812. Biological interfaces carried 2.5 times the hydrophobic carbon-pair density of crystal contacts, 1.91 versus 0.76 pairs per 100 Å2. Post hoc analysis identified hydrophobic density as the main contributor; this descriptor alone reached AUC 0.829. On the same panel, unchanged PRODIGY-cryst reached AUC 0.8475 and the lineage-linked current EPPIC score reached 0.876. Contact organization therefore discriminated the curated classes after area matching and sequence-cluster separation. The inference applies to EPPIC-derived labels; protein chain size remained unmatched and associated with the score.

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Cite

BibTeXRIS
BibTeX
@misc{lavinda2026contact,
  title = {{Contact organization separates biological from crystal protein interfaces matched on area and disjoint in sequence}},
  author = {Olga Lavinda},
  howpublished = {ChemRxiv},
  year = {2026},
  month = oct,
  doi = {10.26434/chemrxiv.15010687/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010687/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - Contact organization separates biological from crystal protein interfaces matched on area and disjoint in sequence
AU  - Olga Lavinda
PY  - 2026
DA  - 2026/10/20
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15010687/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010687/v1
AB  - Interface area can dominate discrimination between physiological protein interfaces and crystal contacts. We tested whether local contact organization remains informative after area matching and sequence-cluster separation. In 2,000 balanced BioMany/XtalMany interfaces, sequence cluster aware cross validation gave ROC AUC 0.904 for area and 0.937 after adding five normalized contact descriptors (difference 0.033; bootstrap 95% interval 0.015–0.058). We then fixed 40 biological and 40 crystal homomeric interfaces from the Duarte–Capitani collection, matched pairwise on area within 800–2000 Å2 and sharing no 30%-identity cluster with development. Area reached AUC 0.523; the frozen contact score reached 0.849 (dependency-component bootstrap 95% interval 0.751–0.927) and average precision 0.812. Biological interfaces carried 2.5 times the hydrophobic carbon-pair density of crystal contacts, 1.91 versus 0.76 pairs per 100 Å2. Post hoc analysis identified hydrophobic density as the main contributor; this descriptor alone reached AUC 0.829. On the same panel, unchanged PRODIGY-cryst reached AUC 0.8475 and the lineage-linked current EPPIC score reached 0.876. Contact organization therefore discriminated the curated classes after area matching and sequence-cluster separation. The inference applies to EPPIC-derived labels; protein chain size remained unmatched and associated with the score.
ER  -