Survey of the geometric association of domain-domain interfaces

Wan Kyu Kim, Jon C. Ison

Research output: Contribution to journalReview articlepeer-review

24 Scopus citations


Considering the limited success of the most sophisticated docking methods available and the amount of computation required for systematic docking, cataloging all the !mown interfaces may be an alternative basis for the prediction of protein tertiary and quaternary structures. We classify domain interfaces according to the geometry of domain-domain association. By applying a simple and efficient method called "interface tag clustering," more than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define "face" as the set of interacting residues in each single domain and the pair of interacting faces as an "interface." We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2-1.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In general, a family tends to use distinct faces for each partner when the family lias diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserved within the same type of interface even between remote homologs. The classification result is available at

Original languageEnglish
Pages (from-to)1075-1088
Number of pages14
JournalProteins: Structure, Function and Bioinformatics
Issue number4
StatePublished - 1 Dec 2005


  • Domain association
  • Interaction specificity
  • Interface conservation
  • Interface diversity
  • Protein interface
  • Protein-protein interaction


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