Contact patterns between helices and strands of sheet define protein folding patterns

Akhil P. Kamat, Arthur M. Lesk

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


Comparing and classifying protein folding patterns allows organizing the known structures and enumerating possible protein structural patterns including those not yet observed. We capture the essence of protein folding patterns in a concise tableau representation based on the order and contact patterns of secondary structures: helices and strands of sheet. The tableaux are intelligible to both humans and computers. They provide a database, derived from the Protein Data Bank, mineable in studies of protein architecture. Using this database, we have: (i) determined statistical properties of secondary structure contacts in an unbiased set of protein domains from ASTRAL, (ii) observed that in 98% of cases, the tableau is a faithful representation of the folding pattern as classified in SCOP, (iii) demonstrated that to a large extent the local structure of proteins indicates their complete folding topology, and (iv) studied the use of the representation for fold identification.

Original languageEnglish (US)
Pages (from-to)869-876
Number of pages8
JournalProteins: Structure, Function and Genetics
Issue number4
StatePublished - Mar 1 2007

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology


Dive into the research topics of 'Contact patterns between helices and strands of sheet define protein folding patterns'. Together they form a unique fingerprint.

Cite this