Analysis of a data set of paired uncomplexed protein structures: New metrics for side-chain flexibility and model evaluation

Shanrong Zhao, David S. Goodsell, Arthur J. Olson

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

We compiled and analyzed a data set of paired protein structures containing proteins for which multiple high-quality uncomplexed atomic structures were available in the Protein Data Bank. Side-chain flexibility was quantified, yielding a set of residue- and environment-specific confidence levels describing the range of motion around X1 and X2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side-chain motion and estimating the extent of side-chain motion in protein structure prediction. We compare the performance of a simple 40° threshold with these quantitative confidence levels in a critical evaluation of side-chain prediction with the program SCWRL.

Original languageEnglish (US)
Pages (from-to)271-279
Number of pages9
JournalProteins: Structure, Function and Genetics
Volume43
Issue number3
DOIs
StatePublished - May 15 2001
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Keywords

  • Protein structure prediction
  • Side-chain flexibility

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