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Analysis of a data set of paired uncomplexed protein structures: New metrics for side‐chain flexibility and model evaluation
Author(s) -
Zhao Shanrong,
Goodsell David S.,
Olson Arthur J.
Publication year - 2001
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.1038
Subject(s) - side chain , flexibility (engineering) , chemistry , protein data bank , biological system , protein structure , computer science , computational biology , crystallography , statistics , mathematics , biochemistry , biology , organic chemistry , polymer
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 χ 1 and χ 2 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. Proteins 2001;43:271–279. © 2001 Wiley‐Liss, Inc.