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An automated classification of the structure of protein loops.
J Mol Biol
266 (4): 814-830 (Mar 7 1997)
Conformational clusters and consensus sequences for protein loops have
been derived by computational analysis of their structures in a
non-redundant set of 233 proteins with less than 25% sequence homology
(X-ray resolution better than 2.5 A). Loops have been classified into
five types (alpha-alpha, beta-beta links, beta-beta hairpins, alpha-beta
and beta-alpha) according to the secondary structures they embrace. Four
variables have been used to describe the loop geometry, three angles
and one distance between the secondary structure elements embracing
the loop. Ramachandran angles (phi, psi) are used to define the loop
conformations within each brace geometry. All loops from the
non-redundant set have been clustered by means of these geometric features.
A total of 56 classes (9 alpha-alpha, 11 beta-beta links, 14 beta-beta
hairpins, 13 alpha-beta and 9 beta-alpha) were identified with consensus
Ramachandran angles in the loops. These classes were divided into
subclasses based on the brace geometry. This clustering procedure
captures most of the clusters analysed by predominantly visual
inspection methods and finds other clusters that have hitherto not
been described. Consensus sequence patterns were identified for the
subclasses. An extensive characterisation of loop conformations has
therefore been achieved and the computational approach is readily open
to the incorporation of information from newly determined structures.
These clusters should also enhance model building by comparison studies.
[ alpha-alpha
| alpha-beta
| beta-alpha
| beta-beta links
| beta-hairpins ]
Last modified: Mon, 11-Aug-1997