Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.

Abstract:

:The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the chi 1 distribution for most side-chains in an alpha-helix showed an absence of the g- conformation and a shift towards the t conformation when compared to the non-alpha/beta structures. The exceptions to this tendency were for short polar side-chains that form hydrogen bonds with the main-chain which prefer g+. Shifts in the chi 1 preferences for residues in the beta-sheet were observed. Other side-chain dihedral angles (chi 2, chi 3, chi 4) were found to be influenced by the main-chain. This paper presents more accurate distributions for the side-chain dihedral angles which were obtained from the increased number of proteins determined to high resolution. The means and standard deviations for chi 1 and chi 2 angles are presented for all residues according to the secondary structure of the main-chain. The means and standard deviations are given for the most popular conformations for side-chains in which chi 3 and chi 4 rotations affect the position of C atoms.

journal_name

J Mol Biol

authors

McGregor MJ,Islam SA,Sternberg MJ

doi

10.1016/0022-2836(87)90314-7

subject

Has Abstract

pub_date

1987-11-20 00:00:00

pages

295-310

issue

2

eissn

0022-2836

issn

1089-8638

pii

0022-2836(87)90314-7

journal_volume

198

pub_type

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