Jump to ContentJump to Main Navigation
Show Summary Details

Statistical Applications in Genetics and Molecular Biology

Editor-in-Chief: Stumpf, Michael P.H.

6 Issues per year

IMPACT FACTOR increased in 2015: 1.265
5-year IMPACT FACTOR: 1.423
Rank 42 out of 123 in category Statistics & Probability in the 2015 Thomson Reuters Journal Citation Report/Science Edition

SCImago Journal Rank (SJR) 2015: 0.954
Source Normalized Impact per Paper (SNIP) 2015: 0.554
Impact per Publication (IPP) 2015: 1.061

Mathematical Citation Quotient (MCQ) 2015: 0.06

See all formats and pricing

30,00 € / $42.00 / £23.00

Get Access to Full Text

Log-Linear Modelling of Protein Dipeptide Structure Reveals Interesting Patterns of Side-Chain-Backbone Interactions

Kerstin Hommola
  • University of Leeds
/ Walter R. Gilks
  • University of Leeds and Rothamsted Research
/ Kanti V. Mardia
  • University of Leeds
Published Online: 2011-01-25 | DOI: https://doi.org/10.2202/1544-6115.1579

It has long been known that the amino-acid sequence of a protein determines its 3-dimensional structure, but accurate ab initio prediction of structure from sequence remains elusive. We gain insight into local protein structure conformation by studying the relationship of dihedral angles in pairs of residues in protein sequences (dipeptides). We adopt a contingency table approach, exploring a targeted set of hypotheses through log-linear modelling to detect patterns of association of these dihedral angles in all dipeptides considered. Our models indicate a substantial association of the side-chain conformation of the first residue with the backbone conformation of the second residue (side-to-back interaction) as well as a weaker but still significant association of the backbone conformation of the first residue with the side-chain conformation of the second residue (back-to-side interaction). To compare these interactions across different dipeptides, we cluster the parameter estimates for the corresponding association terms. This reveals a striking pattern. For the side-to-back term, all dipeptides which have the same first residue jointly appear in distinct clusters whereas for the back-to-side term, we observe a much weaker pattern. This suggests that the conformation of the first residue affects the conformation of the second.

This article offers supplementary material which is provided at the end of the article.

Keywords: amino-acid sequence; bioinformatics; circular variables; cluster analysis; contingency table; dipeptide; protein structure; side-chain interactions

Published Online: 2011-01-25

Citation Information: Statistical Applications in Genetics and Molecular Biology. Volume 10, Issue 1, ISSN (Online) 1544-6115, ISSN (Print) 2194-6302, DOI: https://doi.org/10.2202/1544-6115.1579, January 2011

Supplementary Article Materials

Comments (0)

Please log in or register to comment.