Structural features can be unconserved in proteins with similar folds

An analysis of side-chain to side-chain contacts, secondary structure and accessibility

Robert B. Russell &Geoffrey J. Barton

University of Oxford
Laboratory of Molecular Biophysics
The Rex Richards Building
South Parks Road
Oxford OX1 3QU U.K.
Tel: 44 865 275368 FAX: 44 865 510454
INTERNET: geoff@biop.ox.ac.uk
Subject classification: Proteins, Nucleic Acids and other biologically important macromolecules: Molecular structure
Keywords: amino acid side-chain interactions; substitutions; protein evolution; protein structure
Running title: Conservation of protein structural features
To whom correspondence should be addressed.
Present Address:
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund Laboratories
Lincoln's Inn Fields
P.O. Box 123
London, WC2A 3PX
(The published version of this preprint appeared in Journal of Molecular Biology (1994), 244, 332-350)

• Contents
• Introduction
• Methods
  • Multiple alignment of protein 3D structures
  • Sequence similarity
  • Structural similarity
  • Secondary structure and accessibility
  • Side-chain to side-chain interaction potential
  • Comparison of interacting residues within protein structure pairs
• Results
  • Structural similarity
  • Accessibility
  • Core structure
  • Secondary structure
  • RMS deviation
  • Residue-residue interactions within single structures
  • Shared interactions
  • Complementary changes
  • Homologous vs. analogous proteins
• Discussion
• Acknowledgements
• References
• About this document ...