Journal of Molecular Modeling

, Volume 14, Issue 8, pp 769–775 | Cite as

A reexamination of the propensities of amino acids towards a particular secondary structure: classification of amino acids based on their chemical structure

  • Saša N. Malkov
  • Miodrag V. Živković
  • Miloš V. Beljanski
  • Michael B. Hall
  • Snežana D. Zarić
Original Paper

Abstract

The correlation between the primary and secondary structures of proteins was analysed using a large data set from the Protein Data Bank. Clear preferences of amino acids towards certain secondary structures classify amino acids into four groups: α-helix preferrers, strand preferrers, turn and bend preferrers, and His and Cys (the latter two amino acids show no clear preference for any secondary structure). Amino acids in the same group have similar structural characteristics at their Cβ and Cγ atoms that predicts their preference for a particular secondary structure. All α-helix preferrers have neither polar heteroatoms on Cβ and Cγ atoms, nor branching or aromatic group on the Cβ atom. All strand preferrers have aromatic groups or branching groups on the Cβ atom. All turn and bend preferrers have a polar heteroatom on the Cβ or Cγ atoms or do not have a Cβ atom at all. These new rules could be helpful in making predictions about non-natural amino acids.

Keywords

Amino acid Protein Protein secondary structure Statistical correlation 

Notes

Acknowledgements

This work was supported under projects, No 142037 and No 144030 by the Ministry of Science of the Republic of Serbia. M.B.H. acknowledges the support of the National Science Foundation, USA (CHE-0518074).

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Saša N. Malkov
    • 1
  • Miodrag V. Živković
    • 1
  • Miloš V. Beljanski
    • 2
  • Michael B. Hall
    • 3
  • Snežana D. Zarić
    • 4
  1. 1.Department of MathematicsUniversity of BelgradeBelgradeSerbia
  2. 2.Institute of General and Physical ChemistryBelgradeSerbia
  3. 3.Department of ChemistryTexas A&M UniversityCollege StationUSA
  4. 4.Department of ChemistryUniversity of BelgradeBelgradeSerbia

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