Amino acid classes and the protein folding problem
  We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic stability in and kinetic accessibility to the native state. A simple interpretation of the groups is obtained by eigenanalysis of the interaction matrix. 
Marek Cieplak, Neal S. Holter, Amos Maritan and Jayanth R. Banavar