you can measure hydrophobicity by the distribution coefficient
of a given molecule between a polar and a nonpolar phase, let's say
water and hexan.
So there are two aspects of hydrophobicity: first, there are
favorable interactions between the molecule and other nonpolar
molecules (which can be a nonpolar solvent or neighbouring
hydrophobic side chains in a protein), and second, there are
unfavorable interactions with other polar molecules like water.
The water will form an ordered surface around an hydrophobic
AA side chain, which is highly unfavorable from the entropy.
Peter
--- Peter Slickers slickers@imb-jena.de Institut fuer Molekulare Biotechnologie Beutenbergstrasse 11, Jena Tel.: +49-3641-65-6202 Postfach 10 08 13, D-07708 Jena, Germany Fax: +49-3641-65-6210