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hydrophobicity scales
Hydrophobicity scales are values that define relative hydrophobicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly used to predict the transmembrane alpha-helices of membrane proteins. When consecutively measuring amino acids of a protein, changes in value indicate attraction of specific protein regions towards the hydrophobic region inside lipid bilayer.
==Hydrophobicity and the hydrophobic effect==
(詳細はwater to exclude non-polar molecules. The effect originates from the disruption of highly dynamic hydrogen bonds between molecules of liquid water. Polar chemical groups, such as OH group in methanol do not cause the hydrophobic effect. However, a pure hydrocarbon molecule, for example hexane, cannot accept or donate hydrogen bonds to water. Introduction of hexane into water causes disruption of the hydrogen bonding network between water molecules. The hydrogen bonds are partially reconstructed by building a water "cage" around the hexane molecule, similar to that in clathrate hydrates formed at lower temperatures. The mobility of water molecules in the "cage" (or solvation shell) is strongly restricted. This leads to significant losses in translational and rotational entropy of water molecules and makes the process unfavorable in terms of free energy of the system.〔Tanford, C., The hydrophobic effect(New York:Wiley.1980).〕〔〔〔W . Kauzmann, Adv. Protein Chem. 14 (1959) 1.〕〔Charton, M. and Charton, B.I. (1982) J. Theor. Biol., 99, 629–644.〕
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