Re: Hydrophobicity of residues

Phil Cunningham (
Fri, 2 Feb 1996 11:52:58 +0000 (GMT)

Re hydrophobicity of amino acids

there is a data collection the **Amino Acid Index** Nakai et al Prot Eng 2
93-100 (1988)

which lists many physical values for amino acids
1 Bull and Breese use surface tension to measure hydrophobicity 1974
2 Charton and Charton use a 'polarizability' parameter
3 Eisenburg 1984 reported a 'normalised hydrophobicity ' scale
4 Fauchere and Pliska use 'hydrophobic parameters pi of amino acid side
chains from the patitioning of N acetyl amino acid amides 1983
5 Goldsack and Chalifoux report hydrophobicity factors derived (I think)
from free energy of mixing considerations 1983
6 Hopp and Woods report a Hydrophilicity Value 1981
7 Jones 1975 another set of hydrophobcity values
8 Kyte and Doolittle 1982 report a Hydropathy Index

and so on
Altough the data is 'old' a guess physical properties don't alter much (as
opposed to data re contribution of each amino acid to protein structure and

The question the become just what do we mean by hyrophobic? it is
obviously not a 'physical constant' associated with any particular
molecule as say mol wt or net charge in pH 7 would be.

Regarding the original question, which is most/least hyrophobic

then perhaps we can resort to the Venn Diagram reproduced in"Nucleic Acid
and Protein Sequence analysis ed M Bishop and C Rawlings" P 313

Chapter 12 Protein structure prediction W R Taylor where hydrophic
residues are ILV M FYW H and AGTC ( spacing to reflect inclusion)
where ILM are regarded as 'most likely' to be buried residues.

Just my 5 pence (or are we pee now) worth

Phil Cunningham

PS apologies for the missed MOO yesterday, other commitments ie teaching
took me away... I also had it in my my that the meeing was at 4.00pm
hence my brief sortie at 1630 hours!