VMD-L Mailing List

From: Ramya Gamini (ramyabhargavi_at_gmail.com)
Date: Thu Mar 05 2009 - 20:36:34 CST

Hey !Would like to add:

The Kyte& Doolittle (1982) hydropathy index uses water to vacuum transfer
free energy to assign a hydrophobicity to each amino acid.

The Goldman, Engelman and Steitz (GES) scale (1986) reflects the free energy
cost for transferring amino acids from water to non-aqueous environment of
dielectric 2 (reflecting inside membrane or core of protein)

Eisenberg scale : normalized average of five different scales (1982 b)

von Heijne scale (vH) has statistic origin; derived based on analysis of
transmembrane segments from bacterial inner membrane proteins

Wimley-white (2001): host-guest peptide partitioning into n-octanol (this is
a whole residue hydrophobicity scale whereas all other scales are based on
amino acid side chains)

A table of hydrophobicity index is provided in the book referred below:
ref: computational methods for protein structure prediction and modeling
(authors: Xing Xu, Dong Xu
)

hope this helps.
Ramya

On Thu, Mar 5, 2009 at 8:20 PM, Ramya Gamini <ramyabhargavi_at_gmail.com>wrote:

> hi!hydropathy index was first proposed by kyte &doolittle (you can google
> for some papers, how they arrived at such indexing)
>
> I found some info in the wiki that may be useful for quick reference.
> http://en.wikipedia.org/wiki/Hydropathy_index
>
> best
> Ramya
>
> On Thu, Mar 5, 2009 at 7:17 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>> Hi,
>> Yes, they are just a list of residue names.
>> You'll see that "hydrophobic" isn't actualy a hard-coded
>> atom selection keyword, but rather an atom selection macro:
>> vmd > atomselect macro hydrophobic
>> resname ALA LEU VAL ILE PRO PHE MET TRP
>>
>> This one is provided by default in one of the VMD startup
>> scripts, it was written by Andrew Dalke, one of the original
>> VMD developers, here's his comment on their origination:
>>
>> # APD's hydrophobic residue list, from Branden and Tooze (pp6-7).
>> hydrophobic resname ALA LEU VAL ILE PRO PHE MET TRP
>>
>> Perhaps someone else can comment on the hydrophobicity in terms
>> of a numerical scale as you've asked for.
>>
>> Cheers,
>> John
>>
>> On Thu, Mar 05, 2009 at 04:58:41PM -0800, Goutham wrote:
>> > Hey,
>> > I am trying to find the hydrophobicity of the residues in the protein.
>> The
>> > hydrophobic keyword just acts like a boolean switch. Is there a way to
>> find
>> > the extent of hydrophobicity?
>> >
>> > Thanks
>> > Goutham
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>
>