How To Find Hydrophobic And Hydrophilic Regions In Protein?

Question

[vibhanim.21]

I have a protein. I want to analyse whether the tryptophan and tyrosin molecules fall in hydrophobic or hydrophilic region of my protein. please can anybody help me in this?

Answer 1

[justinhaselbach]

May be a KYTE DOOLITTLE HYDROPATHY PLOT will help solve your problem- if it is integrated to the tools you use for protein analysis/ visualization. However many are free to use and available through a divergent web servers:

1.http://web.expasy.org/protscale/ 2. http://www.ibi.vu.nl/programs/scoobywww/ 3. http://bioinf.cs.ucl.ac.uk/psipred/ 4. http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py?form=HCA#welcome 5. http://gcat.davidson.edu/DGPB/kd/kyte-doolittle.htm 6. http://www.vivo.colostate.edu/molkit/hydropathy/index.html

and so on !

Thanks,

Answer 2

[aravind ramesh]

Calculate PSA(Percent solvent accessibility) values for the residues, It only works when you have structure of a protein. Otherwise(only sequence is available), then Trp and tyr are considered as hydrophobic, check for enrichment of charged and hydrophobic residues neighbouring these residues.

Hope this helps.