I am working on a novel gene which supposed to be present in the apoplast. I am trying to figure out to see if the protein is hyrophilic. I have tried a couple of website online but they give me a graph which I am not able to interpret. I am wondering if anyone knows a better website or software which can give me the direct answer or if anyone can help me to interpret this graph.
It gives output for the regions (eg. 295-305 amino acids in your figure) in your protein which are hydrophobic in nature. high positive score means highly hydrophobic region.
I realize this is an old question but for those still interested:
The hydropathy index of an amino acid is a number representing the hydrophobic or hydrophilic properties of its sidechain and was proposed in 1982 by Jack Kyte and Russell F. Doolittle:
Kyte J, Doolittle RF (1983). "A simple method for displaying the hydropathic character of a protein". J. Mol. Biol. 157 (1): 105–32.
The larger the number is, the more hydrophobic the amino acid. In their scale the most hydrophobic amino acids is isoleucine (4.5) and the most hydrophilic one is arginine (-4.5).
Since this several other hydrophobicity scales are introduced, see for a little overview:
Data keller3biotech2015suppl.docx
One of the other scales is:
-Fauchère, J., and Pliska, V. (1983). Hydrophobic parameters {pi} of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 8: 369–375
This scale is used in the program Heliquest. Perhaps it is worthwhile for you to check your protein with Heliquest in order to see what kind of protein you have. Does it contains (net) charged regions (of for example positively charged) amino-acid. Does it contain regions that are overall hydrophobic and so. All you need is the FASTA form of your protein sequence. See for Heliquest:
http://heliquest.ipmc.cnrs.fr/
In combination with the so-called Heliquest based Eisenberg Plot method you can also determine whether your protein will probably act as a water-soluble, surface bound or even transmembrane peptide. See for more details:
Article New User-Friendly Approach to Obtain an Eisenberg Plot and I...
Hope this answers this matter to some degree.
Best regards.
PS. How to interpret the figure(s): Stretches of AA (10-20) above zero indicate a possible hydrophobic stretch. The second figure (in purple) seems to be a (moderate) hydrophobic protein since virtually all values are above zero.
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