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Hydropathy Plot Help

Sequences:

You can find a sequence at NCBI (National Center for Biotechnology Information) or at Stanford's SGD (Saccharomyces Genome Database).  Search NCBI's "Proteins" for any known protein name (or its accession number) or an organism in general.  A list of links will appear and in each one there should be an amino acid sequence which you may copy and then paste onto the web page.  SGD can be searched for yeast (S.cerevisiae) gene or protein sequences.

Window Size:

      Recommended window sizes: odd integers between 5 and 29.  The window size sets the number of positions that are averaged for each point on the plot. That means that larger window sizes make smoother plots. If your plot doesn't have any distinct peaks, you might try a smaller window size. If your plot has many peaks very close to each other, you might try a larger window size. The window size should be odd so that the window is not centered between two sequence positions. The closest odd positive window size will be used if the input is not appropriate.  If the window size is larger than the length of the sequence no plot will appear.  If you fail to enter a window size, the graph will be plotted with a default window size of 11.

Unknown Amino Acids:

    Any unknown amino acids (represented by 'X') will be given a neutral hydropathy value.  All characters that are not abbreviations for amino acids will be removed from the sequence before plotting (i.e. punctuation, spaces, numbers, 'J', 'O', or 'U').

Hydropathy indexes (Kyte, 1982):

A

Alanine

Ala

1.8

R

Arginine

Arg

-4.5

N

Asparagine

Asn

-3.5

D

Aspartic Acid

Asp

-3.5

C

Cysteine

Cys

2.5

Q

Glutamine

Gln

-3.5

E

Glutamic Acid

Glu

-3.5

G

Glycine

Gly

-0.4

H

Histadine

His

-3.2

I

Isoleucine

Ile

4.5

L

Leucine

Leu

3.8

K

Lysine

Lys

-3.9

M

Methionine

Met

1.9

F

Phenylalanine

Phe

2.8

P

Proline

Pro

-1.6

S

Serine

Ser

-0.8

T

Threonine

Thr

-0.7

W

Tryptophan

Trp

-0.9

Y

Tyrosine

Tyr

-1.3

V

Valine

Val

4.2

B

Asparagine or Aspartic Acid

Asn or Asp

-3.5

Z

Glutamine or Glutamic Acid

Gln or Glu

-3.5

X

Unknown

XXX

0.0

Sources Cited:

Kyte, Jack, and Russel F. Doolittle.  "A Simple Method for Displaying the Hydropathic Character of a Protein."  Journal of Molecular Biology 1982; (157) 105-132.

.NCBI. 23 Jan. 2002. National Center for Biotechnology Information. 28 Feb. 2002 <http://www.ncbi.nlm.nih.gov/>.

Saccharomyces Genome Database (SGD). 2002. Stanford U. 28 Feb. 2002 <http://genome-www.stanford.edu/Saccharomyces/>.

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