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By inputting a known amino acid sequence of interest, you will be redirected to a page displaying a graph of the hydrophilicity values versus the amino acid position. The table of assigned hydrophilicity values is given below with values derived by Hopp and Woods(1981).
A window size must be given to the program. Doing this will tell the program how many amino acids to average before moving on to the next set. Hopp and Woods researched that a window size of 6 is optimal for yielding the most likely protein antigenic determinant locations
The start and stop amino acid boxes come in handy if you wish to zoom in on a particular string of the polypeptide chain. Just input the starting amino acid position and the position at which you'd like to stop. In order to analyze the entire amino acid sequence, just leave these fields blank.
These are the Hydrophilicity values assigned to each amino acid by Hopp and Woods (1981)
Amino Acid | Hydrophilicity Value |
G | 0.0 |
P | 0.0 |
A | -0.5 |
V | -1.5 |
L | -1.8 |
I | -1.8 |
M | -1.3 |
C | -1.0 |
F | -2.5 |
Y | -2.3 |
W | -3.4 |
H | -0.5 |
K | 3.0 |
R | 3.0 |
Q | 0.2 |
N | 0.2 |
E | 3.0 |
D | 3.0 |
S | 0.3 |
T | -0.4 |
Hopp, Thomas P. and Kenneth R. Woods. 1981. "Prediction of protein antigenic determinants from amino acid sequences." Proc. Natl. Acad. Sci. USA. Vol. 78, No. 6, pp 3824-8.