Hydrophobicity

Where:

Placing the cursor above this element: pop-up area will show the position (sequence number and AA three letter code) for selected amino acid and the numerical value for Hydrophobicity for this amino acid.
Left mouse click: no action
Right mouse click: on any of the "Hydrophobicity" will generate following menu and actions:

A) STING it : This option generates structural presentation with color coding of the amino acids corresponding to the "Hydrophobicity" color coding. Amino acids are presented in CPK rendering.

B) The Hydrophobicity values shown at the picture below, were generated using the folowing table (Radzicka et al. (1988)). Figure below shows the difference in concept when data display is in question: GRASP does it one parameter at the time shown at the molecular surface. BLUE STAR STING JPD does it all parameters at the same time for all amino acids (including those at the surface).

The hydrophobicity is very important to consider when analyzing protein folding because it was shown that the hydrophobic forces dominate the process. Also, hydrophobic patches at the surface (see above HOT_SPOTS), are potentially important for identification of surface portions which can engage in the protein interactions/binding.

Table of hydropobicity values assigned to each amino acid

The table is taken from the work by Radzicka et al (1988)