Chain(s) and Parameter Area

 

 

Entropy Density

 

The sum of values is calculated for the relative entropy (according to HSSP (7) data) of the amino acids encountered within the sphere of a given radius, and then divided by the volume of that sphere.


Placing the cursor above this element: pop-up area will show the position (sequence number and amino acid three letter code) for selected amino acid and the 3 numerical values for Entropy Density (@IFR, Internal and Sliding window) for given amino acid.
Left mouse click: no action
Right mouse click: on any of the "Entropy Density" will generate following menu and actions:


A) A user may select either Ca or Last Heavy Atom (LHA) in the side chain as a center of the sphere for calculating "Entropy Density"


B) A user may select among 5 possible radius values for the sphere:


C) A user may select among 4 possible values for the sliding window size (for the size of 5: a value for this parameter is collected over the central residue and other 2 from the each side of the central one, summed and divided by 5):


D) STING it "Entropy Density": This option generates structural presentation with color coding of the amino acids corresponding to the JPD row "Entropy Density" color coding. The area of gaps (as well as ligands) is where the colors are going to be different from the rest of the protein. Amino acids are presented in CPK rendering.


E) STING it "Entropy Density IFR ": This option generates structural presentation with color coding of the amino acids corresponding to the JPD row "Entropy Density" color coding. The area of interface between the two chains is where the colors are going to be different from the rest of the protein. Amino acids are presented in CPK rendering.


F) STING it "Sliding Window Entropy Density": This option generates structural presentation with color coding of the amino acids corresponding to the JPD row "Entropy Density" color coding. The area of gaps is where the colors are going to be different from the rest of the protein. Amino acids are presented in CPK rendering. A ligand here is presented in cyan color.