Accessibility

The Amino acid accessibility is calculated according to SurfV (10) program. JPD shows 3 values: for the protein chain in isolation, for the protein chain in complex with the other chain (if) present in the PDB file and finally, a relative accessibility (the last one given by the table of absolute solvent accessible area for amino acids).

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 Accessibility values for the chain in complex with the other chain, for the chain in isolation and for the relative accessibility.
Left mouse click: no action
Right mouse click: on any of the "Accessibility" will generate following menu and actions:

A) "Accessibility X-Y Graphics" will produce following Java X-Y graphics (X= sequence number, Y= Accessibility in Complex) with the interactive possibilities described in dedicated HELP manual:




B) "Accessibility X-Y Graphics" will produce following Java X-Y graphics (X= sequence number, Y= Accessibility in Isolation) with the interactive possibilities described in dedicated HELP manual:





C) This option will call FORMIGA component of BLUE STAR STING and by running the software SurfV, produce following output (see HELP on FORMIGA):




D) "STINGit - Complex" will induce CHIME window to show the values of accessibility in color coding corresponding to the same color code used by this specific JPD row. The accessibility displayed is for the protein chain in complex with the other chain (if) present in the PDB file.




E) "STINGit - Isolation" will induce CHIME window to show the values of accessibility in color coding corresponding to the same color code used by this specific JPD row. The accessibility displayed is for the protein chain in isolation.




F) "STINGit - Relative" will induce CHIME window to show the values of Relative accessibility in color coding corresponding to the same color code used by this specific JPD row. The accessibility displayed is for the relative accessibility calculated as a ratio of the value for the accessibility of a selected amino acid belonging to the protein chain in isolation and divided by the value given in the table of absolute solvent accessible area for amino acids which basically shows SurfV output with the calculated accessibility of a single amino acid standing in the solvent all by itself.