SPACE CLASH

Definition:
This STING component is computing a steric clash occuring among amino acids. Often, the measure for the steric (or space) clash is a "overlap factor", which is defined as the ratio of the distance between two atom centers to the sum of their van der Waals radii. The överlap factor" numerical value will be less than 1 if the two atom spheres penetrate each other. Some penetration is normal, for example in a hydrogen bonding arrangement. Overlap factors of 0.8 or even 0.75 are common in high resolution x-ray crystal structures. An overlap factor of 0.7 would be a relatively minor steric clash, while 0.65 or lower would be more severe. We have calculated the degree of such penetration of van der Waals spheres and call it Space Clash. The numerical value shown in JPD is a penetration expressed as a percent value of the sum of two atomic van der Waals spheres.

We have calculated 5 different space cklash values for:
1. Internal chain space clashes
2. Inter chain space clashes (two amino acids in space clash, each one belonging to a different chain)
3. Protein_water space clash
4. Protein Ligand space clash
5. water_water space clash (this one is not shown in JPD, but is available in the table form).

Table of Space Clash Data:

There are 5 TYPES of space clash calculated by the STING DB Generator:

0 - Interface
1 - Internal
3 - Atom - HOH
4 - Atom - HetAtm

Note:
Types 2 and 5 are not painted into the JPD window.
2 - HOH - HOH
5 - HetAtm - HOH

At the Window Title, STING displays the central residue data (in this particular case: Residue 26 (ARG) of chain A). In the table, STING displays the space clash type, Atom of the central residue that is involved in the specific space clash type, data of the second atom involved in the space clash: Chain, Residue and atom. Finally, last three columns show:
1. size of atom clash (expressed in Angstroms),
2. the expected SUM of van der Waals radii (expressed in Angstroms), and
3. Percent of penetration (or overlap factor but expressed in percent of the total sum of van der Waals radii where two atoms are not penetrating into each others space).