Occluded Surface (OS) calculates the atomic packing of a protein. The result may be displayed on a residue by residue basis or as an average value for the protein. Below we only look at the whole protein average. Evaluation of the OS packing on a protein depends on whether or not the structure of a homologous protein exists.
Below is a comparison of the packing values for a series of homologous protein structures. It is apparent from this figure that the packing of a protein is conserved through evolution even if the sequence drifts significantly. One could compare the packing of a new structure to the packing of similar structures and the values should be within approximately 0.5%.
The values for the pyrococcus woesei TATA-binding protein are unusually high - presumably due to the fact that this protein is from a hyperthermophile whereas the other TATA-binding proteins shown are from mesophiles.
If there are no structures of proteins homologous to yours, the criterion for "normal" packing is less stringent. Below is a plot of the packing values obtained for a data set of non-homologous proteins. Anything outside of the range shown would indicate an unusual structure.
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Revised: Tuesday, 20-Oct-1998 14:51:43 EDT