One question that relates to the packing of a protein is the number of cavities. These are usually defined as a buried void space large enough to contain a water molecule. MSROLL, a program in the Molecular Surface Package (MSP), provides an accurate method to calculate these cavities.
Below is shown the ASCII output of MSROLL run on the pyrococcus woesei TATA-binding protein using the recommended probe radius of 1.2 Å.
molecule name = pwtbp_mnra
number of atoms = 1403
probe radius = 1.200
contact area = 3526.316
reentrant area = 5145.646
molecular area = 8671.963
accessible area = 9882.129
solvent-excluded volume = 21881.217
component center volume molecular accessible
number x y z area area
1 55.661 41.272 92.172 21941.732 8559.518 9877.404
2 55.820 41.271 107.826 -10.337 23.050 0.204
3 59.363 43.173 86.590 -11.556 24.965 0.312
4 56.799 41.497 74.607 -38.621 64.430 4.209
The four surface components are represented by the outer molecular surface and three small cavity surfaces of approximately the volume of a water molecule or larger. The locations of the cavities are shown by the green spheres in the image below.
Return to Post-structure Analysis
Revised: Tuesday, 20-Oct-1998 14:51:30 EDT