Protein surface
Last update on the 13th of December, 2019Here we study surface area of transhydrogenase NMR model (2BRU, fig. 1) and chain interface surface.
![2BRU surface.](./surface_1.png)
Surface area
2BRU consists of 10 models with 3 chains. MS area and SAS area were calculated with PyMol get_area
for each model (fig. 2).
![2BRU surface areas.](./surface_areas.png)
MS and SAS areas are generally correlated (Pearson's r=0.765, Kendall's τ=0.689). Area differences between models might be explained with little conformation changes. In addition, MS area values have lower standard deviation than SAS area values (98Å and 419Å, respectively) thus indicating more dramatic SAS changes over conformations.
Chain interface
Chain interface residues were estimated with interfaceResidues.py script from PyMol Wiki for each pair of chains.
![Interface surfaces.](./interface_surfaces.png)
Discovered residues reveal rich interface between chains (fig. 3). PyMol builds unified surface in case chains comprise single object. In case chains are split in multiple objects (with PyMol extract
command), interface surfaces intersect each other as it should be defined by the algorithm of interface discovery.
![Interface complementarity.](./interface_complementarity.png)
However, it is not the case in general (fig. 4): not all surfaces of interacting residues intersect each other. That's definitely a bug. Nonetheless, interacting surfaces complement each other.