What is the buriedness of an amino acid?

Is a measure based on the proximity of the amino acid to the surface of the protein.
The surface is modeled by the convex hull of the atomic coordinates of the protein.
Formally, if we let amino acid $r$ be composed of three atoms $a_1, a_2, a_3$ and $dist(a)$ be the shortest distance of an atom $a$ to the convex hull of the protein, then the buriedness of $r$ is equal to $(dist(a_1) + dist(a_2) + dist(a_3))/3$.

Why bother with buriedness when we have the ASA?

Buriedness by definition does not have 0 values, as opposed to the accessible surface area. This allows to a comparison between midly buried to buried to very buried residues.

To compute the buriedness in a protein, use the pdb file of the structure, suppose it is called file.pdb. Just type in the terminal:

$ python buriedness.py file.pdb > output.csv

Clone the repository and listo!

$ git clone https://github.com/rodogi/buriedness.git