A computer implemented method of engineering a variant protein relative to a parent protein, the parent protein comprising a first residue comprising one or more residue atoms, the method comprising: (a) calculating a summation of one or more close contact potentials of the parent protein based on respective distances between the one or more residue atoms of the first residue of the parent protein and one or more environment atoms of the one or more residue atoms of the first residue of the parent protein, in accordance with a close contact potential formula of the form: U ab r ab = { 1 if r ab < r c 1 d r c − r ab if r c < r ab < r c + d 0 if r ab < r c + d 0 if β wherein, U ab ( r ab) is the close contact potential between a residue atom a of the first residue and an environmental atom b, d is a non-zero offset, r c is equal to or greater than 2.8 Å, r ab is the distance between a residue atom a of the first residue and an environmental atom b, β refers to atoms a and b that are either members of the same residue or that are bonded either directly (1-2 bonded), through one intervening atom (1-3 bonded) or through two intervening atoms (1-4 bonded), (b) calculating a first contact area of the one or more residue atoms of the first residue of the parent protein that are exposed to the one or more environment atoms, (c) calculating a first close contact surface density (CCSD) by dividing the summation of the one or more close contact potentials of the parent protein by the first contact area, (d) mutating one or more residues of the parent protein to provide the variant protein, (e) calculating a summation of one or more close contact potentials of the variant protein based on respective distances between the one or more residue atoms of the first residue of the variant protein and one or more environment atoms of the one or more residue atoms of the first residue of the variant protein in accordance with the close contact potential formula of step (a), (f) calculating a second contact area of the one or more residue atoms of the first residue of the variant protein that are exposed to the one or more environment atoms, (g) calculating a second CCSD by dividing the summation of the one or more close contact potentials of the variant protein by the second contact area, (h) making the variant protein if the second CCSD compared to the first CCSD indicates comparable or improved stability of the variant protein relative to the parent protein, wherein steps (a) through (g) of the method are performed on a computer system comprising a clock, a memory, and a processor, and are performed utilizing the processor. (a) calculating a summation of one or more close contact potentials of the parent protein based on respective distances between the one or more residue atoms of the first residue of the parent protein and one or more environment atoms of the one or more residue atoms of the first residue of the parent protein, in accordance with a close contact potential formula of the form: U ab r ab = { 1 if r ab < r c 1 d r c − r ab if r c < r ab < r c + d 0 if r ab < r c + d 0 if β wherein, U ab ( r ab) is the close contact potential between a residue atom a of the first residue and an environmental atom b, d is a non-zero offset, r c is equal to or greater than 2.8 Å, r ab is the distance between a residue atom a of the first residue and an environmental atom b, β refers to atoms a and b that are either members of the same residue or that are bonded either directly (1-2 bonded), through one intervening atom (1-3 bonded) or through two intervening atoms (1-4 bonded), U ab ( r ab) is the close contact potential between a residue atom a of the first residue and an environmental atom b, d is a non-zero offset, r c is equal to or greater than 2.8 Å, r ab is the distance between a residue atom a of the first residue and an environmental atom b, β refers to atoms a and b that are either members of the same residue or that are bonded either directly (1-2 bonded), through one intervening atom (1-3 bonded) or through two intervening atoms (1-4 bonded), (b) calculating a first contact area of the one or more residue atoms of the first residue of the parent protein that are exposed to the one or more environment atoms, (c) calculating a first close contact surface density (CCSD) by dividing the summation of the one or more close contact potentials of the parent protein by the first contact area, (d) mutating one or more residues of the parent protein to provide the variant protein, (e) calculating a summation of one or more close contact potentials of the variant protein based on respective distances between the one or more residue atoms of the first residue of the variant protein and one or more environment atoms of the one or more residue atoms of the first residue of the variant protein in accordance with the close contact potential formula of step (a), (f) calculating a second contact area of the one or more residue atoms of the first residue of the variant protein that are exposed to the one or more environment atoms, (g) calculating a second CCSD by dividing the summation of the one or more close contact potentials of the variant protein by the second contact area, (h) making the variant protein if the second CCSD compared to the first CCSD indicates comparable or improved stability of the variant protein relative to the parent protein,