Amino Acid Substitution Matrices (continued)
Other similarity scoring matrices might be constructed
from any property of amino acids that can be quantified -partition coefficients
between hydrophobic and hydrophilic phases
-molecular volume, etc.
Unfortunately, all these biophysical quantities suffer from the fact that they provide only a partial view of the picture - there is no guarantee, that any particular property is a good predictor for conservation of amino acids between related proteins.