Does Hydrophobic exclusion determine the polarity of proteins in a tertiary structure?
I don’t think I would use the term polarity in describing a tertiary structure of a protein, which is highly folded and in ribbons and sheets. What you have are hydrophobic areas where a lipid or other non hydrogen bonding compound portion can associate with, whether it is an enzyme portion or a drug. And there may be close areas with hydrogen binding that orient the lipid or enzyme into that pocket of the tertiary structure. Think in terms of three dimensions, where there will be pockets of hydrogen binding and non-hydrogen binding, which all serves a purpose of orienting the target molecule into that pocket.
