Now we assign positions to the inside of the folded structure.
Interior algorithms are the opposite of surface algorithms.
Instead of looking for hydrophilic amino acids, we look for hydrophobic amino acids. For example, we might assign to the inside all positions where a hydrophobic amino acid is conserved over the entire alignment. At 5 positions, one finds a hydrophobic amino acid that is conserved throughout. However, although the assignments are very reliable, only a few assignments are made because only a few residues are this highly conserved.