  Protein-protein interactions (protein functionalities) are mediated by water,
which compacts individual proteins and promotes close and temporarily stable
large-area protein-protein interfaces. Proteins are peptide chains decorated by
amino acids, and protein scientists have long described protein-water
interactions in terms of qualitative amino acid hydrophobicity scales. Here we
examine several recent scales and argue plausibly (in terms of self-organized
criticality) that one of them should be regarded as an absolute scale (within
the protein universe), analogous to the dielectric scale of bond ionicity in
inorganic octet compounds. Applications to repeat proteins (containing upwards
of 900 amino acids) are successful, far beyond reasonable expectations, in all
cases studied so far. While some of the results are obvious and can be obtained
from the ex vitro spatial structures alone, many are hidden from plain view,
and can be called phantom relations. As a byproduct, the network theory
explains the exceptional functionality of leucine in zippers, heptads, and
repeat consensus sites.
