  We describe the representation of the chemical affinity between the
antigen-combining site of the immunoglobulin molecule and the antigen molecule
as the probability of the two molecules existing in a bound state. Our model is
based on the identification of shape attractors in the configuration space for
the joint antibody / antigen combining site sequence. We parameterize
configuration space in terms of Ramachandran angles. The shape attractors allow
us to construct a Markov chain whose steady state distribution gives rise to
the desired attachment probability. As a result we are able to delineate the
enthalpic, entropic and kinetic components of affinity and study their
interactions.
