We consider the interval constrained coloring problem, which appears in the interpretation of experimental data in biochemistry. Monitoring hydrogen-deuterium exchange rates via mass spectroscopy experiments is a method used to obtain information about protein tertiary structure. The output of these experiments provides data about the exchange rate of residues in overlapping segments of the protein backbone. These segments must be re-assembled in order to obtain a global picture of the protein structure. The interval constrained coloring problem is the mathematical abstraction of this re-assembly process.