Quenching of protein fluorescence can be used to monitor protein dynamics or biomolecular associations. This quenching can be interpreted to afford valuable structural information with a resolution that depends on the size of the quenching probe used. We have shown that backbone thioamides effectively quench several fluorophores, including tryptophan and tyrosine, in a distance-dependent manner. We have used this method to monitor the binding of thioamide-containing peptides to the protein calmodulin, protein unfolding in model systems, and other biological processes. Since thioamide analogs of the natural amino acids can be incorporated at any position in the peptide backbone, they can function as a valuable, minimally-perturbing probe of protein interactions.