The protein folding problem is one of the great challenges of computational biology. To better understand the nature of known protein structures, an analysis of atomic bond lengths in structures in the Protein Data Bank was performed. A bimodal population distribution was found for many bond distances. Additionally, an association between amino acid atomic bond lengths was revealed. These results suggest new parameters for protein modeling and structure refinement programs. (C) 2003 Elsevier Science (USA). All rights reserved.