A graphical representation of the intramolecular hydrogen bonding in a protein is described, which provides a direct and easily interpretable display of its secondary and tertiary structural elements. The representation is constructed by scanning the coordinate list for all potential proton donor (PD)--proton acceptor (PA) pairs, and any pair which satisfies certain preset distance and angle criteria is classified as being H-bonded. The resulting list of H-bonds is mapped onto an N x N matrix, where N is the number of residues in the protein, by assigning an element ij of the matrix to all the PA-PD pairs between atoms of residues i and j. Subsequently graphical objects are generated for all elements which are labeled as representing one or more H-bonds, and which can then be plotted or displayed in a way analogous to the graphical representation of the distance matrix (DM). In contrast to the DM, the hydrogen bonding matrix (HBM) is sparse, which allows the patterns representing secondary and tertiary structural motifs to be quickly and clearly recognized. In addition, changes in structure are easily identifiable from changes in the H-bonding patterns. The analysis and interpretation of the HBM is discussed using aspartate amino-transferase and calmodulin as examples.