Knowledge of the relationship between a protein’s structure and its dynamic behavior is essential for understanding protein function. Secondary interactions have been widely investigated and were shown to play a key role in protein structure and flexibility. In HB plot application a novel approach for studying hydrogen bond networks is used and this analysis of protein structures yields significant new information on protein function. Hydrogen bonds stabilizing secondary structural element and those formed between distant amino residues (tertiary polar interaction) were distinguished and further focus of the work was on the network of tertiary polar interactions. Characterizing the network of tertiary polar interaction reveals structural motifs at a higher level, i.e. that even the secondary structural motifs are organized in a pseudo-secondary structural level (pseudo parallel beta sheet and pseudo antiparallel beta sheets). Moreover, further analysis of the network shows that one conformation of a protein structure contains all the information needed for identifying flexible parts important for function and suggests specific amino residues involved in structural rearrangement during conformational changes. Generating HB plot of proteins could be a new approach for an analysis of protein structure and conformational changes, which is fundamental to many areas of active biological research.