Niche (protein structural motif)

In the area of protein structural motifs, niches are three or four amino acid residue features in which main-chain CO groups are bridged by positively charged or d+ groups. The d+ groups include groups with two hydrogen bond donor atoms such as NH₂ groups and water molecules. In typical proteins, 7% of amino acid residues belong to niches bound to a d+ group, while another 7% have the conformation but no single cationic bridging group is detected. Two websites are available for examining niches in proteins, Motivated Proteins: [1] or PDBeMotif: [2]