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 NH
2 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]