Geometry of interaction of the histidine ring with other planar and basic residues.
Among the aromatic residues in protein structures, histidine (His) is unique, as it can exist in the neutral or positively charged form at the physiological pH. As such, it can interact with other aromatic residues as well as form hydrogen bonds with polar and charged (both negative and positive) residues. We have analyzed the geometry of interaction of His residues with nine other planar side chains containing aromatic (residues Phe, Tyr, Trp, and His), carboxylate (Asp and Glu), carboxamide (Asn and Gln) and guanidinium (Arg) groups in 432 polypeptide chains. With the exception of the aspartic (Asp) and glutamic (Glu) acid side-chains, all other residues prefer to interact in a face-to-face or offset-face-stacked orientation with the His ring. Such a geometry is different from the edge-to-face relative orientation normally associated with the aromatic-aromatic interaction. His-His pair prefers to interact in a face-to-face orientation; however, when both the residues bind the same metal ion, the interplanar angle is close to 90 degrees. The occurrence of different interactions (including the nonconventional N-H...pi and C-H...pi hydrogen bonds) have been correlated with the relative orientations between the interacting residues. Several structural motifs, mostly involved in binding metal ions, have been identified by considering the cases where His residues are in contact with four other planar moieties. About 10% of His residues used here are also found in sequence patterns in PROSITE database. There are examples of the amino end of the Lys side chain interacting with His residues in such a way that it is located on an arc around a ring nitrogen atom.
Bhattacharyya
Rajasri
R
Department of Biochemistry and Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054, India.
Saha
Rudra Prasad
RP
Samanta
Uttamkumar
U
Chakrabarti
Pinak
P
D020816:Amino Acid Motifs; D024322:Amino Acids, Aromatic / Q000378:metabolism*; D024361:Amino Acids, Basic / Q000378:metabolism*; D006639:Histidine / Q000378:metabolism*; D006860:Hydrogen Bonding; D008239:Lysine / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000378:metabolism*
D024322:Amino Acids, Aromatic; D024361:Amino Acids, Basic; D011506:Proteins; D006639:Histidine; D008239:Lysine; D009584:Nitrogen