Ligand-protein interactions hydroxylation

Twenty two amino acids come within 5.1 A of the bound retinol molecule. Five of them are within 3.6 A—Lys-40, Thr-53, Arg-58, Trp-104, and Gin-106. In fact, the polar side chains of these residues are close to the bound retinol and again it seems that at least part of the lipid-protein interactions occur through polar atoms. Of particular interest are Lys-40 and Gln-106. As in CRBP, Lys-40 is located above the isoprene tail of the retinol and could interact with the ir-electron field of the ligand. Gln-106, on the other hand, makes a hydrogen bond with the only polar group, the hydroxyl group of the retinol molecule. 

Three types of interaction between ligand and protein heavy atoms arising from different atom types. Primary and secondary amines are defined to be donors while oxygen and nitrogen atoms with no bound hydrogens are defined to be acceptors. Crystallographic water molecules and hydroxyl groups are defined to be both donor and acceptor. Carbon and sulfur atoms are defined to be nonpolar... 

Also based on porous silica support, the so-called Biomatrix phases contain a ligand that combines both hydrophilic and hydrophobic properties in the same molecule. Nonpolar analytes interact with the hydrophobic phenyl and alkyl moieties of the ligand, while the hydrophobic outer part of the ligand is supposed to be the result of hydroxyl groups that prevent the adsorption of proteins. 

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