Hydrogen-bonding contacts

Figure C3.2.18.(a) Model a-helix, (b) hydrogen bonding contacts in tire helix, and (c) schematic representation of tire effective Hamiltonian interactions between atoms in tire protein backbone. From [23].

The Liskamp group also examined the ability of peptoid-peptide hybrids to be bound by the MHC Class II receptor, an important component of the human immune system [39]. Two of three peptoid substitutions in the 14-residue peptide caused substantial decreases in binding affinity, despite the fact that these were solvent-exposed residues. These results were attributed to a loss of hydrogen-bond contacts as well as to steric clashes caused by unfavorable positioning of the new side chain groups. 

Waals and hydrogen bond contacts associated with the substrate and the surroundings during the proton transfer were analyzed and described below. 

Table 3 Mean values and ranges (in parentheses) for the hydrogen-bonded contacts in the extended structures of the structurally characterised bis(AT-alkylamidino-0-alkylurea)copper(II) nitrates, tetrafluoroborates, halides and sulfates...

The pyridinyl amide makes two hydrogen-bonding contacts to the main chain of Cys531, while the central aryl ring occupies the gatekeeper pocket—... 

The amino acid side chains which serve as zinc ligands in a metallo-protein are densely packed within the protein structure and often make hydrogen bond contacts with other residues. Argos et al. (1978) pointed out that such interactions orient the metal ligands, and these interactions may also enhance the electrostatic interaction between the metal ion and its ligands. 

Fig. 3. S-adenosyl-L-methionine (SAM) 8 bound to the fluorinase showing hydrogen bonding contacts [10],...

Fig. 32a and b. The conformation of the ligand 5c in its thiourea complex and the disorder of the chain ends. Side view of the 5e-thiourea complex showing hydrogen bond contacts (parts of the aliphatic chain have been omitted for clarity)421... 

The S2 pocket is a large shallow depression offering no real binding cavities. One side of the pocket is made up from the conserved histidine at position 228 and the main chain from residue 227. The bottom of the pocket is formed by histidine 222. Both of these histidines are liganded to the catalytic zinc. The other side consists mostly of the residue 186 side chain with some hydrogen-bonding contacts possible from the tip of the glutamine side chain in the case of HFC and HNC. 

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