S–H···N Contacts between Side Chains of Cys and Backbone Nitrogen Atoms in Proteins Are Weak Interactions and Not Hydrogen Bonds

The thiol group of the Cys side chain is known to participate in hydrogen bonds as an acceptor or donor. Similarly, the backbone nitrogens in proteins are involved in forming hydrogen bonds as donors that provide stability to protein secondary structures. In this study, we have identified more than 400 examples of self-contacting and inter-residue contacts from nearly 6000 high-resolution protein crystal structures in which the S-H group of the Cys side chain and the backbone nitrogen satisfy the geometric criteria to form hydrogen bonds. Very few studies have investigated the role of backbone nitrogen as a hydrogen-bond acceptor. Relative energy profiles calculated by varying the Cys χ1 side chain dihedral angle of self-contacting Cys residues revealed that the energy difference between crystal structure and minimum energy conformations is between 0-3 kcal/mol. Quantum chemical calculations using DFT and MP2 theories indicated that the interaction energies of model systems with S-H···N self-contacts were only marginally favorable. However, the model systems representing S-H···N inter-residue contacts showed reasonably stable interaction. Natural bond orbital (NBO) analysis and NCIPLOT studies do not exhibit any hydrogen-bond interaction between the S-H donor and acceptor backbone nitrogen. The favorable interaction energies may be due to electrostatic and dispersion interactions. We found that the interactions due to S-H···N inter-residue contacts stabilize two secondary structural elements, and a large number of them occur between two β-strands. The structural role of S-H···N interactions can be further investigated by mutation studies of specific Cys residues involved in S-H···N contacts.