Although single hydrogen bonds are a weak force in comparison to the other interactions which occur in proteins, they collectively forms very strong interactions. Hydrogen bonding exclusively occurs between a hydrogen atom and either nitrogen, oxygen or fluorine. A classic example of how a hydrogen bond is formed is shown in the interaction of two water molecules. The oxygen atom is relatively electronegative in comparison to the hydrogen atoms, so that it gains a slight negative charge. This causes it to attract an adjacent hydrogen atom which is subsequently positive.
As a protein's secondary structure forms, intermolecular forces adopt their role in holding together substructures. The Alpha helix is the most common secondary structure found proteins. It is a right-handed helix held together by hydrogen bonding, with 3.6 residues occurring per turn (meaning that there is a residue every 100o). Hydrogen bonds occur between the oxygen of carbonyl groups and hydrogen of amino groups, 4 residues away, creating the compact helical shape as residues are pulled tightly together. These interactions form between the atoms of the polypeptides main chain, so that all side chains extend outwards.
The Beta-pleated sheet is the second most common structure found within a protein. Unlike the Alpha-helix, Beta sheets are composed of adjacent polypeptide chains, called Beta strands, which are held together by hydrogen bonding. These strands can run parallel or antiparallel and often twist to form structures such as a Beta barrel. Anti-parallel sheets are slightly stronger than parallel sheets, as the hydrogen bonds are planar and line up more efficiently to form more stable interactions.
Turns are a common motif in proteins which allow a loop to form in the secondary structure. The most common type of turn is the beta turn which allows a polypeptide chain to double-back on itself. For example, it can be used to link beta strands in a beta sheet, forming a hairpin-like shape.