This is shown most dramatically in patterns of hydrogen bonding between the carboxyl groups and the amino groups in the peptide backbone that give rise to alpha helix and beta strand conformations. In particular, the bond angles between two adjacent bonds on either side of a single atom, or the dihedral angles between three contiguous bonds and two atoms control the geometry of the protein folding. The preferred dihedral angles for different secondary structural elements are discussed below. They are generally between 5 and 20 residues in length, but some proteins and coiled-coil structures can be considerably longer. The carboxyl groups of the backbone hydrogen bond to the amino group of a residue four amino acids distant along the chain.
Alpha helices can span membranes either singly or in groups.
Beta-strands are an extended form in which the side chains alternate on either side of the extended chain. Longer loops are occasionally found where the loop plays an important role in substrate binding or an active site. The antigen-combining site of the immunoglobulins is an important example of this. Plots of phi versus psi dihedral angles for amino acid residues are called Ramachandran plots. Principles of Protein Structure.