Protein secondary structure

In biochemistry and structural biology, protein secondary structure is the general three-dimensional form of local segments of proteins. Secondary structure can be formally defined by the pattern of hydrogen bonds of the protein (such as alpha helices and beta sheets) that are observed in an atomic-resolution structure. More specifically, the secondary structure is defined by the patterns of hydrogen bonds formed between amine hydrogen and carbonyl oxygen atoms contained in the backbone peptide bonds of the protein. The secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot; thus, a segment of residues with such dihedral angles may be called a helix, regardless of whether it has the correct hydrogen bonds. The secondary structure may be provided by crystallographers in the corresponding PDB file.