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.