A protein loop is any stretch of non-regular polypeptide chain connecting secondary structures.

Short loops commonly have little structure and are often found joining two adjacent beta strands . They are often referred to as reverse turns.

Long loops are often flexible and are able to adopt a number of different conformations, effectively making them invisible in x-ray crystal structures. These loops are likely to be involved in protein function and can switch from a 'open' conformation (frequently to allow access to an active site) to a 'closed' conformation (to protect reactive groups from bulk solvent).