Assingments of Tri- and Tetrapeptide Sequences in Globular Proteins to the 18 Kinds of Local Structures along Helices and Their Propensities for Specific Local Structures

Abstract The genetic information for local structures along helices, encoded in local sequences of protein chains, was statistically investigated for tri- and tetrapeptide sequences (3- and 4-letter words) using the 411 analyzed protein chains. The 18 kinds of local structures adopted by tri- and tetrapeptide sequences were represented 1-dimensionally by using a single helix element and pairs of helix elements in parentheses, respectively. The local sequences have propensities for none to some specific local structures along helices. A local structure (LS)-value is introduced for the evaluation of the normalized preference (NP)-value of a local sequence for a particular local structure. It should be emphasized that N-capping tetrapeptide sequences of helices do not necessarily prevent helix elongation. Local structures adopted by tetrapeptide sequences are plastic, and a particular local structure along helices is determined by the sequence context of helices.