Secondary struture is determined from course grained mesostate definitions using the match hieirarchy below:

SS Type SS Code Mesostates Description
α-helix H O, P A region is identified as helix if there are five or more contiguous residues in the mesostate set.
β-strand E L, G, F, A, R, M A region is defined as strand if there are three or more contiguous residues in the mesostate set.
β-turn T OO, OP, OJ, PO, PP, PJ, JO, JP, JJ, Mo, Mp, Mj, Ro, Rp, Rj, oo, op, oj, po, pp, pj, jo, jp, jj, mO, mP, mJ, rO, rP, rJ All dipeptide pairs which match a combination in the mesostate set are defined as a β-turn.
PII-conf P M, R Residues that have not already been classified as strand, yet match any of the elements in the mesotate set, are categorized as polyproline-II conformation.
Coil C All All other residues not classified as P, T, E, or H are assigned as coil.