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. Author manuscript; available in PMC: 2019 Dec 10.
Published in final edited form as: Prog Biophys Mol Biol. 2019 Sep 27;147:92–102. doi: 10.1016/j.pbiomolbio.2019.09.003

Figure 3: Relationship between structure element keys and threading model.

Figure 3:

A SE defines a secondary structure designation, a set of Cα coordinates and four keys that map these coordinates to residues in the primary sequence. SE1 defines the Cα coordinates of ten residues of a helix and the set of four keys map the six blue coordinates onto sequence. The start residue, 4, denotes that the threaded sequence begins at residue four, the length, 6, means six total coordinates from the SE are assigned, a polarity of 1 assigns the coordinates in advancing order and an offset of 2 begins from coordinate 3 in the structure element. SE2 shows a similar assignment, beginning at residue 21; however, the polarity of −1 flips the assignment, such that the last assigned coordinate in the SE is threaded to the sequence at residue 21 and the remainder of the SE is assigned backwards.