Fig. 2.

The closure operation extends the concept of locality to residues that are close in space though not necessarily in sequence. For example, on hairpin formation the first and the last residues in the hairpin become three-dimensional neighbors, as illustrated here. A conceptual shortcut through the sequence is introduced when this occurs, illustrated by the red line. In general, two secondary structures are considered to be neighbors when they are consecutive in the sequence or when they become neighbors via a shortcut established by the closure operation.