Every chain may run in the same direction to form a parallel sheet, every other chain in the reverse direction to form an antiparallel sheet, or the chains may be parallel and antiparallel to form a mixed sheet. As illustrated in the Figure, the pattern of h bonding is different in the parallel and antiparallel configurations. The F and Y angles of the amino acids in b sheets vary considerably in one region of the Ramachandran plot. Previously, it was more difficult to predict the location of b sheets than a helices, but the situation improved when the amino acid variation in multiple sequence alignments was taken into account. Hairpin loops which represent a complete turn in the polypeptide chain joining two antiparallel b strands may be as short as two amino acids in length .
Loops interact with the surrounding aqueous environment and other proteins.
Since amino acids in loops are not constrained by space and environment as are amino acids in the core region, and do not have an effect on the arrrangement of secondary structures in the core, more substitutions, insertions and deletions may occur. Thus, in a sequence alignment, the presence of these features may be an indication of a loop. The position of introns in genomic DNA sometimes corresponds to the location of loops in the encoded protein. Loops also tend to have charged and polar amino acids and are frequently a component of active sites. A detailed examination of loop structures has shown that they fall into distinct families.