Parallel and antiparallel β-strands differ in amino acid composition and availability of short constituent sequences

One of the important secondary structures in proteins is the β-strand. However, due to its complexity, it is less characterized than helical structures. Using the 1641 representative three-dimensional protein structure data from the Protein Data Bank, we characterized β-strand structures based on strand length and amino acid composition, focusing on differences between parallel and antiparallel β-strands. Antiparallel strands were more frequent and slightly longer than parallel strands. Overall, the majority of β-sheets were antiparallel sheets; however, mixed sheets were reasonably abundant, and parallel sheets were relatively rare. Notably, the nonpolar, aliphatic hydrocarbon amino acids, valine, isoleucine, and leucine were observed at a high frequency in both strands but were more abundant in parallel than in antiparallel strands. The relative amino acid occurrence in β-sheets, especially in parallel strands, was highly correlated with amino acid hydrophobicity. This correlation was not observed in α-helices and 3(10)-helices. In addition, we examined the frequency of 400 amino acid doublets and 8000 amino acid triplets in β-strands based on availability, a measurement of the relative counts of the doublets and triplets. We identified some triplets that were specifically found in either parallel or antiparallel strands. We further identified "zero-count triplets" which did not occur in either parallel or antiparallel strands, despite the fact that they were probabilistically supposed to occur several times. Taken together, the present study revealed essential features of β-strand structures and the differences between parallel and antiparallel β-strands, which can potentially be applied to the secondary structure prediction and the functional design of protein sequences in the future.