do alpha helices have a lot of hydrophobic amino acids

As expected, the large majority was composed of helices with fewer than two helical turns, but a significant number spanned more than seven residues: 53 helices were 8 residues long, 13 helices were 9 residues long, 4 helices spanned 10 residues, and 1 helix was 11 residues long. More recently, a structural analysis of 689 protein chains with low sequence identity (≤20%) and solved at better than 1.6-Å resolution found 1,774 3 10 helices spanning five residues or more ( Enkhbayar et al., 2006). A 1999 survey found 132 cases of 3 10 helices with six amino acids or more ( Pal and Basu, 1999). The very large number of protein structures currently available has revealed that long 3 10 helices are present in proteins. The authors also concluded that 3 10 helices in proteins differed from the canonical conformation by having an average of 3.2 residues per turn instead of three residues, and noticed that 3 10 helices are in general irregular, presenting a wide variability in their main-chain torsion angle distribution. In contrast, they found that the 3 10 conformation was present in only 3.4% of the total number of residues 3 10 helices had a mean length of 3.3 residues, with just one helix spanning six residues.

Later, in a comparative study of protein structures, Barlow and Thornton (1988) analyzed 57 protein structures and showed that 32% of the total number of residues were involved in the formation of α helices α helices presented a mean length of 10 residues, with the longest extending over 27 residues. When Pauling, Corey, and Branson proposed the α-helical and the 3 10-helical conformations as protein structural motifs, they concluded that the 3 10 helix had a distorted hydrogen bond network and was most likely unstable ( Pauling et al., 1951). This idea has its origins in the classical studies of the helical conformation of polypeptides. There is a generalized belief among structural biologists that 3 10 helices are inherently unstable and are, therefore, relatively rare and short, not spanning more than three to four residues.

Because of their potential functional impact, it is worthwhile focusing our attention on two characteristics of 3 10 helices, stability and dynamics.

Do alpha helices have a lot of hydrophobic amino acids