Exploring Secondary Structure Elements
In the previous chapter, we investigated the structure of the polypeptide backbone in the two main types of secondary structure elements, the α-helix and the β-sheet. In this chapter, the secondary structure elements themselves will be presented in more detail. First, we will learn how residues are assigned to such elements by different algorithms. This will reveal that the assignments of secondary structures are subject to some uncertainty and may vary depending on whether an algorithm uses torsional angles or hydrogen-bonding possibilities or both to make assignments. We will compare and contrast the hydrogen-bonding properties of α-helices and β-sheets and examine some variations of these structures that occur in protein structures. The chapter will also introduce the various types of turns that link the secondary structure elements together and show how the turns can be characterized by their torsion angles and hydrogen-bonding properties. A discussion of preferences of the amino acids to be found in α-helices, β-sheets, or turns will round off the chapter.
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