Hydrogen bond types chain atoms

The p Sheet Another type of secondary structure, the p sheet, consists of laterally packed p strands. Each p strand is a short (5- to 8-residue), nearly fully extended polypeptide segment. Hydrogen bonding between backbone atoms in adjacent p strands, within either the same polypeptide chain or between different polypeptide chains, forms a p sheet (Figure 3-4a). The planarity of the peptide bond forces a p sheet to be pleated hence this structure is also called a 3 pleated sheet, or simply a pleated sheet. Like a helices, p strands have a directionality defined by the orientation of the peptide bond. Therefore, in a pleated sheet, adjacent p strands can be oriented in the same (parallel) or opposite (antiparallel) directions with respect to each other. In both arrangements, the side chains project from both faces of the sheet (Figure 3-4b). In some proteins, p sheets form the floor of a binding pocket the hydrophobic core of other proteins contains multiple P sheets. 

A rarer type is a helix 2.2-j (the hydrogen bond is between atoms 1 and 7 of the polypeptide chain). A right-handed hehx 3 (three units per turn, pitch height 0.6 nm), which is narrower and also steeper than an a-helix (the hydrogen bond is between atoms 1 and 10 of the polypeptide chain), sometimes occurs as an a-hehx junction with another part of the polypeptide chain. The so-cahed hehx 4.4jg (n-helix) only exists at the end of several hehces (4.4 units per turn, pitch height 0.52 nm, the hydrogen bond is between atoms 1 and 16 of the polypeptide chain). 

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

There are several other far less common types of helices found in proteins. The most common of these is the Sjq helix, which contains 3.0 residues per turn (with 10 atoms in the ring formed by making the hydrogen bond three residues up the chain). It normally extends over shorter stretches of sequence than the a-helix. Other helical structures include the 27 ribbon and the 77-helix, which has 4.4 residues and 16 atoms per turn and is thus called the 4.4ig helix. 

As a result of the bonding between sulfur atoms, several hydrogen compounds exist in which there are several sulfur atoms in a chain with a hydrogen atom bonded to the terminal sulfur atoms. These compounds include H2S2 (m.p. —88, b.p. 74.5 °C) and H2S6. Compounds of this type are known as sulfanes, and they are discussed in the next section. 

The second structural element to be proposed by Pauling and Corey was the P-pleated sheet (Figure 4.7). These sheets are made up of P-strands, typically from 5 to 10 residues long, in an almost fully extended conformation, aligned alongside one another with hydrogen bonds formed between the C=0 bonds of one strand and the NH of the other, and vice versa. The P-sheets are pleated (i.e. they undulate) with the Ca atoms alternatively a little above, or a little below the plane of the P-sheet, which means that the side chains project alternatively above and below the plane. P-Strands can interact to form two types of pleated sheets. 

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