Alpha-Helices
Alpha-helices are formed by hydrogen bonding amino acids via their carbonly carbons and amide protons. In a helix each peptide carbonyl groups is hydrogen bonded to the amide proton four residues up the chain. Such an association of amino acids gives rise to a structure that resembles a cork screw. Each turn of the helix is made up of 3.6 amino acids (residues). Each turn of the helix propagates 5.4 angstroms along the helical axis. This distance is also known as the pitch of the helix. On average the phi angle in an alpha helix is -60 degrees while the psi angles can be in the range of -45 to -50 degrees.

Let's look at a model of an alpha-helix.

(1). into the JMol window (left).

(2) In this depiction only the backbone atoms are shown. None of the side chain atoms are shown. Move the molecule around and observe the polypeptide backbone of the helix.

Notice that in this depiction the center of the helix appears to be hollow. This is not the case (see space filling model below). When you illustrate the atoms as a space filling objects (atoms represented at their van der waals radi) then we can see that there is no hollow core to the helix.

In some illustrations the helix is illustrated as a ribbon. The ribbon follows the path of the polypeptide backbone.

Use the controls to the left to render the helix in different formats. Move the molecule around and observe the differences.

(3). Notice that all of the backbone carbonyl and amide groups of amino acids four residues apart are pointing towards each other. This arrangement facilitates hydrogen bonding between backbone carbonyls and amide protons four residues up the chain. Also notice that all the backbone carbonyls are pointing towards the C-temnius of the helix and the amide hydrogens are pointing towards the N-terminus of the helix.

Use the controls to the left to show hydrogen bonding. Move the molecule around and observe the arrangement of these hydrogen bonds.

Q1. Are all of the carbonyl and amide groups in the helix involved in hydrogen bonding? Which ones are not? Why?

(4). The side chains of amino acids extend outward from the helix axis. Use the controls below to view the side chains in the helix. Observe how they are arranged.

Hemoglobin is a classic example of a protein which contains predominantly alpha-helical secondary structure. into the JMol window (left).

Beta-Sheets
Although beta-sheets also contain hydrogen bonds between residues, the bonds in beta sheets are interstrand rather than intrastrand as in the case of a helix. In beta sheets hydrogen bonds exist between the residues of two separate beta strands. In beta-strands the phi and psi angles are about -150 and 150 degrees respectively.

(5).into the JMol window (left).

Use the controls to the left to manipulate the molecule as you did with the model of the helix.

Q2. What differences do you observe between the structure of the helix and the structure of the beta-sheet (hydrogen bonding, beta-strand axis and side chain distirbution, etc)?

Tenascin is an example of a protein which contains beta-sheet secondary structure. into the JMol window (left).