Two atoms cannot occupy the same space. That simple principle determines a great deal of protein molecular structure. Most proteins consist almost entirely of alpha helices and beta sheets, connected by turns and coil shown here in white. It is the avoidance of clashes between atoms that forces proteins to adopt these common secondary and tertiary structures. To understand the Rommet-Jundren principle, we'll use this small atomic model. In the center is a single complete alanine amino acid, all of whose atoms are marked by clouds of black dots. The atoms that are outside the black dots are fragments of adjacent amino acids that are connected to the central alanine and a polypeptide chain. Here is the main chain or backbone of the polypeptide, and over here is the side chain of the central alanine, the methyl group. The central alanine is connected to these other two amino acids by the two peptide bonds that are shown in magenta. In a polypeptide chain, each amino acid has two bonds that can rotate. Those bonds are part of the backbone or main chain. Each of those bonds defines a dihedral or torsion angle, something I'll explain next. Those two bonds are called phi and psi. A dihedral angle is determined by four atoms numbered here, one through four. These particular four determine the phi angle. Notice the relative positions of atoms one and four when the angle is zero degrees. Here we'll do a clockwise rotation around the phi bond, so we'll pass through 90 degrees, we'll reposing for a moment, and then we'll continue arriving at a dihedral angle of 180 degrees. If we rotate counterclockwise around the phi bond, by convention the angles are considered to be negative, here we're pausing at minus 90 degrees. And we'll continue rotating up to minus 135 degrees. If we continue to minus 180 degrees, that would be the same as plus 180 degrees. Peptide bonds have a double bonded character, this prevents them from rotating. They have this character because they resonate with the adjacent oxygen double bond. As a result of their inability to rotate, each peptide bond holds six atoms in a plane. An actuality, most phi or psi angles are impossible due to clashes between atoms. Remember that the atoms in this fallen stick model are much smaller than the true atom sizes. Here are the actual sizes of the atoms in our model. These are the so-called Vander Waal's radii. Here the psi angle is fixed at 165 degrees, and we're rotating the phi angle a full turn through 360 degrees. As the atoms get close to each other and begin to overlap, which would be physically impossible, but is allowed in this model, they clash with each other. And these clashes are shown as the yellow and red objects that appear in disappear during rotation. Wherever these yellow and red objects appear, the clashes, that angle of phi would be impossible when psi is 165 degrees. Here is a Rammachandrin plot. Along the bottom we have the phi angles from 0 to plus 180 and 0 to minus 180. And along this axis we have the psi angles from 0 to minus 180 and clockwise from 0 to plus 180. Inside the plot we have 100,000 tiny dots. Each dot represents the phi and psi angles that actually occurred in a single amino acid in one of a large number of reliable protein structures. This cluster of dots represents alpha helices, while this cluster of dots represents beta strands that form beta sheets, and here we have turns. Notice that there are large areas of the plot completely devoid of dots. These confirmations simply do not occur. Now let's compare our rotating phi animation with the Rammachandrin plot. Remember that psi is fixed at 165 degrees. You'll notice that as phi rotates, there's only one region that has no clashes. Let's watch it. Here's a big clash. And just as it disappears another clash, but starting here and going to there, there are no clashes. And that no clash region represents phi angles of minus 170 degrees to minus 70 degrees, namely the confirmation of beta strands. Here is another animation in which we're rotating psi. In this animation, phi is fixed at minus 80 degrees. As you watch psi rotate, you see there are two regions with no clashes. The first one starts here and goes to here, and the second one is shorter starting there and going to there. Those two areas of no clashes represent psi angles of minus 55 to 10 degrees, which is alpha helix, and 90 degrees to 180 slightly higher than 180, which would be minus 175, perhaps. And that region represents beta strands. In this third and final animation, I've set phi at zero degrees, an angle that does not occur in real proteins. Indeed, as you watch psi rotate, you see that there are clashes at all psi angles. Thus, phi of zero degrees is physically impossible. In conclusion, we've seen how atomic clashes limit the possible combinations of phi and psi angles, and how the permissible combinations represent the common secondary structures of alpha helices, beta sheets, turns, and coil. Would you like to try a little nine question quiz to see if you got the main points? This tutorial is also available as a slide show, so you can pick the slides that you want and narrate it for your audience. Would you like to have buttons to control the rotations of phi and psi, and be able to rotate the molecular model with your mouse? All of these options and more are available with the links below this video.