Ramachandran Plot - Online Tutor, Practice Problems & Exam Prep

Ramachandran plots illustrate the permissible phi (φ) and psi (ψ) bond angles in polypeptides, excluding the omega (ω) bond due to its restricted rotation. The plot reveals regions of steric hindrance, indicating non-permissible angles. Key secondary structures, such as α-helices and β-sheets, occupy specific areas within the plot, aiding in protein structure prediction. Understanding these angles is crucial for analyzing protein conformation and interactions, as they influence the overall stability and functionality of proteins.

Ramachandran Plot

In this video, we're going to begin our discussion on Ramachandran plots. In our last lesson video, we said that peptide bond rotation is limited and restricted due to its partial double bond character. However, bond rotations, specifically around the alpha carbon bonds, are still possible even though the peptide bond rotation is restricted. It turns out that there are three bond rotation angles that you should be familiar with, and they're symbolized with these Greek letters. In our example below, we're going to distinguish between these three bond angles in the peptide that's being shown.

In this peptide, we have a free amino group on the far left. On the far right, what we have is a little squiggly line which is a continuation of the peptide. We're not being shown the C-terminal end, and we're only being shown a small snippet of our peptide. Notice that the R groups of our peptide here are in blue. The first amino acid residue has a hydrogen as its R group, which means that we have a glycine amino acid residue. The second amino acid residue has a methyl group as its R group, which means that we have an alanine amino acid residue.

To distinguish between these three bond angles, the first bond angle that you should know is the phi bond angle. Phi is symbolized with the Greek letter phi, and it represents the rotation angles around the alpha carbon-nitrogen bond in the backbone. Taking a look at our alanine amino acid residue below in our peptide, notice that the alpha carbon is this carbon here, which is attached to the R group. The alpha carbon, bonded to the nitrogen, represents the phi bond. This bond right here is the phi bond, representing the bond rotation angles around the phi bond.

The second bond rotation angle that you should know is the psi bond. Psi is symbolized with the Greek letter psi and represents rotation angles around the alpha carbon-carbonyl group carbon bond in the backbone. Looking again at our alanine amino acid residue, here is our alpha carbon, and the carbonyl group carbon is over here. The bond between the alpha carbon and the carbonyl group carbon represents the psi bond, indicating the bond rotation angles around the psi bond.

The last bond rotation angle that you should be familiar with is omega. Omega, symbolized with the Greek letter omega, represents rotation angles of the peptide bond. Looking below at our peptide, we see that the peptide bond is in red here and notice that it has partial double bond character with this dotted line. Omega represents the bond rotation angles around the peptide bond. Omega and the bond rotation angles around the peptide bond are severely limited and restricted because of the partial double bond character. This makes it not interesting to plot omega on a Ramachandran plot. When plotting a Ramachandran plot, we only focus on the phi and the psi bond rotation angles.

Looking over at our other figure, which is a ball and stick figure of a peptide, notice that the alpha carbon is this black ball in the center. The bonds around the alpha carbon are all able to still rotate. So bond rotations around the alpha carbon are still possible. You see that the alpha carbon-nitrogen bond, the blue ball over here, represents the nitrogen, phi bond. Here, this bond in green is analogous to this bond in green, which is the phi bond, and then the psi bond is between the alpha carbon and the carbonyl group carbon, shown in yellow. These arrows indicate that these bonds are able to freely rotate, whereas, the peptide bonds, which would be this bond over here in red, are restricted and limited. That's why we see the plane behind them that indicates the peptide group that is planar.

What we need to understand, because we're mainly going to focus on phi and psi bonds, is that each individual amino acid residue has its own phi and psi bonds. If we take a look at our glycine amino acid residue over here, notice that its alpha carbon is right here. The alpha carbon-nitrogen bond, which would be this bond right here, is going to be the phi bond, as we said before. The alpha carbon-carbon bond over here is going to be the psi bond, drawn in as well. And, of course, the peptide bonds are always going to be, so this bond right here is going to be the peptide bond, representing omega.

Moving forward, we're going to talk more about Ramachandran plots, and we'll be able to get a lot more practice understanding phi and psi bond angles. I'll see you guys in our next video where we'll be able to get a little bit of practice distinguishing between phi and psi bond angles. See you there.

Ramachandran Plot

So now that we've talked about the phi, psi and omega bond angles, we can talk about Ramachandran plots. Since the peptide bond rotation or omega is hindered by the double bond nature, really it's just the phi and the psi bond angles that determine the structure of a polypeptide. Because it's phi and psi that determine the structure of a polypeptide, that is what the plot focuses on plotting. The omega bond angle is actually excluded from the Ramachandran plot, so it's not part of the Ramachandran plot. Even though the phi and the psi bond angles are free to rotate, they're still somewhat restricted by steric hindrance, specifically between the R groups and the backbone carbonyl oxygens.

The rotation angles for phi and psi range from -180° to 0°, or counterclockwise angles, as well as from 0° to 180° which would be clockwise angles. A Ramachandran plot shows the permissible and the non-permissible bond angles for phi and psi. You can think of it as showing just the phi and psi angles for a single amino acid residue, or it could be showing all of the phi and psi angles for all of the amino acid residues in an entire protein.

In the example below, we discussed a typical Ramachandran plot for almost all amino acids with just two exceptions. On the x-axis, the phi bond angles are plotted, ranging from -180° to 180°. On the y axis, we have the psi bond angles which also range from -180° to 180°. The blue regions on the plot represent permissible bond angles, and the white regions symbolize non-permissible bond angles due to steric hindrance. Most permissible bond angles are found in the top-left and bottom-left of the Ramachandran plot, with fewer structures falling on the right side.

By examining a Ramachandran plot, we can reveal some of the secondary structures of a protein, such as beta sheets and alpha helices. Beta sheets are typically found in the upper-left quadrant, whereas alpha helices are in the bottom-left quadrant of a Ramachandran plot.

When discussing bond angles in terms of Newman projections, remember that a Newman projection is a molecular depiction where you're looking down the length of a bond. The bond angles that we measure might be between specific groups, providing specific angles between these groups, essentially reflecting the concepts behind Newman projections. However, this might be more detailed than necessary for an introductory explanation.

A Ramachandran plot shows:

• A. The likelihood that proline bond angles allow it to form hydrogen bonds.
• B. The stability of the pKa of amino acids in a hydrophobic environment.
• C. The values of the torsional angles and allows prediction of the protein/amino-acid conformation.
• D. The probability for a protein to be soluble or insoluble in polar solutions.

Why are some regions of a Ramachandran plot shaded while others are unshaded? Circle all true answers.

a) Shaded regions correspond to the most common permissible conformations and bond angles.

b) Unshaded regions correspond to the ΔG values for each combination of phi & psi bond angles.

c) Unshaded regions correspond to restricted bond angles that are non-permissible & less common.

d) Shaded regions can be analyzed to reveal the full primary structure of a peptide.

So this practice problem asks, why are some regions of a Ramachandran plot shaded while others are unshaded? Circle all true answers. And so there may be more than one true answer below. I'm not sure. Let's go through them and find out. So A says, Shaded regions correspond to the most common permissible confirmations and bond angles. And this is actually true. A is true because we know that the shaded or the colored regions, those are the permissible bond angles and the permissible bond angles are going to have permissible confirmations. And by permissible, what we mean is they are allowable and that they can occur. And they can occur because they encounter very little resistance when they try to take on these confirmations. And so A here is correct, and we can go ahead and circle it as it says to do. B says, unshaded regions correspond to the delta g values for each combination of phi and psi bond angles. And this is not true. We never said anything about delta g or the change in Gibbs free energy or thermodynamics or anything like that when it came to the unshaded regions of a Ramachandran plot. So B here is false, and we can scratch it off our list. Now, C says that unshaded regions correspond to restricted bond angles that are non-permissible and less common. And C is actually true. The unshaded regions or the white regions on a Ramachandran plot correspond to bond angles that are not permissible because they're restricted. So they are restricted. And because they are restricted, it means that they are probably encountering steric hindrance when they try to achieve these confirmations. So the R groups are probably preventing the steric hindrance between the R groups which are preventing these conformations or, potentially, the steric hindrance between carbonyl group oxygens are preventing these conformations. So these unshaded regions are non-permissible and because they are non-permissible, they are going to be less common. So this is all true here, so we can circle C as well as being true. So, D here says, shaded regions on a Ramachandran plot can be analyzed to reveal the primary structure of a peptide. This is incredibly difficult to do or probably impossible to do with a Ramachandran plot. So the shaded regions only tell you the phi and psi bond angles, but there is overlap between different amino acid residues, so it would be very difficult and probably impossible to do something like this. But if this were to say secondary structure, then it might be true. It would be true. So the shaded regions can be analyzed to reveal the secondary structure of a peptide, such as the alpha helices and beta sheets. But for the primary structure, that would be the exact sequence of amino acids and that would not be possible with a Ramachandran plot. So, D here is incorrect as written because it says primary. But if it were to say secondary, it would be true. And that concludes this practice problem. A and C here are correct, so we can mark it as A and C as being correct here. And that concludes this practice, and I'll see you guys in our next video.

The predominate structure in α-keratin, a mammalian protein that makes up large portions of hair & nails, is the α-helix. Mark the approximate locations on a Ramachandran plot you might expect to find φ and ψ angles for α-keratin amino acid residues.

So this practice problem says, the predominant structure of alpha keratin, which is a mammalian protein that makes up large portions of hair and nails, is the alpha helix. And then it says, mark the approximate locations on a Ramachandran plot you might expect to find the phi and psi bond angles for alpha keratin amino acid residues. And so, basically, the key here is the alpha helix that we highlighted above. And so, what we have here is the alpha helix structure, which you guys may be somewhat familiar with from your previous courses. And so, the alpha helix structure requires a very specific set of phi and psi bond angles, and that specific set of phi and psi bond angles happens to fall in the bottom left quadrant of a Ramachandran plot. So that means that we would expect the region to be right in this region somewhere, in the bottom left. So it’s a pretty large region because there is a little bit of flexibility that is allowed. And so sometimes, you'll see different textbooks have slightly different ranges that are allowable for the alpha helix, but the main point is that it's found somewhere in the bottom left quadrant. So if you know that, you'll be set and good to go. And again, once we get to talking about the alpha helix secondary structures a little bit later in our course, we'll bring this back up and, we'll talk a little bit more about it. So, that concludes this practice problem, and I'll see you guys in our next practice.

The principal component of silk is the protein fibroin, which is a classic example of β-sheet structure. Mark the approximate locations on a Ramachandran plot you might expect to find φ and ψ angles for silk amino acid residues.

So this practice problem says, the principal component of silk is protein fibroin which is a classic example of a beta sheet structure. Mark the approximate locations on a Ramachandran plot that you might expect to find the phi and psi bond angles for silk amino acid residues. And so down below, what we have is the structure of a beta sheet, which you guys might recognize from your old courses. And so, the key to this practice problem is recognizing the beta sheet structure here, and we know that Ramachandran plots reveal secondary structure, such as alpha helices and beta sheets. Now, beta sheets require a very particular set of phi (φ) and psi (ψ) bond angles, and that particular set of φ and ψ bond angles happens to fall into the upper left quadrant of a Ramachandran plot, so somewhere up in this region up here. And so, the region is pretty wide because there is a little bit of flexibility that is allowed for the phi (φ) and psi (ψ) bond angles for a beta sheet. And again, you'll see that the regions change somewhat, from Ramachandran plot to Ramachandran plot and from textbook to textbook. But, if you know that the beta sheet structure falls in the upper left-hand quadrant, then you'll be good for those practice problems. And so, when we get to secondary structures and beta sheets a little bit later in our course, we'll revisit this idea of beta sheets and Ramachandran plots. But for now, this concludes this practice problem and I'll see you guys in our next practice video.

Which of the following statements is true for the portion of the peptide shown in the figure below?

• A. Arrow A is pointing to the phi bond, B is pointing to the psi bond.
• B. Arrow B is pointing to the phi bond, C is pointing to the psi bond.
• C. Arrow C is pointing to the phi bond, A is pointing to the psi bond.
• D. Arrow C is pointing to the phi bond, B is pointing to the psi bond.

Here’s what students ask on this topic:

What is a Ramachandran plot and what does it show?

A Ramachandran plot is a graphical representation used in biochemistry to visualize the permissible phi (φ) and psi (ψ) bond angles in polypeptides. It excludes the omega (ω) bond due to its restricted rotation. The plot reveals regions of steric hindrance, indicating non-permissible angles, and permissible regions where the bond angles are allowed. Key secondary structures, such as α-helices and β-sheets, occupy specific areas within the plot, aiding in protein structure prediction. Understanding these angles is crucial for analyzing protein conformation and interactions, as they influence the overall stability and functionality of proteins.

Why are omega (ω) bond angles excluded from the Ramachandran plot?

Omega (ω) bond angles are excluded from the Ramachandran plot because the rotation around the peptide bond is severely restricted due to its partial double bond character. This restriction limits the ω bond angle to around 180° (trans configuration) or 0° (cis configuration), making it uninteresting to plot. The Ramachandran plot focuses on the phi (φ) and psi (ψ) bond angles, which have more freedom to rotate and thus play a more significant role in determining the structure of polypeptides.

What are the typical regions for α-helices and β-sheets on a Ramachandran plot?

On a Ramachandran plot, α-helices typically occupy the bottom left quadrant, where the phi (φ) angles are around -60° and the psi (ψ) angles are around -45°. β-sheets, on the other hand, are found in the upper left quadrant, where the phi (φ) angles are around -135° and the psi (ψ) angles are around 135°. These regions indicate the permissible bond angles for these secondary structures, aiding in the prediction and analysis of protein conformations.

How do steric hindrance and bond angles affect the Ramachandran plot?

Steric hindrance, caused by the spatial arrangement of atoms, restricts the rotation of phi (φ) and psi (ψ) bond angles in polypeptides. This hindrance is primarily due to interactions between the R groups and the backbone carbonyl oxygens. As a result, the Ramachandran plot shows permissible regions where these angles can exist without causing steric clashes. Non-permissible regions, indicated by white areas on the plot, represent angles that cannot be achieved due to steric hindrance. Understanding these constraints is essential for predicting protein structures and their stability.

What is the significance of the phi (φ) and psi (ψ) bond angles in protein structure?

The phi (φ) and psi (ψ) bond angles are crucial in determining the three-dimensional structure of proteins. These angles describe the rotation around the bonds between the alpha carbon and the nitrogen (φ) and the alpha carbon and the carbonyl carbon (ψ). The specific values of these angles dictate the folding and conformation of the polypeptide chain, influencing the formation of secondary structures like α-helices and β-sheets. Accurate knowledge of these angles helps in understanding protein stability, function, and interactions.