Ramachandran Map

A Ramachandran plot is a way to examine the backbone conformation of each residue in a protein. It was first used by G.N. Ramachandran et al. in 1963 to describe stable arrangements of individual residues of a protein. Today, a Ramachandran plot is frequently used by crystallographers to identify protein models with an unrealistic backbone.

As many of you may recall, each residue of a protein has two rotatable bonds, which we designate φ and ψ. If we take a protein structure and measure the rotations about these bonds (between -180 and 180 degrees), then we can plot each residue with respect to its φ (x-axis) and ψ (y-axis). The result is a Ramachandran plot, where each black point is a residue of the protein:

Certain rotations are more stable than others: white areas of the Rama plot are unstable, and a residue in this space will have a bad backbone score; colored areas of the Rama plot are more stable, and a residue in this space will have a better backbone score.

The stable areas of the Rama Map in Foldit are divided into four regions, called ABEGO regions, and are colored accordingly:

  • Red: Right-handed helix (characteristic of α-helix)
  • Blue: Right-handed strand (characteristic of β-strand)
  • Green: Left-handed helix (uncommon, except for GLY)
  • Yellow: Left-handed strand (very uncommon, except for GLY)

Because the 20 different amino acid types have different properties, each amino acid type has a slightly different Rama profile. For example, most amino acids have a side chain that would clash with the backbone in a left-handed helix, so maps of these residues have only a faint green region. However, glycine has no side chain and can easily adopt a left-handed helix conformation, so its map has a large, intense green region.

Mouse over a point in the Rama Map to see its residue type and number in the upper right corner.
Click on a point to see the specific Rama profile for its amino acid type; this also selects the residue in Selection Mode.
Click and drag a point to change the φ and ψ rotations of a single residue's backbone.

The viewport at the top of the Rama Map will focus on a selected residue, and simply shows the local configuration of the protein backbone around the selected residue. Each residue in the viewport is colored according to the ABEGO region in which it lies. The ABEGO coloring scheme can also be applied to the main Foldit console in the View Options with View->AbegoColor.

Ideal Loops

When designing a protein, there are usually a number of different loop backbones that can connect α-helices and β-strands. However, we've found that certain types of loops occur frequently in native proteins, and that these "ideal" loops can be distinguished by ABEGO patterns. For example, the most common way to connect two β-strands is by a short hairpin, with two residues in left-handed helix (green) conformation.

The Foldit Rama Map includes a gallery of ideal loops, located in the drop menus in the upper right corner. Each drop menu displays a handful of ideal loops that can be used to connect some combination of α-helices and β-strands. These are provided as a reference for Foldit players, and we encourage players to try to incorporate these loop structures in their designs. Within each drop menu, the most common loops are listed at the top, but a less common loop may be preferred depending on the precise layout of α-helices and β-sheets in a design!

The Rama Map will be available to use in selected design puzzles. It can be accessed from the Actions menu in the Original Interface; or from the Main menu in Selection Interface. Try out the new Rama Map in the latest design puzzle!

( Posted by  bkoep 85 1289  |  Wed, 03/16/2016 - 01:53  |  10 comments )
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Joined: 03/30/2013
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generously allowed

I am hugely in favor of this new addition to our folding tools. I am still learning to make the best use of it (like all of us). I am thinking the color scheme is based on observed hi-res, hi-quality protein structures in the database. Or is it based on an energy calculation?
I was also wondering if you might show us some generalized plot, so we could see our whole range of options in one graph (in case we want to mutate). Even more, I was wondering if you might give us a better indication of where the allowed, and generously allowed regions are, like possibly drawing a perimeter around these regions. Then i would get an idea if I am near enough to a colored region, if i am not quite in it for a particular residue.

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Good questions

The color scheme is arbitrary, and the four colors only serve to delineate the different ABEGO regions. We use this particular color scheme because it has been used in the literature, and many scientists that use Foldit are familiar with these ABEGO colors. The color intensity is proportional to the Foldit backbone score.

If no points are selected on the Rama Map, the default plot is a "generalized" plot that shows the average map for all 20 amino acids—but I understand that this does not show the full "range of options" (for instance, the yellow region is practically non-existent, even though GLY is perfectly happy in that space). We could think about displaying something like a "tolerant" plot like you suggest.

I'm hesitant to draw bounds around the areas the crystallographers refer to as "favored" and "allowed" (like this). The color intensities of the Rama Map come from the distribution of points observed in native proteins, and the distribution is pretty continuous—there is not a switch that flips at the transition from "favored" to "allowed."

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legibility

I think this would be far more useful if once you select a residue on the map that the same residue on the protein is highlighted with something obvious. Recognizing parts by a three segment length of loop is, ummm, less than ideal.

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Great suggestion!

For now, I would recommend using the Selection Interface (accessed from the Menu tab) if you're comfortable with it. In Selection Interface, selecting a residue on the Rama Map will also select the residue on your protein (the residue swells and turns magenta).

As you suggest, we can probably add some type of highlighting for those using the Original Interface.

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Ideal loops too small

It would really help if we could make the ideal loop rectangles bigger - they are hard to see, especially when I zoom out a little to see more of the backbone. (I was happy to learn the ideal loops are zoomable and rotatable.)

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Add another sheet-sheet loop

Could you please add a sample 4-residue sheet-sheet loop that turns the other way (opposite chirality)? Koga & Koga found that a 4-residue sheet-sheet loop has almost equal likelihood of turning left or right, and you have only given us one of the two options.

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Show ideal loops in Rama map

I really like this idea from jmbrownlee: Let us click on an ideal loop, and show the rama dots for that loop in a different color in the rama map. (There would have to be some way to tell which dot is which residue in the ideal loop.) Then we can see which ideal loop is closest to our current position, and we could drag our own dots closer to the ideal loop dots.

Also several people have said stick view is hard to see; could you let us toggle the ideal loops to cartoon thin? Don't get rid of stick view (IMO stick view is necessary if you want to copy the ideal loops accurately by eye), but let us pick.

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re ideal loops seeing/copying

re ideal loops

seeing/copying these by eye is at best time consuming. For many (not regular users of stick mode) it is almost impossible.

Since there is now the facility for 'residue count', can we not have the ability to click on an 'ideal loop' and have it imported into the solution - exactly as it should be folded? This would save so much time and effort.

Joined: 04/28/2015
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TRAJECTORY MOTION OF ATOMS ( THEORY OF IDEAS )

THEORY OF IDEAS

let rama card has 4 corners

if you are a programmer implement the trajectory of the atoms with the best assembly

Joined: 04/28/2015
Groups: Go Science
random arrangement of atoms

---Can the implementation of the script, random arrangement of atoms in the rama map? ---

For the moment I don't see how to do this. I think we have to suggest a LUA command in oder to "command" the turn of the atoms. That would be a good idea, may be for the feedback suggestions.

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