Before understandind Ramachandran plot It is very  important to  understand the structure of a peptide bond which is rigid and planar in nature .Simply   A  Ramachandran plot  is a  plot  to visualize energetically allowed regions for a polypeptide backbone torsion  angles  psi (ψ ) against (phi)  φ of amino acid residues  present in a  protein structure.It is used to analyze  the structure of  a protein , the conformation of the amino acid present in the protein  and close contacts between the atoms

Ramachandran plot is when on x-axis You put value of phi torsion angle, and on y-axis psi angle is. Both from one residue of protein. By comparing position of your residue on that plot, with a model plot where allowed and favourite areas are marked You can evaluate structure of Your protein.

So should we call it a phi-psi scatter plot or phi-psi energy diagram.

I would use scatter plot. For sure not energy - it is about degrees

OK, RP could be useful in following ways:

1. for determine protein structure and the position of amino acids (aa)

2. If the % of aa is more than 88 % in allowed region the protein model is good for in silico studies

3. It tells about allowed and dis allowed regions of the aa that reflects the stability of protein structure.

A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure. A Ramachandran plot can be used in two somewhat different ways. One is to show in theory which values, or conformations, of the ψ and φ angles are possible for an amino-acid residue in a protein. A second is to show the empirical distribution of datapoints observed in a single structure

The colouring/shading on the plot represents the different regions described in Morris et al. (1992): the darkest areas correspond to the "core" regions representing the most favorable combinations of phi-psi values.

Ideally, one would hope to have over 90% of the residues in these "core" regions. The percentage of residues in the "core" regions is one of the better guides to stereochemical quality. The different regions were taken from the observed phi-psi distribution for 121,870 residues from 463 known X-ray protein structures. The two most favoured regions are the "core" and "allowed" regions which correspond to 10° x 10° pixels having more than 100 and 8 residues in them, respectively. The "generous" regions were defined by Morris et al. (1992) by extending out by 20° (two pixels) all round the "allowed" regions. In fact, the authors found very few residues in these "generous" regions, so they can probably be treated much like the "disallowed" region and any residues in them investigated more closely.

I would add "to confirm that either any structure is possible or not we use RP". On the basis of phi and psi angles, we decide that either this kind of rotation and torsion is possible theoretically in the periphery of structure biology. In RP we call it as allowed regions and non allowed regions on the basis of these torsion angles.

Thank you all... its been very informative

Its a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.

Thank you everyone for such valuable Information.

I am not from BioInfo, but i m doing some in silico work now. So is it worth while to check the protein structure using Ramachandran Plot?

I mean the proteins i download from RCSB PDB.. Nothing that i modelled personally. Just the protein structures that i downloaded from PDB site. Is it worth while to check the Favoured, allowed and generous regions in a protein structure, before going into Docking studies??

Thanks in Advance..

All the above answers are very good but it is also important first to know the structure of peptide bond which is planar or rigid in nature .The peptide bond between the carbon and nitrogen shows the partial double bond characteristic .Although it is rigid but free rotation can take place about C alpha-N and C alpha-C.As the backbone  of a protein is a linked sequence of planar structure  of peptide bond. The conformation of  polypeptides backbone is specified by the rotation angles about the C alpha-N,( phi) and C alpha-C bond (psi) of each of its amino acid residues. The phi & psi will be at  180 degree when polypeptide is in its fully extended form and it will be  clockwise rotation when seen from C alpha. The conformation range of the two angles in polypeptide chain  backbone is restricted by the steric hindrance ( Steric hindrance between adjacent groups can also restrict torsional bond angles )The values (sterically allowed) of these two angles can be determind by calculating the distance between the atoms of the tripeptide   or oligopeptid   at all the values of two angles for central peptide unit  these values can be visualized in a steric contour  diagram which all we know is the Ramachandran plot .

What is the difference in the extreme and normal limit of Ramachandran Plot?

I use RAMPAGE and I'm happy with it...

  Before understandind Ramachandran plot It is very  important to  understand the structure of a peptide bond which is rigid and planar in nature .Simply   A  Ramachandran plot  is a  plot  to visualize energetically allowed regions for a polypeptide backbone torsion  angles  psi (ψ ) against (phi)  φ of amino acid residues  present in a  protein structure.It is used to analyze  the structure of  a protein , the conformation of the amino acid present in the protein  and close contacts between the atoms

If one allows for slight distortions of the bond angles around the C-alpha atom, some regions that would be considered unfavorable become more favorable.

A paper from 2007 noted in its abstract, "Thus, it appears that the rare tolerance of disallowed conformations is possible by gentle and acceptable deviations in a number of bond lengths and angles, from ideal geometry, over a series of bonds resulting in a net gross effect of acceptable non-bonded inter-atomic distances."

If you like molecular models, here is a YouTube video:  https://www.youtube.com/watch?v=Kewhg5spUjs

Thank u to all. Very informative

is ramachandran plots base only on amino acids (protein)

Ramachandran is used for the measurement of angles in amino acids (proteins), however, the principle can be adapted to measure angles in other types of molecules. E.g. CARP - Carbohydrate Ramachandran Plot - you get the idea what it does :)

http://glycosciences.de/tools/carp/

Thanks Muhamed, can u please tell me how long did it take for you to get the result from Rampage?

A few seconds only...

I left it even overnight but nothing has happened, even when I hit the ''For high-resolution output,  Adobe PDF'' the PDF is just a white page , Could you please send me the link which you used? I am using http://mordred.bioc.cam.ac.uk/~rapper/rampage.php 

That is the exact same link that I've been using.

I upload .pdb file, submit it and in a few seconds I have results.

I also have a problem with .pdf file, though (just checked it).

But I do get the results in the webpage (I am using latest Chrome version). I get Ramachandran plot together with textual output, e.g.:

Number of residues in favoured region (~98.0% expected) : 263 ( 89.5%)

Number of residues in allowed region ( ~2.0% expected) : 19 ( 6.5%)

Number of residues in outlier region : 12 ( 4.1%)

If you don't manage it, I can try running your .pdb file, to see where is the issue. My email is [email protected].

Please downlod the Swiss-PdbViewer and then it can be plotted. You can use this forum for sharing ideas, questions, and concerns about Swiss-PdbViewer and its applications in research, teachingan publishing.The Ramachandran Plot Window plots only values for the currently selected amino-acids of the current layer. The name of the current layer is drawn at the bottom left of the window.

i really appreciate all for the valuable answers.....

Does it mean that the protein in the allowed region has phi- psi angles are in the extended form and free to rotate and flexible.

No, a perfectly extended polypeptide has phi = psi = 180, but that pair of values is not among the lowest in energy. Phi and psi are each defined for single bonds; therefore, they can take multiple values because single bonds can rotate. However, not every pair of angles is equal in energy (think about gauche and anti butane in organic chemistry). The forbidden regions are places in which the pair of values is associated with high energy, sometimes very high. What happens in the forbidden regions is that the electron clouds of atoms that are not joined by a covalent bond get too close to each other.

OK, thanks a lot.....