User:Angel Herraez/Sandbox 8

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Dihedral angles (ϕ and ψ) in proteins and Ramachandran plot

Structure Ramachandran plot
Drag the structure with the mouse to rotate
(drag the purple point around)
ϕ
ψ

ϕ = phi ; ψ = psi

While dragging in the plot, restrict to:
<input type="radio" name="fixAng" onClick="fix_a(0)" id="freeA" checked>none <input type="radio" name="fixAng" onClick="fix_a('phi')">constant phi <input type="radio" name="fixAng" onClick="fix_a('psi')">constant psi

Or enter values:

ϕ = <input type="text" id="phi_V" style="width:4.5ex;"> ψ = <input type="text" id="psi_V" style="width:4.5ex;"> <input type="button" value="apply" onClick="setStruct()">

Structure rotation changing one angle:
<button onClick="rotate('phi');return false;">ϕ play/pause</button> <button onClick="rotate('psi');return false;">ψ play/pause</button>

<input type="checkbox" id="bumps"> Highlight collisions or clashes

(steric hindrance)
(does not work during rotation)

Legend for Ramachandran plot:

  • boundary of rather stable conformations (favoured)
  • boundary of moderately stable conformations (allowed)
  • α alpha helix (right-handed, the usual one)
  • Lα left-handed alpha helix (less common)
  • 310 3_10 helix
  • β beta strand, beta sheet
  • poly P polyproline helix (also collagen)


Image of Ramachandran plot areas modified from “[1]” by Dcrjsr [CC-BY license]

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Angel Herraez

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