An Animated Look at Phi and Psi Angles
Each amino acid in a peptide or protein has two degrees of backbone
freedom. The angle denoted phi describes rotation about the C(alpha)-N
bond of the amino acid, and the angle psi denotes rotation about the bond
linking the alpha carbon and the carbonyl carbon.
The phi and psi angles in a peptide backbone are difficult to
visualize for most students. This exercise provides a three-dimensional,
animated look at phi and psi angles in a peptide and enables the user to
compare a data point on a Ramachandran plot (of psi versus phi) with
actual angles between a pair of peptide planes.
In this exercise, the first image that appears shows two peptide
planes arranged about an alpha carbon, such that phi = 0 and psi = 0.
The user has several options:
1) Click on the indicated buttons to observe positive and negative phi
and psi rotations. If you begin here, the selected plane will rotate in the
indicated direction until the selected angle (phi or psi) is 180 degrees.
2) Select a numerical value for phi or psi from the lists of available
values. When the value is selected, the molecule will begin to rotate to
adopt the selected value.
3) Click and drag the data point in the Ramachandran plot. When the
point is dragged around the plot, the phi and psi angles in the displayed
peptide will follow the data point.
4) Click Reset to return the phi and psi values to 0 degrees.
Note that at any time during this exercise, you can click an drag in the
black area to rotate the molecule to your own desired orientation.
Technical note: This exercise uses a Virtual Reality scene, constructed with
the Virtual Reality Modeling Language (VRML). The VRML scene is linked
to a Java applet, which presents the clickable buttons, the menu boxes
and the graph. The Java applet written for this exercise by Edward K.
O'Neil utilizes the External Authoring Interface (EAI), which permits
Java applets to communicate with and control VRML scenes.
Also note that you must have an appropriate VRML browser installed on your computer. Our
recommendation is the Cosmo Player
browser by SGI.
Click here to begin the exercise.