Warning - If you have dial-up internet service, this applet may take a inordinate amount of time to load!
This applet displays all of the (103 346) possible conformations of a 27-mer on the points of a 3 × 3 × 3 lattice. Lattice models are useful for the computation of biophysical properties, because such computations are "tractable" (i.e., we can do them, with our current computers).
Click on st+ to view the next structure, and st- to view the previous structure. To quickly find a specific structure, click on +100 to increase the structure number by 100, or +1000 to increase the number by 1000. Clicking on -100 will decrease the structure number by 100, and -1000 by 1000.
You can also define a new sequence to be displayed, by typing into the box after sequence:. Be sure to click the mouse within the box before typing, or the letters won't appear in the box when you type.
This applet recognized only two types of amino acid, either hydrophobic (abbreviated "H", colored blue), or polar (abbreviated "P", colored red). Be sure to type in at least 27 consecutive letters, each of which is an "H" or a "P". The gray lines show the connectivity of the protein.
Click on right to rotate the cube a quarter turn to the right, and left to rotate a quarter turn to the left. Click on cw ("clockwise") to twist the cube a quarter-turn clockwise, and on ccw ("counter-clockwise") to twist counterclockwise. It is possible to view all 24 possible orientations of the cubic lattice this way.
For each structure, the applet calculates the number of HH, HP, and PP contacts. Two residues are considered to be in contact if the are adjacent on the cube, but are not connected by a gray line.
Proteins tend to fold in such a way that the hydrophobic amino acids are in the middle of the protein, and the polar acids are on the surface (in contact with the water solvent).
© 2004-2011 by Lawrence T. Sein. All rights reserved.
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