Sandbox 1742

The structure at the right is an 11-amino acid peptide fragment of a larger protein. Use the green links in the text below to view different representations of this peptide to help you answer the questions in your activity handout.

Representations

Ball and stick representations: , or

Space fill representations: , or

Ribbon representation:

Displaying Hydrogen Bonds

Let's view the hydrogen bonds that can be calculated from optimal distances/angles in this structure: for the structure , or . Use one of these representations to measure the distances necessary to complete the table in your activity.

A Reminder on Measuring Distances Between Atoms

• You might want to toggle off the spinning of the molecule (see spin button in lower left corner of the structure box).
• Put your cursor in the structure window.
• Decide on two atoms for which you would like to measure the distance between them.
• Using your cursor, hover over one atom and double-click on that first atom.
• Drag the cursor to the next atom and double click on the second atom. A distance label should now appear on the structure.

• Note that if the model gets cluttered, you may want to remove the distance labels. You can do this (and many other things!) by accessing the JSmol menu in the structure window. Hover the cursor inside the structure window, right click (control-click on your macbook), and scroll down to "Measurements" and choose "Delete measurements". You can also use this JSmol window to change the distance units.