Sandbox 1742

Peptide 1 is an 11-amino acid 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

The default representation is called . This is an end-on orientation of the peptide.

Another representation that is useful for viewing peptides includes only the .

If you use a representation, it more accurately represents the space occupied by each of the atoms. This representation only shows the spacefill of the heteroatoms of the protein backbone, and starts from an end-on orientation.

A more simplified rendering is called and is often used to trace the backbone location in large protein structures.

Displaying Hydrogen Bonds

Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules. Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:

Measuring Distances Between Atoms

Be sure to go back to a representation of this Model that will allow you to see which atoms are WITHIN one water molecule and which atoms are in DIFFERENT water molecules. Once you have selected a representation (by clicking on one of the green text options in the "Representations" section above), to measure distances between two atoms you can follow these steps:

• You might want to stop the spinning of Model 2 (click the +/-spin button at the bottom of the structure window).
• 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.

Measuring Angles formed by 3 Atoms

To measure the angle formed by three atoms in the Model, you can follow steps very similar to those for measuring distances:

• Stop the spinning of the Model.
• Hover your cursor over the first atom and double-click on that atom.
• Single-click on the second atom (the middle one).
• Finish by double-clicking on the third atom. An angle label should now appear on the structure.