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 is the same as the default representation above, but just an end-on orientation of the peptide.
Protein backbone is another representation that is useful for viewing just the backbone atoms of peptides and proteins.
The spacefill representation more accurately represents the space occupied by the electron cloud of 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 ribbon representation is a more simplified rendering that 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
- 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.
