More on the chemistry of secondary structure and amino acid preferences.
Here is a link to the example protein used in the lecture.
Click on domain 3 of chain A - you will see a multiple sequence alignment. Use the pull-down menus to choose "up to 50 ... of the most diverse members" and then click on "View 3D Structure ... using all atoms" (with Cn3D).
When the structure viewer comes up, you can change the colouring (to "By Hydrophobicity" for example) using the "Style" menu.
You can look at patterns of hydrophobicity in helices and strands, in the protein of known structure, and the 50 homologous proteins.
For a better example of alternating hydrophobicity in a semi-exposed beta sheet, see this structure of sonic hedgehog. (Click on "View 3D Structure").
To see an example of the structural similarity between two distantly related proteins, go to this Ribonuclease H protein, and click on the magenta chain graphic. Now you'll see a list of structurally similar proteins (found using the program "VAST"). Change the "subset sorted by" to "Seq. Identity" and hit "List".
Now you can see that there are many structral neighbours with very low sequence identity (suggesting that share a distant ancestor). Check the box next to "1ASU" and then hit the "View 3D structure" (all atoms) button. Now you will see the two structures (Ribonuclease H and a viral integrase protein) aligned in 3D space. Look carefully at both the similarities and differences between the two structures.