Figures for Notes on Helix Supersecondary Structures

This page contains all the figures used in the notes on helix supersecondary structures. You may want to keep this page open, or print this page when going through the notes.

Please also note that this page contains pdb files and you will need to use jmol to view the files. Simply click on the link to view the file.

Figure 5.0 Helix Hairpin

Manipulate the sequence, using Jmol with appropriate commands or scripts, to see the alpha helices, the hairpin structure, and the distribution of hydrophobic residues.

Coordinates from single chain of ROP (Repressor of Primer) 1rop.pdb. ROP usually occurs as a dimer of identical subunits (homodimer).

Figure 5.1 Alpha-alpha Corner

Figure 5.2 Helix-loop-helix structure

Figure 5.3 Helix-loop-helix

Manipulate the protein with Jmol and see if you can show the calcium binding to the helix-loop-helix in this protein.

Shown here is the helix-loop-helix from parvalbumin 5pal.pdb

Figure 5.4 Helix-turn-helix motif

The motif can be found fitting neatly in between the major groove of the DNA

Figure 5.5 Helix-turn-helix in DNA Binding Protein

The figure shows the protein bound to DNA. Manipulate the protein with Jmol and see if you can show the helix-turn-helix in this protein and its relationship with and without the DNA.

The coordinates are from DNA Binding Protein (1lmb.pdb)