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Hydrophilic Coil Structure

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The hydrophilic residues are located on the solvent accessible surface of the leucine zipper, enabling these residues to interact with the water in the surrounding. This arrangement reduces the free-energy of protein folding by burying the hydrophobic residues in the interior of the protein, while exposing the hydrophilic residues to the water containing environment and thereby, stabilizing the coiled-coil structure.

Q37. The α helices of the leucine zipper motif can recognize and bind to DNA specifically, providing a scaffold for interaction of proteins with DNA.

Q38. The coiled coil structure contains approximately 3.5 residues per turn, with every seventh residue having an equivalent position as related to the helix axis. In addition, the
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Yes. The DNA-binding residues are located within the zipper motif, at the basic regions of the helices.

Q41. There are several hydrogen bonds between the protein and the base pairs of the DNA such as the cytosine at position 34, cytosine at position 12, and tyrosine at position 29. In addition, there seem to be several hydrogen bonds between the protein and the phosphate backbone of the DNA such as the oxygen in the phosphate group at position 33.

Q42. The arginine-234 forms two hydrogen bonds with the phosphate backbone at position 27.
The arginine-241 forms three hydrogen bonds with the phosphate backbone at position 28.
The arginine-245 forms one hydrogen bonds with the phosphate backbone at position 29. The arginine-243 forms two hydrogen bonds with the phosphate backbone at position 9. The arginine-232 forms one hydrogen bonds with the phosphate backbone at position 33. The arginine-240 forms three hydrogen bonds with the phosphate backbone at position 32.

Q43. Yes. The asparagine that hydrogen bond with two contiguous base pairs at the center of each half-state is located at position 235.

Q44. Yes. The two alanine that make van der Waals contact with the thymine methyl group
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