Myoglobin contains 8 alphahelices one of which has the follo

Myoglobin contains 8 alpha-helices, one of which has the following sequence: -Gln-Gly-Ala-Met-Asn-Lys-Ala-Leu-Glu-His-Phe-Arg-Lys-Asp-lle-Ala-Ala Which side groups are likely to be on the side of the helix that faces the interior of the protein? Which are likely to be facing the aqueous solvent? Account for the spacing of the residues facing the interior.

Solution

a) The hydrophobic amino acids face the interior side of the helix. In the given amino acid sequence hydrophobic residues include Alanine, Methionine, Leucine, Phenylalanine and Isoleucine amino acids.

b) The amino acids that are hydrophilic face the aqueous side. In the given amino acid sequence hydrophilic residues include Aspargine, Lysine, histidine and Lysine.

c) The spacing of residues facing the interior is accounted by total number of amino acid residues / number of hydrophobic residues = 17/5 = 3.4