What sections of the embedded protein chain are most likely to contain amino acids with hydrophobic r-groups? explain your reasoning?

Alpha helices are likely to form when there are hydrophobic R-groups. This is because the cell is a water matrix, therefore all of the hydrophobic R-groups will "face" each other and will be willing to bond with each other because they are non-polar and will not react with water. Alpha helices are the shape that they would assume because they are not interfacing with water.