Alpha/Beta Structures. Beta strands. 3 type of Alpha/Beta structure exists Barrels Open sheets Horseshoe (I don’t believe we covered this)
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In alpha/beta barrels the side chains of the alpha helices are packed against the h-phobic side chains of the B-sheet and this packing interaction between the alpha and beta are dominated by branched h-phobic residues (V, I, L)
The alpha helices are anti-parallel to the adjacent B-strands
In a given sequence of beta strand, it is known that h-phobic residues and h-philic residues alternate, thus the h-phobic residues face inward of the barrel forming the h-phobic core
Also, the formation of the interior of the barrel is not limited to h-phobic residues, because the top and bottom surface can comprise of polar/charged group as the polar end will be in contact with the solvent whereas the h-phobic parts of the side chain will interact with the core of the protein
In these barrels the active site is commonly found in very similar positions, usually situated at the bottom of the funnel-shaped pocket created by eight loops that connect the carboxy end of the beta-strand to the amino end of the alpha helices.