Minimizing steric clashes of mainchain and sidechain atoms.Maximize van der Waals interactions of mainchain atoms.These conformations are stable because they: A left-handed alpha helix is also stable, but relatively rare. Only two are commonly observed in proteins, the right-handed alpha helix and beta-structures. Given the possible values of \(\Phi\) and \(\Psi\) angles, many different shapes of the amino acid building block are possible and therefore many different three dimensional structures are possible. If the building block is a perfect rectangular prism, then the structure will remain linear. In the case of three dimensional building blocks that have some degree of curvature on both faces, the two dimensional circular structure becomes a helix. The radius of the circle is related to the degree of curvature. A straight chain occurs if the is no curvature in the block, while a circle will result if there is any degree of curvature. In two dimensions there are two possibilities, either a straight chain or some type of circle (which may or may not be closed). If a series of identically shaped objects are laid end-to-end they will form some type of geometrical structure. In regular secondary structures these angles are the same for each residue, and thus the shape of each building block, or amino acid, is the same. The shape of each block depends on the \(\Phi\) and \(\Psi\) angle of each residue. Proteins consist of a linear chain of amino acids, with each amino acid representing a build block.
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