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For example, residue i may form hydrogen bonds to residues j − 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The hydrogen bond arrangement in parallel beta sheet resembles that in an amide ring motif with 11 atoms.
In one sort, the beta bulge loop, one of the hydrogen bonds of the beta-bulge also forms a beta turn or alpha turn, such that the motif is often at the loop of a beta hairpin. [5] In the other sort, the beta link, the beta bulge occurs in combination with, and overlaps, a type II beta turn.
T = hydrogen bonded turn (3, 4 or 5 turn) E = extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues. B = residue in isolated β-bridge (single pair β-sheet hydrogen bond formation) S = bend (the only non-hydrogen-bond based assignment). C = coil (residues which are not in any of the above conformations).
The beta sheet is anti-parallel, and alternate strands run in the same directions. The first strand and last strand are next to each other and bonded by hydrogen bonds. Connecting loops can be long and include other secondary structures. The Greek key motif has its name because the structure looks like the pattern seen on Greek urns.
Consequently, hydrogen bonds between or within solute molecules dissolved in water are almost always unfavorable relative to hydrogen bonds between water and the donors and acceptors for hydrogen bonds on those solutes. [44] Hydrogen bonds between water molecules have an average lifetime of 10 −11 seconds, or 10 picoseconds. [45]
A beta helix is a tandem protein repeat structure formed by the association of parallel beta sheet in a helical pattern with either two [1] or three [2] faces. The beta helix is a type of solenoid protein domain. The structure is stabilized by inter-strand hydrogen bonds, protein-protein interactions, and sometimes bound metal ions. Both left ...
This electrostatic interaction stabilizes the peptide dipoles in a parallel orientation. Much like the contiguous helical hydrogen bonds that stabilize α-helices, high levels of aspartate are just as equally important in the survival of the 3 10-helix.
One hydrogen bond is then removed to create a three-residue loop, which is the secondary hairpin of class 1. Singly bound residues are counted in the loop sequence but also signal the end of the loop, thus defining this hairpin as a three-residue loop. This single hydrogen bond is then removed to create the tertiary hairpin; a five-residue loop ...