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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.
The arrows indicate the hydrogen bonds that were identified in the figures. The relative direction of each strand is indicated by the "+" and "-" at the bottom of the table. Except for strands 1 and 6, all strands are antiparallel. The parallel interaction between strands 1 and 6 accounts for the different appearance of the hydrogen bonding ...
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).
An ubiquitous example of a hydrogen bond is found between water molecules. In a discrete water molecule, there are two hydrogen atoms and one oxygen atom. The simplest case is a pair of water molecules with one hydrogen bond between them, which is called the water dimer and is often used as a model system. When more molecules are present, as is ...
In the A-U Hoogsteen base pair, the adenine is rotated 180° about the glycosidic bond, resulting in an alternative hydrogen bonding scheme which has one hydrogen bond in common with the Watson-Crick base pair (adenine N6 and thymine N4), while the other hydrogen bond, instead of occurring between adenine N1 and thymine N3 as in the Watson ...
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.
Chemical structures for Watson–Crick and Hoogsteen A•T and G•C+ base pairs. The Hoogsteen geometry can be achieved by purine rotation around the glycosidic bond (χ) and base-flipping (θ), affecting simultaneously C8 and C1 ′ (yellow). [1] A Hoogsteen base pair is a variation of base-pairing in nucleic acids such as the A•T pair.
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 ...