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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 ...
Secondary structure is defined by hydrogen bonding, so the exact definition of a hydrogen bond is critical. The standard hydrogen-bond definition for secondary structure is that of DSSP, which is a purely electrostatic model. It assigns charges of ±q 1 ≈ 0.42e to the carbonyl carbon and oxygen, respectively, and charges of ±q 2 ≈ 0.20e to ...
Preliminary binding of a ligand near to the entrance breaks hydrogen bonds S212-E474, S207-H172 in the open form of CYP2B4 and hydrogen bonds E218-A102, Q215-L51 are formed that fix the entrance in the closed form as the HB plot reveals. The second step is the transfer of the first electron from NADPH via an electron transfer chain. For the ...
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 ...
The hydrogen bonds are between the amide hydrogen and carbonyl oxygen of the peptide bond. There exists anti-parallel β pleated sheets and parallel β pleated sheets where the stability of the hydrogen bonds is stronger in the anti-parallel β sheet as it hydrogen bonds with the ideal 180 degree angle compared to the slanted hydrogen bonds ...
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 .
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 ...