Editing Beta sheet (section)

==Structure and orientation==

===Geometry===
The majority of β-strands are arranged adjacent to other strands and form an extensive [[hydrogen bond]] network with their neighbors in which the [[amine|N−H]] groups in the backbone of one strand establish [[hydrogen bond]]s with the [[carbonyl|C=O]] groups in the backbone of the adjacent strands. In the fully extended β-strand, successive side chains point straight up and straight down in an alternating pattern. Adjacent β-strands in a β-sheet are aligned so that their C<sup>α</sup> atoms are adjacent and their side chains point in the same direction. The "pleated" appearance of β-strands arises from tetrahedral chemical bonding at the C<sup>α</sup> atom; for example, if a side chain points straight up, then the bonds to the C′ must point slightly downwards, since its bond angle is approximately 109.5°. The pleating causes the distance between C{{su|p=α|b=''i''}} and C{{su|p=α|b=''i'' + 2}} to be approximately {{cvt|6|Å|nm|lk=on}}, rather than the {{cvt|7.6|Å|nm}} expected from two fully extended ''[[Cis-trans isomerism|trans]]'' [[peptide bond|peptide]]s. The "sideways" distance between adjacent C<sup>α</sup> atoms in [[hydrogen bond|hydrogen-bonded]] β-strands is roughly {{cvt|5|Å|nm}}.
[[File:Ramachandran plot general 100K.jpg|thumb|left|200px| Ramachandran (''φ'',&nbsp;''ψ'') plot of about 100,000 high-resolution data points, showing the broad, favorable region around the conformation typical for β-sheet amino acid residues.]]
However, β-strands are rarely perfectly extended; rather, they exhibit a twist. The energetically preferred [[dihedral angle]]s near (''φ'',&nbsp;''ψ'') = (–135°,&nbsp;135°) (broadly, the upper left region of the [[Ramachandran plot]]) diverge significantly from the fully extended conformation (''φ'',&nbsp;''ψ'') = (–180°,&nbsp;180°).<ref>{{cite book |title=Biochemistry | vauthors = Voet D, Voet JG |year=2004 |edition=3rd |publisher=Wiley |location=Hoboken, NJ |isbn=0-471-19350-X |pages=[https://archive.org/details/biochemistry00voet_1/page/227 227–231] |url=https://archive.org/details/biochemistry00voet_1|url-access=registration }}</ref> The twist is often associated with alternating fluctuations in the [[dihedral angle]]s to prevent the individual β-strands in a larger sheet from splaying apart. A good example of a strongly twisted β-hairpin can be seen in the protein [[BPTI]].

The side chains point outwards from the folds of the pleats, roughly perpendicularly to the plane of the sheet; successive amino acid residues point outwards on alternating faces of the sheet.

===Hydrogen bonding patterns===
{{multiple image
| direction = horizontal
| width = 150
| image1 = Beta sheet bonding antiparallel-color.svg
| image2 = Beta sheet bonding parallel-color.svg
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| caption1 = '''Antiparallel''' β-sheet [[hydrogen bonding]] patterns, represented by dotted lines. [[Oxygen]] atoms are colored <span style="color:red;">'''red'''</span> and [[nitrogen]] atoms colored <span style="color:blue;">'''blue'''</span>.
| caption2 = '''Parallel''' β-sheet [[hydrogen bonding]] patterns, represented by dotted lines. [[Oxygen]] atoms are colored <span style="color:red;">'''red'''</span> and [[nitrogen]] atoms colored <span style="color:blue;">'''blue'''</span>.
}}
Because peptide chains have a directionality conferred by their [[N-terminus]] and [[C-terminal end|C-terminus]], β-strands too can be said to be directional. They are usually represented in protein topology diagrams by an arrow pointing toward the C-terminus. Adjacent β-strands can form [[hydrogen bond]]s in antiparallel, parallel, or mixed arrangements.

In an antiparallel arrangement, the successive β-strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next. This is the arrangement that produces the strongest inter-strand stability because it allows the inter-strand hydrogen bonds between carbonyls and amines to be planar, which is their preferred orientation. The peptide backbone dihedral angles (''φ'',&nbsp;''ψ'') are about (–140°,&nbsp;135°) in antiparallel sheets. In this case, if two atoms C{{su|p=α|b=''i''}} and C{{su|p=α|b=''j''}} are adjacent in two [[hydrogen bond|hydrogen-bonded]] β-strands, then they form two mutual backbone hydrogen bonds to each other's flanking [[peptide bond|peptide groups]]; this is known as a '''close pair''' of hydrogen bonds.

In a parallel arrangement, all of the N-termini of successive strands are oriented in the same direction; this orientation may be slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. The dihedral angles (''φ'',&nbsp;''ψ'') are about (–120°,&nbsp;115°) in parallel sheets. It is rare to find less than five interacting parallel strands in a motif, suggesting that a smaller number of strands may be unstable, however it is also fundamentally more difficult for parallel β-sheets to form because strands with N and C termini aligned necessarily must be very distant in sequence {{Citation needed|date=August 2019}}. There is also evidence that parallel β-sheet may be more stable since small amyloidogenic sequences appear to generally aggregate into β-sheet fibrils composed of primarily parallel β-sheet strands, where one would expect anti-parallel fibrils if anti-parallel were more stable.

In parallel β-sheet structure, if two atoms C{{su|p=α|b=''i''}} and C{{su|p=α|b=''j''}} are adjacent in two [[hydrogen bond|hydrogen-bonded]] β-strands, then they do ''not'' hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue ''i'' may form hydrogen bonds to residues ''j''&nbsp;−&nbsp;1 and ''j''&nbsp;+&nbsp;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.

Finally, an individual strand may exhibit a mixed bonding pattern, with a parallel strand on one side and an antiparallel strand on the other. Such arrangements are less common than a random distribution of orientations would suggest, suggesting that this pattern is less stable than the anti-parallel arrangement, however bioinformatic analysis always struggles with extracting structural thermodynamics since there are always numerous other structural features present in whole proteins. Also proteins are inherently constrained by folding kinetics as well as folding thermodynamics, so one must always be careful in concluding stability from bioinformatic analysis.

The [[hydrogen bond]]ing of β-strands need not be perfect, but can exhibit localized disruptions known as [[beta bulge|β-bulge]]s.

The hydrogen bonds lie roughly in the plane of the sheet, with the [[peptide bond|peptide]] [[carbonyl]] groups pointing in alternating directions with successive residues; for comparison, successive carbonyls point in the ''same'' direction in the [[alpha helix]].

===Amino acid propensities===
Large aromatic residues ([[tyrosine]], [[phenylalanine]], [[tryptophan]]) and β-branched amino acids ([[threonine]], [[valine]], [[isoleucine]]) are favored to be found in β-strands in the ''middle'' of β-sheets. Different types of residues (such as [[proline]]) are likely to be found in the ''edge'' strands in β-sheets, presumably to avoid the "edge-to-edge" association between proteins that might lead to aggregation and [[amyloid]] formation.<ref>{{cite journal | vauthors = Richardson JS, Richardson DC | title = Natural beta-sheet proteins use negative design to avoid edge-to-edge aggregation | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 99 | issue = 5 | pages = 2754–9 | date = March 2002 | pmid = 11880627 | pmc = 122420 | doi = 10.1073/pnas.052706099 | bibcode = 2002PNAS...99.2754R | doi-access = free }}</ref>