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Information about Helical Wheel

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An example of an amino acid sequence plotted on a helical wheel. Aliphatic residues are shown as blue squares, polar or negatively charged residues as red diamonds, and positively charged residues as black octagons.
A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins. The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final representation looks down the helical axis. The plot reveals whether hydrophobic amino acids are concentrated on one side of the helix, usually with polar or hydrophilic amino acids on the other. This arrangement is common in alpha helices within globular proteins, where one face of the helix is oriented toward the hydrophobic core and one face is oriented toward the solvent-exposed surface. Specific patterns characteristic of protein folds and protein docking motifs are also revealed, as in the identification of leucine zipper dimerization regions and coiled coils.

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References

  • Mount DM (2004). Bioinformatics: Sequence and Genome Analysis, 2, Cold Spring Harbor Laboratory Press. ISBN 0879697121. 
alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier ( hydrogen bonding). (See also helix.
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Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
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primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular
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amino acid is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent.
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secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
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hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water [1].
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Chemical polarity, also known as bond polarity or simply polarity, is a concept in chemistry which describes how equally bonding electrons are shared between atoms.
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Hydrophile, from the Greek (hydros) "water" and φιλια (philia) "friendship," refers to a physical property of a molecule that can transiently bond with water (H2O) through hydrogen bonding.
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Globular proteins, or spheroproteins are one of the two main protein classes, comprising globelike proteins that are more or less soluble in aqueous solutions (where they form colloidal solutions).
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hydrophobic effect is the property that nonpolar molecules tend to form intermolecular aggregates in an aqueous medium and analogous intramolecular interactions.[1][2] The name arises from the combination of water in Attic Greek hydro-
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A solvent is a liquid that dissolves a solid, liquid, or gaseous solute, resulting in a solution. The most common solvent in everyday life is water. Most other commonly-used solvents are organic (carbon-containing) chemicals. These are called organic solvents.
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In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]

Relationship to primary sequence


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Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks.

The interactions between proteins are important for many biological functions.
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d represent amino acid leucine , arranged with other amino acids on two parallel alpha helices.]] Found in proteins, a leucine zipper is a type of structural motif which creates adhesion forces in parallel alpha helices.
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coiled coil is a structural motif in proteins, in which 2-7[1] alpha-helices are coiled together like the strands of a rope (Dimers and trimers are the most common types).
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Emboss can refer to:
  • Embossing, the process of pressing creases or designs into substrates such as paper or metal.
  • EMBOSS, an acronym for European Molecular Biology Open Software Suite.

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