Users' questions

What does a Ramachandran plot tell you?

What does a Ramachandran plot tell you?

The Ramachandran plot is a plot of the torsional angles – phi (φ)and psi (ψ) – of the residues (amino acids) contained in a peptide. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.

Which amino acids are not preferable for Ramachandran plot?

Glycine is fundamentally different to the other amino acids in that it lacks a sidechain. In particular, glycine does not have the Cβ atom, which induces many steric clashes in the generic Ramachandran plot.

What is the hydrogen bonding pattern of an 3/10 helix?

Structure. The amino acids in a 310-helix are arranged in a right-handed helical structure. Each amino acid corresponds to a 120° turn in the helix (i.e., the helix has three residues per turn), and a translation of 2.0 Å (0.20 nm) along the helical axis, and has 10 atoms in the ring formed by making the hydrogen bond.

Why proline is not in Ramachandran plot?

Proline has restrictions in phi-psi space that arise from the 5-membered ring. Phi is restricted to approxamatly -60 by the ring and psi angles fall into two groupings near -45 and +135 in the helical and sheet regions of the Ramachandran plot.

Why is glycine not in alpha helix?

Amino-acid propensities Different amino-acid sequences have different propensities for forming α-helical structure. At the other extreme, glycine also tends to disrupt helices because its high conformational flexibility makes it entropically expensive to adopt the relatively constrained α-helical structure.

Why alpha helix is called Alpha?

Alpha helices in coiled coils Alpha helices are named after alpha keratin, a fibrous protein consisting of two alpha helices twisted around each other in a coiled-coil (see Coiled coil). In leucine zipper proteins (such as Gcn4), the ends of the two alpha helices bind to two opposite major grooves of DNA.

Why is proline more conformationally restricted?

proline because its side chain is bonded to both the nitrogen and the α-carbon atoms proline because its side chain is aliphatic glycine because it is achiral proline because its side chain is bonded to both the carboxyl carbon and the α-carbon atom glycine because two hydrogen atoms are.

Why is proline Ramachandran plot different?

Its van der Waals radius is smaller and is thus less restricted. Proline, on the other hand has a 5-membered ring as a side chain. Therefore it is much more restricted than the other amino acids and allows for only a limited number of ψ and φ. Gly is the least restricted, Pro is the most restricted.

Where does the 3 ( 10 ) helix occur in Ramachandran plot?

These residues are usually glycine but can also be asparagine or aspartate where the side chain forms a hydrogen bond with the main chain and therefore stabilises this otherwise unfavourable conformation. The 3(10) helix occurs close to the upper right of the alpha-helical region and is on the edge of allowed region indicating lower stability.

What are the edges of the Ramachandran plot?

Because dihedral angle values are circular and 0° is the same as 360°, the edges of the Ramachandran plot “wrap” right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left.

What does the Ramachandran plot show about an amino acid?

The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ. In theory, the allowed regions of the Ramachandran plot show which values of the Phi/Psi angles are possible for an amino acid, X, in a ala-X-ala tripeptide (Ramachandran et al., 1963 ).

Why is glycine disallowed in the Ramachandran plot?

Disallowed regions generally involve steric hindrance between the side chain C-beta methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence it frequently occurs in turn regions of proteins where any other residue would be sterically hindered.