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The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined ...
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm, [2] where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.
The alpha helix is also commonly called a: Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure); 3.6 13-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen)
A beta bend ribbon can be regarded as an aberrant 310 helix (3/10-helix) that has lost some of its hydrogen bonds. [9] Two websites are available to facilitate finding and examining these features in proteins: Motivated Proteins; [10] and PDBeMotif. [11] A beta bend ribbon with 12 alanine residues. Colors of atoms: carbon, green; oxygen red ...
Carbon atoms grey, oxygen atoms red and nitrogen atoms blue. The defining hydrogen bond is shown as a magenta line. The hydrogen bond criterion for beta turns, applied to polypeptides whose amino acids are linked by trans peptide bonds, gives rise to just four categories, as shown by Venkatachalam in 1968. They are called types I, II, I’ and ...
The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.
Their number and arrangement is called the secondary structure of the protein. Alpha helices are regular spirals stabilized by hydrogen bonds between the backbone CO group of one amino acid residue and the backbone NH group of the i+4 residue. The spiral has about 3.6 amino acids per turn, and the amino acid side chains stick out from the ...
[1] [2] [3] The hydrogen bonding pattern in an alpha sheet is similar to that of a beta sheet, but the orientation of the carbonyl and amino groups in the peptide bond units is distinctive; in a single strand, all the carbonyl groups are oriented in the same direction on one side of the pleat, and all the amino groups are oriented in the same ...