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A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i {\displaystyle i} and j {\displaystyle j} , the i j {\displaystyle ij} element of the matrix is 1 if the two residues are closer than a predetermined ...
The Chou–Fasman method takes into account only the probability that each individual amino acid will appear in a helix, strand, or turn. Unlike the more complex GOR method, it does not reflect the conditional probabilities of an amino acid to form a particular secondary structure given that its neighbors already possess that structure. This ...
A codon table can be used to translate a genetic code into a sequence of amino acids. [1] [2] The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. [2] [3] The mRNA sequence is determined by the sequence of ...
Protein sequence is typically notated as a string of letters, listing the amino acids starting at the amino-terminal end through to the carboxyl-terminal end. Either a three letter code or single letter code can be used to represent the 22 naturally encoded amino acids, as well as mixtures or ambiguous amino acids (similar to nucleic acid ...
The mass of b 2-ion = mass of two amino acid residues + 1. Table 2. Mass of b2-ions in peptide fragmentation [16] Identify a sequence ion series by the same mass difference, which matches one of the amino acid residue masses (see Table 1). For example, mass differences between a n and a n-1, b n and b n-1, c n and c n-1 are the same.
The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns). The alignment of the H-bonds creates a dipole moment for the helix with a resulting partial positive charge at the amino end of the helix.
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers – specifically polypeptides – formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a
The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a protein strand. Each group of three bases, called a codon , corresponds to a single amino acid, and there is a specific genetic code by which each possible combination of three bases corresponds to a specific amino acid.