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The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were calculated for distances between -25 and 25. Shapes of the diagrams indicate that amino acids polarity and capability for hydrogen bonding have influence on the secondary structure at some distances. Clear preference of most of the amino acids towards certain secondary structure type classifies amino acids into four groups: alpha-helix admirers, strand admirers, turn and bend admirers and the others. Group four consists of His and Cis, the amino acids that do not show clear preference for any secondary structure. Amino acids from a group have similar physicochemical properties, and the same structural characteristics. The results suggest that amino acid preference for secondary structure type is based on the structural characteristics at Cb and Cg atoms of amino acid. alpha-helix admirers do not have polar heteroatoms on Cb and Cg atoms, nor branching or aromatic group on Cb atom. Amino acids that have aromatic groups or branching on Cb atom are strand admirers. Turn and bend admirers have polar heteroatom on Cb or Cg atoms or do not have Cb atom at all. Our results indicate that polarity and capability for hydrogen bonding have influence on the secondary structure at some distance, and that amino acid preference for secondary structure is caused by structural properties at Cb or Cg atoms.
This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V, I)], all w
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic
In several previous works, I presented the mirror symmetry in the set of protein amino acids, expressed through the number of atoms. Here, however, the same thing is shown but over the number of nucleons and molecules mass. Compared to the previous v
A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current w
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 golden amino acids, 7 of their complements, and