dorsal/arxiv
View SchemaCorrelations of Amino Acids with Secondary Structure Types: Connection with Amino Acid Structure
| Authors | Sasa Malkov, Miodrag V. Zivkovic, Milos V. Beljanski, Snezana D. Zaric |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0505046 |
| URL | https://arxiv.org/abs/q-bio/0505046 |
Abstract
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.
{
"annotation_id": "9ca7754f-8078-41a1-aaa5-886559c70602",
"date_created": "2026-03-02T18:01:31.814000Z",
"date_modified": "2026-03-02T18:01:31.814000Z",
"file_hash": "e9520260df5f90ef0dc5305d66ea613d36a250c6938e9f6702d9752795f65128",
"private": false,
"record": {
"abstract": "The correlations of primary and secondary structures were analyzed using\nproteins with known structure from Protein Data Bank. The correlation values of\namino acid type and the eight secondary structure types at distant position\nwere calculated for distances between -25 and 25. Shapes of the diagrams\nindicate that amino acids polarity and capability for hydrogen bonding have\ninfluence on the secondary structure at some distances. Clear preference of\nmost of the amino acids towards certain secondary structure type classifies\namino acids into four groups: alpha-helix admirers, strand admirers, turn and\nbend admirers and the others. Group four consists of His and Cis, the amino\nacids that do not show clear preference for any secondary structure. Amino\nacids from a group have similar physicochemical properties, and the same\nstructural characteristics. The results suggest that amino acid preference for\nsecondary structure type is based on the structural characteristics at Cb and\nCg atoms of amino acid. alpha-helix admirers do not have polar heteroatoms on\nCb and Cg atoms, nor branching or aromatic group on Cb atom. Amino acids that\nhave aromatic groups or branching on Cb atom are strand admirers. Turn and bend\nadmirers have polar heteroatom on Cb or Cg atoms or do not have Cb atom at all.\nOur results indicate that polarity and capability for hydrogen bonding have\ninfluence on the secondary structure at some distance, and that amino acid\npreference for secondary structure is caused by structural properties at Cb or\nCg atoms.",
"arxiv_id": "q-bio/0505046",
"authors": [
"Sasa Malkov",
"Miodrag V. Zivkovic",
"Milos V. Beljanski",
"Snezana D. Zaric"
],
"categories": [
"q-bio.BM"
],
"title": "Correlations of Amino Acids with Secondary Structure Types: Connection with Amino Acid Structure",
"url": "https://arxiv.org/abs/q-bio/0505046"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "2c109f54-0f31-4354-b052-3a8f8cffa811",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}