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Updated: Oct 13, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Hydrophilic framework in proteins?
1TIMC Laboratory, Institut Albert Bonniot, Faculté de Médecine, La Tronche, France. jean-claude.jesior@imag.fr
Abstract:
The spatial neighborhood composition of residues was determined in a 511-structure set by taking only side-chain atoms into account to generate a hydrophobicity scale. This scale is symmetrical and has been divided into seven functional groups. Hydrophobic (LIVFMCAWYG) and hydrophilic (PTHSQRNKED) residues obey an equipartition rule: not only are they found in equal proportions, but they play equivalent roles in many of their properties. The nearest neighbors of all residues are always hydrophilic. However, hydrophobic residues are mostly surrounded by other hydrophobic residues located at a peak at 3.9 A, while hydrophilic residues show three peaks at 5.0, 6.5, and 8.0 A, suggesting a hydrophilic structural framework. This leads us to question the importance of hydrophobic cores believed to be at the origin of protein folding.
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