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Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
Biomolecules · Submitted 8 Dec 2003
abstract compiled · 2026-09-23 · no language-model review
The authors' main claim We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate.
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The abstract, sentence by sentence
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity and we quantify this by analyzing the surface exposure distributions of all amino acids. Lastly we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.
background contribution method result interpretation main claim
| # | sentence | role | the authors' own work | states the main conclusion | strength |
|---|---|---|---|---|---|
| s0 | Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. | background 1.00 | 0.03 | 0.02 | hedged possibility 0.91 |
| s1 | On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. | background 1.00 | 0.06 | 0.05 | asserted 0.94 |
| s2 | By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. | contribution 0.65 | 0.96 | 0.06 | asserted 0.96 |
| s3 | We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. | result 0.99 | 0.97 | 0.24 | asserted 1.00 |
| s4 | We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. | interpretation 0.95 | 0.91 | 0.51 | asserted 1.00 |
| s5 | Lesser effects are due in part to forces other than hydrophobicity and we quantify this by analyzing the surface exposure distributions of all amino acids. | interpretation 0.56 | 0.93 | 0.08 | asserted 0.86 |
| s6 | Lastly we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding. | result 0.93 | 0.87 | 0.10 | hedged possibility 0.54 |
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The paper
Original abstract
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By analyzing the known protein structures, we quantify the degree to which the hydrophobicity sequence of a protein correlates with its pattern of surface exposure. We have assessed the statistical significance of this correlation for several hydrophobicity scales in the literature, and find that the computed correlations are significant but far from optimal. We show that this less than optimal correlation arises primarily from the large degree of mutations that naturally occurring proteins can tolerate. Lesser effects are due in part to forces other than hydrophobicity and we quantify this by analyzing the surface exposure distributions of all amino acids. Lastly we show that our database findings are consistent with those found from an off-lattice hydrophobic-polar model of protein folding.
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