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Figure 1 | BMC Bioinformatics

Figure 1

From: Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

Figure 1

1D log-odds scores as a function of C β separation for Ala-Ala, Cys-Cys, and Glu-Glu residue pairs. The Cys-Cys function has a peak near the typical C β separation for disulfide bonds, in the range of 3.5-4.0 Å and is negative for large separations. On the contrary, the score for the same-charge Glu-Glu pairs is negative for small separations and positive for large separations, reflecting the electrostatic energy penalty for close proximity. Both the Cys-Cys and Glu-Glu scores are among the most accurate because of these physical constraints on their separations. The Ala-Ala score, shown for comparison, manifests an oscillatory behavior with a peak near that of the Cys-Cys score.

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