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Hydropathy Plot (Kyte-Doolittle)
*Recently, a colleague from Lunds university pointed out that the extinction coefficients from the paramater calculation and those from the spectrum prediction are different. Here's why:
The parameter algorithm uses the following simple equation to predict the extinction at 280 nm:
A = 5690 * #Trp + 1280 * #Tyr + 60 * #Cys
The UV spectrum prediction program models a Gaussian curve around the various transitions; (following with their maxima):
Cys-Cys: 250 nm
Phe: 257 nm
Tyr - OH: 274 nm
Tyr - ring: 222 nm
Trp - indole: 280 nm
Trp - ring: 219 nm
His - imid.: 211 nm
Peptide bonds: 211 nm
The contributions are summed to predict an absorbance at each wavelength - including the extinction at 280 nm. I'm not sure which one is more accurate in the real world, but if any one knows, please comment.
Thank you to Dr. Groening and others for reporting possible bugs. Keep them coming!