In Chimera, amino acid residues are automatically assigned an attribute named kdHydrophobicity, with values according to the hydrophobicity scale of Kyte and Doolittle.
Other hydrophobicity scales are not assigned automatically, but input files to define wwHydrophobicity and hhHydrophobicity with Define Attribute are provided below.
| Residue Type | kdHydrophobicitya | wwHydrophobicityb | hhHydrophobicityc |
|---|---|---|---|
| Ile | 4.5 | 0.31 | -0.60 |
| Val | 4.2 | -0.07 | -0.31 |
| Leu | 3.8 | 0.56 | -0.55 |
| Phe | 2.8 | 1.13 | -0.32 |
| Cys | 2.5 | 0.24 | -0.13 |
| Met | 1.9 | 0.23 | -0.10 |
| Ala | 1.8 | -0.17 | 0.11 |
| Gly | -0.4 | -0.01 | 0.74 |
| Thr | -0.7 | -0.14 | 0.52 |
| Ser | -0.8 | -0.13 | 0.84 |
| Trp | -0.9 | 1.85 | 0.30 |
| Tyr | -1.3 | 0.94 | 0.68 |
| Pro | -1.6 | -0.45 | 2.23 |
| His | -3.2 | -0.96 | 2.06 |
| Glu | -3.5 | -2.02 | 2.68 |
| Gln | -3.5 | -0.58 | 2.36 |
| Asp | -3.5 | -1.23 | 3.49 |
| Asn | -3.5 | -0.42 | 2.05 |
| Lys | -3.9 | -0.99 | 2.71 |
| Arg | -4.5 | -0.81 | 2.58 |
a J. Kyte and R.F. Doolittle, "A Simple Method for Displaying the Hydropathic Character of a Protein" J Mol Biol 157:105 (1982).
b W.C. Wimley and S.H. White, "Experimentally determined hydrophobicity scale for proteins at membrane interfaces" Nature Struct Biol 3:842 (1996). Attribute assignment file wwHydrophobicity.txt.
c T. Hessa, H. Kim, K. Bihlmaier, C. Lundin, J. Boekel, H. Andersson, I. Nilsson, S.H. White, and G. von Heijne, "Recognition of transmembrane helices by the endoplasmic reticulum translocon" Nature 433:377 (2005), supplementary data. Attribute assignment file hhHydrophobicity.txt. In this scale (unlike the others), more negative values reflect greater hydrophobicity.