Chem3D 8.0 Manual - CambridgeSoft

The Map Property provides color-codedvisualization of Atom Colors, Group Colors,Hydrophobicity, Partial Charges, or ElectrostaticPotential (derived from partial charges)superimposed upon the solvent-accessible surface.Hydrophobicity is displayed according to awidely-used color convention derived from aminoacid hydrophobicities 1 , where the most hydrophobic(lipophilic) is red and the least hydrophobic(lipophobic) is blue. The following table showsmolecule hydophobicity.Molecule HydrophobicityPro –0.2Tyr –0.7His –3.0Gln –4.1Asn –4.8Glu –8.2MoleculeHydrophobicityLys –8.8Phe 3.7 Most hydrophobic (Red)Met 3.4Ile 3.1Leu 2.8Val 2.6Cys 2.0Trp 1.9Ala 1.6Thr 1.2Gly 1.0Ser 0.6 Middle (White)1. Engelman, D.M.; Steitz, T.A.; Goldman, A., “Identifyingnonpolar transbilayer helices in amino acidsequences of membrane proteins”, Annu. Rev. Biophys.Biophys. Chem. 15, 321-353, 1986.Asp –9.2Arg –12.3 Least hydrophobic (Blue)The Partial Charges and Electrostatic Potential(derived from the partial charges) properties aretaken from the currently selected calculation. If youhave performed more than one calculation on themodel, you can specify which calculation to use bychoosing the Partial Charges or MolecularElectrostatic Potential dialog boxes from the Viewmenu and choosing a Calculation from theCalculation pop-up menu in that dialog box.Connolly Molecular SurfaceThe Connolly surface, also called the molecularsurface, is similar to the solvent-accessible surface.Using a small spherical probe to simulate a solvent,it is defined as the surface made by the contact of thesolvent sphere with the van der Waals surface. Thevolume enclosed by the Connolly surface is calledthe solvent-excluded volume. These surfaces areshown in the following illustration.Chem3D 8 Chapter 6: Displaying Models • 87Displaying Molecular Surfaces