hydrophobicity {Peptides} | R Documentation |
This function calculates the GRAVY hydrophobicity index of an amino acids sequence using one of the 38 scales from different sources.
hydrophobicity(seq, scale = "KyteDoolittle")
seq |
An amino-acids sequence |
scale |
A character string specifying the hydophobicity scale to be used; must be one of |
The hydrophobicity is an important stabilization force in protein folding; this force changes depending on the solvent in which the protein is found. The hydrophobicity index is calculated adding the hydrophobicity of individual amino acids and dividing this value by the length of the sequence.
The computed GRAVY index for a given amino-acid sequence
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# COMPARED TO GRAVY Grand average of hydropathicity (GRAVY) ExPASy # http://web.expasy.org/cgi-bin/protparam/protparam # SEQUENCE: QWGRRCCGWGPGRRYCVRWC # GRAVY: -0.950 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Aboderin") #[1] 3.84 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "AbrahamLeo") #[1] 0.092 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Argos") #[1] 1.033 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "BlackMould") #[1] 0.50125 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "BullBreese") #[1] 0.1575 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Casari") #[1] 0.38 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Chothia") #[1] 0.262 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Cid") #[1] 0.198 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Cowan3.4") #[1] 0.0845 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Cowan7.5") #[1] 0.0605 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Eisenberg") #[1] -0.3265 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Engelman") #[1] 2.31 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Fasman") #[1] -1.2905 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Fauchere") #[1] 0.527 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Goldsack") #[1] 1.2245 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Guy") #[1] 0.193 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "HoppWoods") #[1] -0.14 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Janin") #[1] -0.105 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Jones") #[1] 1.4675 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Juretic") #[1] -1.106 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Kidera") #[1] -0.0405 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Kuhn") #[1] 0.9155 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "KyteDoolittle") #[1] -0.95 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Levitt") #[1] -0.21 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Manavalan") #[1] 13.0445 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Miyazawa") #[1] 5.739 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Parker") #[1] 1.095 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Ponnuswamy") #[1] 0.851 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Prabhakaran") #[1] 9.67 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Rao") #[1] 0.813 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Rose") #[1] 0.7575 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Roseman") #[1] -0.495 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Sweet") #[1] -0.1135 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Tanford") #[1] -0.2905 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Welling") #[1] -0.666 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Wilson") #[1] 3.16 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Wolfenden") #[1] -6.307 hydrophobicity(seq = "QWGRRCCGWGPGRRYCVRWC",scale = "Zimmerman") #[1] 0.943