Physicochemical Properties
1 Introduction
Calculate physicochemical properties of protein sequences.
2 Parameters
Input your protein sequences.
3 Results Explanation
| Field Name | Description |
|---|---|
| Sequence | Protein sequence. |
| Molecular Weight | Molecular weight of the protein sequence, unit is g/mol. |
| Isoelectric Point1,2 | Isoelectric point of the protein sequence, return pH value. |
| Molar Extinction Coefficient (without disulfide bond) | Molar extinction coefficient assuming cysteines are reduced, unit is L/(mol*cm). |
| Molar Extinction Coefficient (with disulfide bond) | Molar extinction coefficient assuming paired cysteines form disulfide bonds, unit is L/(mol*cm). |
| Instability Index3 | Protein instability index; values above 40 indicate that the protein is unstable (short half-life). |
| Aromaticity | The aromaticity index of the protein, which is the relative frequency of Phe + Trp + Tyr. |
| Grand average of hydropathicity (GRAVY)4 | Overall average hydropathcity; a negative value indicates a hydrophilic protein, while a positive value indicates a hydrophobic protein. |
| Helix Fraction5 | The proportion of helix structure in the protein. Amino acids in helix: E, M, A, L, K. |
| Turn Fraction6 | The proportion of turn structure in the protein. Amino acids in turn: N, P, G, S, D. |
| Sheet Fraction7 | The proportion of sheet structure in the protein. Amino acids in sheet: V, I, Y, F, W, L, T. |
| Positive Charge Percentage | The percentage of amino acids with a positive charge. |
| Negative Charge Percentage | The percentage of amino acids with a negative charge. |
| Polar Percentage | The percentage of polar amino acids. |
| Unpolar Percentage | The percentage of nonpolar amino acids. |
4 Reference
[1] Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez, J.-Ch., Frutiger, S. & Hochstrasser, D.F. The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031.
https://doi.org/10.1002/elps.11501401163
[2] Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E. Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions. Electrophoresis 1994, 15, 529-539. https://doi.org/10.1002/elps.1150150171
[3] Guruprasad K, Reddy BV, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. 1990 Dec;4(2):155-61. PMID: 2075190. https://doi.org/10.1093/protein/4.2.155
[4] Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32. PMID: 7108955. https://doi.org/10.1016/0022-2836(82)90515-0
[5] Haimov, B., Srebnik, S. A closer look into the α-helix basin. Sci Rep 6, 38341 (2016). https://doi.org/10.1038/srep38341
[6] Hutchinson EG, Thornton JM. A revised set of potentials for beta-turn formation in proteins. Protein Sci. 1994 Dec;3(12):2207-16. doi: 10.1002/pro.5560031206. PMID: 7756980; PMCID: PMC2142776. https://doi.org/10.1002/pro.5560031206
[7] Kim, C., Berg, J. Thermodynamic β -sheet propensities measured using a zinc-finger host peptide. Nature 362, 267–270 (1993). https://doi.org/10.1038/362267a0