Property

We use 23 indicators to describe physicochemical properties of amino acids as shown in Table 1. You can use pp.fpsite.property to get access to them.

Python 

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import pypropel as pp

property = 'positive'

scale = pp.fpsite.property(property)

print(scale)

Output 

{'A': 1.0, 'C': 1.0, 'D': 1.0, 'E': 1.0, 'F': 1.0, 'G': 1.0, 'H': 0.5, 'I': 1.0, 'K': 0.0, 'L': 1.0, 'M': 1.0, 'N': 1.0, 'P': 1.0, 'Q': 1.0, 'R': 0.0, 'S': 1.0, 'T': 1.0, 'V': 1.0, 'W': 1.0, 'Y': 1.0}

In fact, property can be any of 23 amino acid properties, including

Table 1. amino acid properties

Property Kind Citation Value
positive Russell Betts & Russell1 discrete
negative Russell Betts & Russell1 discrete
charged Russell Betts & Russell1 discrete
polar Russell Betts & Russell1 discrete
aliphatic Russell Betts & Russell1 discrete
aromatic Russell Betts & Russell1 discrete
hydrophobic Russell Betts & Russell1 discrete
small Russell Betts & Russell1 discrete
active Russell Betts & Russell1 continuous
weight Taylor Lundblad & Macdonald2 continuous
pI Taylor Lundblad & Macdonald2 continuous
solubility Taylor Lundblad & Macdonald2 continuous
tm Taylor Lundblad & Macdonald2 continuous
pka Taylor Lundblad & Macdonald2 continuous
pkb Taylor Lundblad & Macdonald2 continuous
hydrophilicity Hopp 3 discrete
hydrophobicity Argos Argos et al.4 continuous
fet Argos Argos et al.4 continuous
hydration Argos Argos et al.4 continuous
signal Argos Argos et al.4 continuous
volume Grantham Grantham 5 continuous
polarity Grantham Grantham 5 continuous
composition Grantham Grantham 5 continuous

Note

pI: pH at the isoelectric point.

Solubility in water in units of grams of compound per kilogram of water.

tm: Melting point.

pKa: Negative of the logarithm of the acid dissociation constants for the COOH and NH2 groups (and, in some cases, other groups) in the molecule (at 25°C)

  1. Betts, M.J. and Russell, R.B. (2003). Amino Acid Properties and Consequences of Substitutions. In Bioinformatics for Geneticists (eds M.R. Barnes and I.C. Gray). https://doi.org/10.1002/0470867302.ch14 ↩↩↩↩↩↩↩↩↩

  2. Lundblad, R.L., & Macdonald, F. (Eds.). (2018). Handbook of Biochemistry and Molecular Biology (5th ed.). CRC Press. https://doi.org/10.1201/b21846 ↩↩↩↩↩↩

  3. Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A. 1981 Jun;78(6):3824-8. doi: 10.1073/pnas.78.6.3824. ↩

  4. ARGOS, P., RAO, J.K.M. and HARGRAVE, P.A. (1982), Structural Prediction of Membrane-Bound Proteins. European Journal of Biochemistry, 128: 565-575. https://doi.org/10.1111/j.1432-1033.1982.tb07002.x ↩↩↩↩

  5. R. Grantham ,Amino Acid Difference Formula to Help Explain Protein Evolution.Science185,862-864(1974).DOI:10.1126/science.185.4154.862 ↩↩↩