Amino Acid Indices

Description Reference A R N D C Q E G H I L K M F P S T W Y V
Bulkiness [1] 11.5 14.28 12.82 11.68 13.46 14.45 13.57 3.4 13.69 21.4 21.4 15.71 16.25 19.8 17.43 9.47 15.77 21.67 18.03 21.57
Isoelectric point [1] 6 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02 5.98 9.74 5.74 5.48 6.3 5.68 5.66 5.89 5.66 5.96
Absolute entropy [2] 30.88 68.43 41.7 40.66 53.83 46.62 44.98 24.74 65.99 49.71 50.62 63.21 55.32 51.06 39.21 35.65 36.5 60 51.15 42.75
Size [3] 2.5 7.5 5 2.5 3 6 5 0.5 6 5.5 5.5 7 6 6.5 5.5 3 5 7 7 5
Polarity [4] 8.1 10.5 11.6 13 5.5 10.5 12.3 9 10.4 5.2 4.9 11.3 5.7 5.2 8 9.2 8.6 5.4 6.2 5.9
Volume [4] 31 124 56 54 55 85 83 3 96 111 111 119 105 132 32.5 32 61 170 136 84
Molecular weight [5] 89.09 174.2 132.12 133.1 121.15 146.15 147.13 75.07 155.16 131.17 131.17 146.19 149.21 165.19 115.13 105.09 119.12 204.24 181.19 117.15
Melting point [5] 297 238 236 270 178 185 249 290 277 284 337 224 283 284 222 228 253 282 344 293
Hydrophobicity index [5] −0.21 2.11 0.96 1.36 −6.04 1.52 2.3 0 −1.23 −4.81 −4.68 3.88 −3.66 −4.65 0.75 1.74 0.78 −3.32 −1.01 −3.5
The stability scale from the knowledge-based atom-atom potential [6] 2.18 2.71 1.85 1.75 3.89 2.16 1.89 1.17 2.51 4.5 4.71 2.12 3.63 5.88 2.09 1.66 2.18 6.46 5.01 3.77
Long range non-bonded energy per atom [7] −0.49 −0.55 −0.382 −0.36 −0.67 −0.405 −0.371 −0.53 −0.54 −0.762 −0.65 −0.3 −0.659 −0.729 −0.463 −0.455 −0.515 −0.839 −0.656 −0.728
Average surrounding hydrophobicity [8] 12.97 11.72 11.42 10.85 14.63 11.76 11.89 12.43 12.16 15.67 14.9 11.36 14.39 14 11.37 11.23 11.69 13.93 13.42 15.71
Hydrophobicity index [9] 1.12 −2.55 −0.83 −0.83 0.59 −0.78 −0.92 1.2 −0.93 1.16 1.18 −0.8 0.55 0.67 0.54 −0.05 −0.02 −0.19 −0.23 1.13
Hydration potential [10] 1.28 2.34 1.6 1.6 1.77 1.56 1.56 0 2.99 4.19 2.59 1.89 2.35 2.94 2.67 1.31 3.03 3.21 2.94 3.67
Smoothed upsilon steric parameter Hydrophobicity index [11] 0.53 0.69 0.58 0.59 0.66 0.71 0.72 0 0.64 0.96 0.92 0.78 0.77 0.71 0 0.55 0.63 0.84 0.71 0.89
Hydrophobicity index [12] 0.61 0.6 0.06 0.46 1.07 0 0.47 0.07 0.61 2.22 1.53 1.15 1.18 2.02 1.95 0.05 0.05 2.65 1.88 1.32
Electron-ion interaction potential Positive charge [13] 0.037 0.096 0.004 0.126 0.083 0.076 0.006 0.005 0.024 0 0 0.037 0.082 0.095 0.019 0.083 0.094 0.055 0.052 0.006
Positive charge [11] 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0
Negative charge [11] 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
Number of hydrogen bond donors Hydropathy index [11] 0 4 2 1 0 2 1 0 1 0 0 2 0 0 0 1 1 1 1 0
Hydropathy index [14] 1.8 −4.5 −3.5 −3.5 2.5 −3.5 −3.5 −0.4 −3.2 4.5 3.8 −3.9 1.9 2.8 −1.6 −0.8 −0.7 −0.9 −1.3 4.2
Average flexibility indices Recognition factors [15] 0.357 0.529 0.463 0.511 0.346 0.493 0.497 0.544 0.323 0.462 0.365 0.466 0.295 0.314 0.509 0.507 0.444 0.305 0.42 0.386
Recognition factors [16] 78 95 94 81 89 87 78 84 84 88 85 87 80 81 91 107 93 104 84 89
Long-range contacts [17] 3.92 3.78 3.64 2.85 5.55 3.06 2.72 4.31 3.77 5.58 4.59 2.79 4.14 4.53 3.57 3.75 4.09 4.83 4.93 5.43
Relative connectivity [18] 1.05 0.94 0.93 0.88 1.17 0.93 0.85 0.99 0.99 1.11 1.07 0.88 1.04 1.07 0.92 0.96 0.99 1.05 1.05 1.12


References

[1] J. ZimmermanNaomi and R. Simha, “The characterization of amino acid sequences in proteins by statistical methods,” Journal of theoret- ical biology, vol. 21, no. 2, pp. 170–201, 1968.
[2] L. Acid, D. Citrulline, and D. HCI, “Heat capacities, absolute entropies, and entropies of formation of amino acids and related compounds,” Handbook of biochemistry and molecular biology, vol. 1, no. 154.33, p. 109, 1984.
[3] O. Mayo and D. Brock, The biochemical genetics of man. Cambridge Univ Press, 1972.
[4] R. Grantham, “Amino acid difference formula to help explain protein evolution,” Science, vol. 185, no. 4154, p. 862, 1974.
[5] G. Fasman, Practical handbook of biochemistry and molecular biol- ogy. CRC, 1989.
[6] H. Zhou and Y. Zhou, “Quantifying the effect of burial of amino acid residues on protein stability,” PROTEINS: Structure, Function, and Bioinformatics, vol. 54, no. 2, pp. 315–322, 2004.
[7] M. Oobatake and T. Ooi, “An analysis of non-bonded energy of proteins,” Journal of Theoretical Biology, vol. 67, no. 3, pp. 567–584, 1977.
[8] P. Manavalan and P. Ponnuswamy, “Hydrophobic character of amino acid residues in globular proteins,” 1978.
[9] R. Wolfenden, P. Cullis, and C. Southgate, “Water, protein folding, and the genetic code,” Science, vol. 206, no. 4418, p. 575, 1979.
[10] R. Wolfenden, L. Andersson, P. Cullis, and C. Southgate, “Affinities of amino acid side chains for solvent water,” Biochemistry, vol. 20, no. 4, pp. 849–855, 1981.
[11] J. FAUCHE`RE, M. Charton, L. Kier, A. Verloop, and V. Pliska, “Amino acid side chain parameters for correlation studies in biology and pharmacology,” International journal of peptide and protein research, vol. 32, no. 4, pp. 269–278, 1988.
[12] P. ARGOS, J. Rao, and P. HARGRAVE, “Structural prediction of membrane-bound proteins,” European Journal of Biochemistry, vol. 128, no. 2-3, pp. 565–575, 1982.
[13] V.Veljkovic,I.Cosic,B.Dimitrijevic,andD.LalovicC,“Isitpossible to analyze DNA and protein sequences by the methods of digital signal processing?” IEEE Transaction on Biomedical Engineering, vol. 32, no. 5, pp. 337–341, 1985.
[14] J. Kyte and R. Doolittle, “A simple method for displaying the hydropathic character of a protein,” Journal of molecular biology, vol. 157, no. 1, pp. 105–132, 1982.
[15] R. Bhaskaran and P. Ponnuswamy, “Positional flexibilities of amino acid residues in globular proteins,” International Journal of Peptide and Protein Research, vol. 32, no. 4, pp. 241–255, 1988.
[16] E. Gasteiger, C. Hoogland, A. Gattiker, S. Duvaud, M. Wilkins, R. Appel, and A. Bairoch, “Protein identification and analysis tools on the expasy server,” The proteomics protocols handbook, pp. 571–607, 2005.
[17] L. Ferna ́ndez, J. Caballero, J. Abreu, and M. Ferna ́ndez, “Amino acid sequence autocorrelation vectors and bayesian-regularized genetic neural networks for modeling protein conformational stability: Gene v protein mutants,” Proteins: Structure, Function, and Bioinformatics, vol. 67, no. 4, pp. 834–852, 2007.
[18] J. Huang, S. Kawashima, and M. Kanehisa, “New amino acid indices based on residue network topology,” Genome Informatics, vol. 18, pp. 152–161, 2007.