Appendix: Tables

1. Argos, et al.
   This table is based on the statistical distribution of specific amino acids in membrane vs. non-membrane segments for a sample set of proteins [Argos, et al., Eur. J. Biochem. 128:55 (1982)]. This Transmembrane Helix analysis is identical to the Membrane Buried Regions analysis.
   
   
2. Bull & Breese
   This table is based on variations in surface tension as a function of amino acid concentration. This is related to the free energy of transfer between surface and solution. Arch. Biochem. Biophys . 161:665 (1974).
   
   
3. Eisenberg, et al.
   This table is based on consensus values obtained in a number of ways - optimized for alpha-helical membrane domains. These values are often used in hydrophobic moment analyses. J. Mol. Biol. 179:125 (1984).
   
   
4. Emini, et al.
   Based on paper by Emini, et al., J. Virol. 55(3):836 (1985), this paper uses the values in Janin, et al. J. Mol. Biol. 125:357 (1978). To indicate surface accessibility, the values in column 5 of table 1 are subtracted from 1. This analysis is different from the Surface Probability analysis which uses a different calculation method.
   
   
5. Engelman & Steitz
   Data from Engelman and Steitz, Cell 23:411 (1981). These data indicate the likelihood that an amino acid will lie in the interior of a protein. This Hydropathy analysis is identical to the Protein Interior analysis.
   
   
6. Engelman, et al.
   This hydropathy table is based on Engelman et al. [Ann. Rev. Biophys. Biophys. Chem . 15:321 (1986)]. This is identical to the Hydropathy analysis with the same table.
   
   
7. Fauchere & Pliska
   This hydropathy table is based on free energy changes in amino acid side chain analogs between water and 1-octanol. Eur. J. Med. Chem. - Chim. Ther . 18:369 (1983).
   
   
8. Fraga
   Based on the data from Fraga, Can. J. Biochem. 60:2606 (1982). These values are modified from the original Hopp-Woods table to include recognition factors. This represents the ability of an amino acid to be recognized by other amino acids.
   
   
9. GES
   From Engelman, Steitz, and Goldman, Ann. Rev. Biophys. Biophys. Chem . 15:321 (1986). This is sometimes called the GES scale. It is designed to show transbilayer helices. This hydropathy analysis is identical to the Engelman, et al. Transmembrane Helix analysis.
   
   
10. Hopp and Woods
    This analysis is based on free energy changes in amino acid side chains between water and ethanol [Proc. Nat. Acad. Sci. USA 78:3824 (1981)]. It was designed to determine antigenicity but has become popular as a standard hydropathy analysis. The Antigenicity and Hydropathy analyses using this table are identical.
    
    
11. Janin
    Based on values in Janin, Nature 277:491 (1979) which determined the surface accessibility of amino acids. The ratio of buried:accessible values in the paper (Table 1, column 4) were converted to the fraction accessible. This Antigenicity analysis is identical to the Accessible Surface Area analysis.
    
    
12. Kyte and Doolittle
    This hydropathy analysis table is based on an aggregate scale obtained by several methods and fine tuned manually. The original paper recommends a window of 7, but 19-21 is also useful for determining membrane spanning segments. J. Mol. Biol. 157:105 (1982).
    
    
13. Manavalan & Ponnuswamy
    Based on data from Manavalan & Ponnuswamy, Nature 275:673 (1978). This data indicates the likelihood that an amino acid will be surrounded by hydrophobic amino acids. Values in Table 1, col 2 were “standardized” to Gln as suggested by the authors. This Hydropathy analysis is identical to the Surrounding Hydrophobicity analysis.
    
    
14. Parker, et al.
    This hydropathy or antigenicity analysis is based on the partitioning of model peptides on an HPLC column. Based on Parker, et al. [Biochemistry 25:5425 (1986)]. The Hydropathy and Antigenicity analyses using this table are identical.
    
    
15. Sweet and Eisenberg
    Based on data from Sweet & Eisenberg [J. Mol. Biol. 171:479 (1983)]. This table of data is derived by correlating data from a number of other hydropathy tables and from observed amino acid replacement rates. This Hydropathy analysis is identical to the Optimal Matching Hydrophobicity analysis.
    
    
16. Thornton, et al.
    This antigenicity table is based on side chain protrusion from the protein backbone. This is based on Thornton, et al. [EMBO J. 5(2):409 (1986)]. The Antigenicity analysis with the Thornton table is identical to the Side Chain Protrusion analysis.
    
    
17. von Heijne
    Based on data from von Heijne [Eur. J. Biochem . 116:419 (1981)]. This table is based on the known occurrences of specific amino acids in both prokaryotic and eukaryotic signal sequences. This Hydropathy analysis is identical to the Signal Sequence analysis.
    
    
18. Welling, et al.
    This antigenicity table is based on known antigenic regions in a sample protein set. See Welling, et al. [FEBS Letts. 188(2):215 (1985)].
    
    
19. Wolfenden, et al.
    This hydropathy analysis is based on free energy of transfer between vapor phase and solution for amino acid side chain analogs. [Wolfenden, et al., Science 206:575 (1979)]. This Hydropathy analysis is identical to the Hydration Potential Analysis.