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Sequence Index

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The purpose of this page is to help you to find your sequence from lists. The lists follow the standard classification of Rawlings & Barrett described in the overview page.To find sequences, click on the link to the corresponding clan or family in the table or click on the link "all serine protease" to access the entire list of serine proteases. Use the "find" tool of your browser to look through the list for the occurence of specified keywords. You can also use the seach tools from the search page or search form the set maker tools in the sequence analyzer page: these tools allow you to group selected sequences into sets. All these facilities allow you to obtain direct links to sequences through corresponding databases to display the selected sequences. This web site does not contain whole sequences and descriptions. The current database is described in the references.

The Overview of the Classification of Serine Proteases describe the organization of the lists and gives statistics and some links to shortcut access to sequence lists and to helpful databases, currently handling serine protease families.

"Clan & family" provides links to the corresponding clan or family sequence list. The "sequence" column show the total number of sequences in the current list- link to the most representative. "Proteases" gives the number of different proteases, i.e. trypsins of different species are counted as 1. "Enzyme" shows the number of enzymes with distinct E.C. entries. "Structures" gives the total number of structures including a serine protease domain from the Protein Databank while "3D" shows number of structures including distinct serine protease domains. HSSP provides a link to the homology-derived secondary structure of the current family. ProSite provides a link to the family card describing the family or function "signatures". ProDom provides a link to a multialignment database of domains of the same family. SCOP and CATH provides links to protein structure classifications of the current family. The representative enzyme allows a shortcut to the corresponding sequence of the most representative protease of the family through the Swiss-Prot database.

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Sequence Analyzer

Ex
Ref

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AC Identify: Enter or paste the Swiss-Prot accession numbers or descriptive codes in the box and click the Identify button and you get a table with the list of corresponding sequence and the associated accession numbers. You can find a shortcut to the sequence in the Swiss-Prot database. The reset button clean the box for a new entry.
Ex
Ref

Number translator : Enter or paste the Swiss-Prot accession numbers or descriptive codes, the position and the sequence used as reference (only one, not necessarly in the selected set) in their respective boxes. Click on the translate button and you get the position of each specified protease according to the numbering from the whole sequence as described in the Swiss-Prot database, as a product from the gene corresponding gene. Of course the specified position is relative to the alignment choice.

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Ref
View&Submit Enter the accession number of a serine protease and display its catalytic domain sequence (the fragment used in the multialignement of the family domain) and submit it to BLAST, PHI-BLAST, gapped-BLAST, Sssearch, FastA and Swiss-Model.
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Ref
Sequence set maker from the whole list: Proteases listed in Swiss-Prot are displayed by alphabetic order per family and Families are ranked by increasing order. Corresponding clans are indicated at the beginning of each family. The links written as numbers (1 for S1,...) may be used as shortcut to the corresponding proteases families in the same table. You can select all the sequences you want to group in the same set by clicking on the corresponding checkbox. You make a set and print a list of the corresponding accession numbers only after clicking the button "go" or stiking "enter" anywhere in the table. The program sends you back a new table that you may use again to reduce the number of the current selection. To be selected, sequences have to be checked. A new validation create a new set and so on...
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Ref
Sequence set maker from keywords: enter one word or a part of one word as a protease name, an organism name, an accession number, whatever that could appear on a line of the protease list. The program sends back a new table that you can use to reduce the number of proteases selected. You can use the set maker with logical operators to filter sequences fished with different keywords.
Ex
Ref
Sequence set maker from a sequence:
Write an accession number or a Swiss-Prot descriptive code of the sequence used as reference to fetch all the other sequences close enough according to the current alignment. Write an accession number or a Swiss-Prot descriptive code to fix the sequence numbering (bovin chymotrypsinogen by default) used to fix the window's limits in which the sequence comparison will be active. These limits are necessarly integer and 60D or 77B by example are not allowed. By default the window cover residues 16 to 238 which defines the heavy chain of chymotrypsin.
Define the minimal percentage of identity (from 0 to 100 float or integer) or the minimal percentage of similarity according to a selected substitution matrix, a threshold and gap pennalties for the gap openning and its extension. The total score is the sum of the score of amino-acid pairs divided by the number of pairs. Lower is the threshold more frequent are the amino acid pairs evaluated as similar. The decision is very sensitive with the cutoff value at the low value of threshold for the PAM256 and at high value for the PAM 32 (non-linearity). All the sequences close enough to the specified sequence will be added in a result table. You can copy either the accession number set or the set of Swiss-Prot descriptive codes.
Ex
Ref
Sequence set maker from a motif: Select a set of sequences from a motif
Write the sequence of amino acids you want to use to as reference to fetch sequences that display a segment close enough, that means higher than the minimal score of identity requested, percentage between 0 and 100 integer or float, or higher than the best score of similarity according to a selected substitution matrix, a threshold and gap pennalties for the gap openning and its extension. The total score is the sum of the score of amino-acid pairs divided by the number of pairs. Lower is the threshold more frequent are the amino acid pairs evaluated as similar. The decision is very sensitive with the cutoff value at the low value of threshold for the PAM256 and at high value for the PAM 32 (non-linearity). All the sequences including a segment close enough to the specified motif will be added in a result table. You can copy either the accession number set or the set of Swiss-Prot descriptive codes.
Ex
Ref
Sequence set maker from constraints:
Write an accession number or a Swiss-Prot descriptive code to fix the sequence numbering (bovin chymotrypsinogen by default). Write the position number according to the specified reference and the imposed amino acid at this position. After pushing the select button you will get a table with all the sequence satifying the specified constraints.
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Sequence set maker from logical operations on sets:
Enter or paste the Swiss-Prot accession numbers or descriptive codes
Set Operation Set
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Save and read sets:
Read a set from a local file (in your computer) note :T2,G2 equivalent
Enter the file name or find it with the browser


Save a set in a temporary file in the server (available during a 6h-period)
Enter the file name or find it with the browser

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Sequence alignment:
  Save and read sets:
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Sequences
This web site use only the catalytic domain of the sequences, so it does not contain the whole sequences and their descriptions. The sequence database used links as reference toward:
Swiss-Prot release 37: Bairoch A., currator(1999), The Swiss Institute of Bioinformatics, Expasy web site.

Family and Clan classification is refering to:
Bairoch A. (1999)The ENZYME data bank in 1999 Nucleic Acids Res. 27:310-311.
Appel R.D., Bairoch A., Hochstrasser D.F. (1994) A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server. Trends Biochem. Sci. 19:258-260.
Rawlings N.D., Barrett A.J. (1993) Evolutionary families of peptidases. Biochem. J. 290:205-218.
Rawlings N.D., Barrett A.J. (1994) Families of serine peptidases. Meth. Enzymol. 244:19-61.
Rawlings N.D., currator(1999) Merops : The Peptide Database, Babraham Institute, Cambridge (UK)
Alignment tools:
Altschul SF, Gish W, Miller W, Myers EWand Lipman DJ (1990).BLAST.Basic local alignment search tool. J Mol Biol .215:403-410
:Altschul, SF., Madden, TL., Schäffer, AA., Zhang, J., Zhang, Z., Miller, W. and Lipman DJ.(1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.
W.R. Pearson & D.J. Lipman (1988) FASTA. PNAS 85:2444-2448
Thompson, J.D. Higgins, D.G. Gibson, T.J. (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalites and weight matrix choice. Nucl. Acids Res. 22:4673-4680
Smith and Waterman,(1981) SSEARCH "Identification of common molecular subsequences", J. Mol. Biol. 147:195-197
Barton, G. J. (1997) "SCANPS Version 2.3.1 User guide", University of Oxford, UK. The underlying algorithm used in scanps is described in: Barton, G. J. (1993) CABIOS, 9, 729-734.
 Substitution matrices:
PAM: (Percent Accepted Mutation) square matrix developed by Dayhoff and co-workers that gives for the 20 amino acids, the frequency to be replaced by each of the 20 amino acids, in sets of sequences globaly aligned, sharing a same ancestor, with 10 amino acids substituted per 100 residue-window for PAM10. Matrices for greater evolutionary distances, ie PAM250, are extrapolated from those lesser ones. The threshold expressed in the same scale unit defines the limit above what an amino acid has similar amino acid properties of the comparated one (or the substituted one if we considere the alignement as an edition of sequences where we count the price of the substitution of the current amino acid to make two sequences identical).
Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. (1978) "A model of evolutionary change in proteins." In "Atlas of Protein Sequence and Structure, vol. 5, suppl. 3." M.O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found., Washington, DC.
Blosum: square matrix developed by Henikoff and co-workers that gives for the 20 amino acids, the frequency to be replaced by each of 20 amino acid, in local ungapped multialignment of sequences with more than 62% of identity for BLOSUM62. All matrices are calculated, no extrapolations are used.
Altshul et al. (1991) Amino acid substitutions matrices from an information theoretic perspective - J. Mol. Biol. 219, 555-565 .

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Structures
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Structure Database used as reference for links:
Protein Databank current release : currated during 27 years by the Brookhaven National Laboratory (Thank you so much to the BNL Staff !) and now by the Research Collaboratory for Structural Bioinformatics (RCSB PDB).

  SCOP: Structural Classification of Proteins. Release 1.39
Murzin AG, Brenner S.E., Hubbard T., Chothia C. (1995) "scop: a structural classification of proteins database for the investigation of sequences and structures" Journal of Molecular Biology 247:536-540.
  HSSP: Database of homology derived protein structures and the structural meaning of sequence alignment. Chris Sander and Reinhard Schneider Proteins, 1991,9, 56-68
  CATH: Version 1.6,Thornton J.M., Biomolecular Structure and Modelling Unit, University College London.
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Mutation
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Evolution
  Phylip : Phylogeny Inference Package programs (see the manual in line)
Go to page top ProDist from Phylip, computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff's PAM matrix, Kimura's 1983 approximation to it, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. PROTPARS. Estimates phylogenies from protein sequences using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished.
  Fitch 3.572c from Phylip, estimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria. Does not assume an evolutionary clock. This program will be useful with distances computed from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.
  Kitch from Phylip, estimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria are assumed. This program will be useful with distances computes from DNA sequences, with DNA hybridization measurements, and with genetic distances computed from gene frequencies
  GCG package
  PileUp
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Amino acid scales of physico-chemical properties
size hydrophobicity hydropholicity 2D-structure micellaneous database-related qualitative
 SIZE
    A        C        D        E        F        G        H        I        K        L
    M        N        P        Q        R        S        T        V        W        Y
 1: Molecular weight of each residue(dalton)= amino acid -H2O. 
Reference: Handbook of Chemistry and Physics (1961).
  71.080  103.140  115.090  129.120  147.180   57.060  137.150  113.170  128.180  113.170 
 131.210  114.110  197.120  128.140  156.200   87.080  101.110   99.140  186.210  163.180 

2: Volume (Angstroem cube). Reference: Prog.Biophys.Mol.Biol.24:107-123(1972). 88.600 108.500 111.100 138.400 189.900 60.100 153.200 166.700 168.600 166.700 162.900 117.700 122.700 143.900 173.400 89.000 116.100 140.000 227.800 193.600 : Volume (Angstroem cube). Authors : Pontius J., Richelle J. & Wodak S.J.
Reference: (Voronoi's method) J. Mol. Biol. 264: 121-136 (1996). 91.500 114.400 135.200 154.600 198.800 67.500 163.200 162.600 162.500 163.400 165.900 138.300 123.400 156.400 196.100 102.000 126.000 138.400 237.200 209.800 : Volume (Angstroem cube). Authors : Harpaz, Y., Gerstein, M. & Chotia, C. Reference: (Richards's B method) Structure,2:611-649 (1994) 90.100 113.200 117.100 140.800 193.500 63.800 159.300 164.900 170.000 164.600 167.700 127.500 123.100 149.400 192.800 94.200 120.000 139.100 231.700 197.100 3: Total accessible surface area of X in GXG tripeptides (Angstroem square). Author(s): Rose T. Reference: Not published. 118.000 132.000 155.000 192.000 232.000 86.000 209.000 196.000 230.000 199.000 185.000 172.000 147.000 200.000 253.000 132.000 154.000 169.000 277.000 247.000 4: Accessible surface area of the X's side chain in GXG tripeptides (Angstroem square). Author(s): Rose T. Reference: Not published. 56.000 70.000 96.000 133.000 176.000 0.000 155.000 141.000 172.000 140.000 147.000 115.000 109.000 142.000 193.000 73.000 97.000 112.000 222.000 192.000
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 HYDROPHOBICITY
     A        C        D        E        F        G        H        I        K        L
     M        N        P        Q        R        S        T        V        W        Y
 5: Proportion of residues 95% buried (in 12 proteins). 
Author(s): Chothia C. 
Reference: J. Mol. Biol. 105:1-14(1976). 
   0.380    0.500    0.150    0.180    0.500    0.360    0.170    0.600    0.030    0.450 
   0.400    0.120    0.180    0.070    0.010    0.220    0.230    0.540    0.270    0.150 

 6: Molar fraction (%) of 2001 buried residues. 
Author(s): Janin J. 
Reference: Nature 277:491-492(1979). 
  11.200    4.100    2.900    1.800    5.100   11.800    2.000    8.600    0.500   11.700 
   1.900    2.900    2.700    1.600    0.500    8.000    4.900   12.900    2.200    2.600 

 7: Mean fractional area loss (f) [average area buried/standard state area]. 
Author(s): Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. 
Reference: Science 229:834-838(1985). 
   0.740    0.910    0.620    0.620    0.880    0.720    0.780    0.880    0.520    0.850 
   0.850    0.630    0.640    0.620    0.640    0.660    0.700    0.860    0.850    0.760 
 
 8: Average area buried on transfer from standard state to folded protein. 
Author(s): Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. 
Reference: Science 229:834-838(1985). 
  86.600  132.300   97.800  113.900  194.100   62.900  155.800  158.000  115.500  164.100 
 172.900  103.300   92.900  119.200  162.200   85.600  106.500  141.000  224.600  177.700 

 9: Hydrophobicity (delta G1/2 cal) 
Author(s): Abraham D.J., Leo A.J. 
Reference: Proteins: Structure, Function and Genetics 2:130-152(1987). 
   0.440    0.580   -0.310   -0.340    2.540    0.000   -0.010    2.460   -2.450    2.460 
   1.100   -1.320    1.290   -0.710   -2.420   -0.840   -0.410    1.730    2.560    1.630 

10: Hydrophobicity (free energy of transfer to surface in kcal/mole). 
Author(s): Bull H.B., Breese K. 
Reference: Arch. Biochem. Biophys. 161:665-670(1974). 
   0.610    0.360    0.610    0.510   -1.520    0.810    0.690   -1.450    0.460   -1.650 
  -0.660    0.890   -0.170    0.970    0.690    0.420    0.290   -0.750   -1.200   -1.430 

11: Normalized consensus hydrophobicity scale. 
Author(s): Eisenberg D., Schwarz E., Komarony M., Wall R. 
Reference: J. Mol. Biol. 179:125-142(1984). 
   0.620    0.290   -0.900   -0.740    1.190    0.480   -0.400    1.380   -1.500    1.060 
   0.640   -0.780    0.120   -0.850   -2.530   -0.180   -0.050    1.080    0.810    0.260 

12: Hydrophobicity scale (pi-r). 
Author(s): Fauchere J.-L., Pliska V.E. 
Reference: Eur. J. Med. Chem. 18:369-375(1983). 
   0.310    1.540   -0.770   -0.640    1.790    0.000    0.130    1.800   -0.990    1.700 
   1.230   -0.600    0.720   -0.220   -1.010   -0.040    0.260    1.220    2.250    0.960 

13: Hydrophobicity scale based on free energy of transfer (kcal/mole) 
Author(s): Guy H.R. 
Reference: Biophys J. 47:61-70(1985). 
   0.100   -1.420    0.780    0.830   -2.120    0.330   -0.500   -1.130    1.400   -1.180 
  -1.590    0.480    0.730    0.950    1.910    0.520    0.070   -1.270   -0.510   -0.210 

14: Hydrophilicity 
Author(s): Hopp T.P., Woods K.R. 
Reference: Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). 
  -0.500   -1.000    3.000    3.000   -2.500    0.000   -0.500   -1.800    3.000   -1.800 
  -1.300    0.200    0.000    0.200    3.000    0.300   -0.400   -1.500   -3.400   -2.300 

15: Free energy of transfer from inside to outside of a globular protein 
Author(s): Janin J. 
Reference: Nature 277:491-492(1979). 
   0.300    0.900   -0.600   -0.700    0.500    0.300   -0.100    0.700   -1.800    0.500 
   0.400   -0.500   -0.300   -0.700   -1.400   -0.100   -0.200    0.600    0.300   -0.400 

16: Hydropathicity 
Author(s): Kyte J., Doolittle R.F. 
Reference: J. Mol. Biol. 157:105-132(1982). 
   1.800    2.500   -3.500   -3.500    2.800   -0.400   -3.200    4.500   -3.900    3.800 
   1.900   -3.500   -1.600   -3.500   -4.500   -0.800   -0.700    4.200   -0.900   -1.300 

17: Average surrounding hydrophobicity 
Author(s): Manavalan P., Ponnuswamy P.K. 
Reference: Nature 275:673-674(1978). 
  12.970   14.630   10.850   11.890   14.000   12.430   12.160   15.670   11.360   14.900 
  14.390   11.420   11.370   11.760   11.720   11.230   11.690   15.710   13.930   13.420 

18: Hydrophobicity scale (contact energy derived from 3D data)
Author(s): Miyazawa S., Jernigen R.L. 
Reference: Macromolecules 18:534-552(1985). 
   5.330    7.930    3.590    3.650    9.030    4.480    5.100    8.830    2.950    8.470 
   8.950    3.710    3.870    3.870    4.180    4.090    4.490    7.630    7.660    5.890 

19: Hydrophobicity scale (pi-r) 
Author(s): Roseman M.A. 
Reference: J. Mol. Biol. 200:513-522(1988). 
   0.390    0.250   -3.810   -2.910    2.270    0.000   -0.640    1.820   -2.770    1.820 
   0.960   -1.910    0.000   -1.300   -3.950    0.000    0.000    0.000    0.000    0.000 

20: Optimized matching hydrophobicity(OMH) 
Author(s): Sweet R.M., Eisenberg D. 
Reference: J. Mol. Biol. 171:479-488(1983). 
  -0.400    0.170   -1.310   -1.220    1.920   -0.670   -0.640    1.250   -0.670    1.220 
   1.020   -0.920   -0.490   -0.910   -0.590   -0.550   -0.280    0.910    0.500    1.670 

21: Hydration potential (kcal/mole) at 25øC 
Author(s): Wolfenden R.V., Andersson L., Cullis P.M., Southgate C.C.F. 
Reference: Biochemistry 20:849-855(1981). 
   1.940   -1.240  -10.950  -10.200   -0.760    2.390  -10.270    2.150   -9.520    2.280 
  -1.480   -9.680    0.000   -9.380  -19.920   -5.060   -4.880    1.990   -5.880   -6.110 

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 HYDROPHILICITY
     A        C        D        E        F        G        H        I        K        L
     M        N        P        Q        R        S        T        V        W        Y
22: Molar fraction (%) of 3220 accessible residues 
Author(s): Janin J. 
Reference: Nature 277:491-492(1979). 
   6.600    0.900    7.700    5.700    2.400    6.700    2.500    2.800   10.300    4.800 
   1.000    6.700    4.800    5.200    4.500    9.400    7.000    4.500    1.400    5.100 

23: Hydrophilicity 
Author(s): Hopp T.P., Woods K.R. 
Reference: Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). 
  -0.500   -1.000    3.000    3.000   -2.500    0.000   -0.500   -1.800    3.000   -1.800 
  -1.300    0.200    0.000    0.200    3.000    0.300   -0.400   -1.500   -3.400   -2.300 

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 2D-STRUCTURES
     A        C        D        E        F        G        H        I        K        L
     M        N        P        Q        R        S        T        V        W        Y
24: Conformational parameter for alpha helix (computed from 29 proteins)
Author(s): Chou P.Y., Fasman G.D. 
Reference: Adv. Enzym. 47:45-148(1978). 
   1.420    0.700    1.010    1.510    1.130    0.570    1.000    1.080    1.160    1.210 
   1.450    0.670    0.570    1.110    0.980    0.770    0.830    1.060    1.080    0.690 

25: Conformational parameter for beta-sheet (computed from 29 proteins) 
Author(s): Chou P.Y., Fasman G.D. 
Reference: Adv. Enzym. 47:45-148(1978). 
   0.830    1.190    0.540    0.370    1.380    0.750    0.870    1.600    0.740    1.300 
   1.050    0.890    0.550    1.100    0.930    0.750    1.190    1.700    1.370    1.470 

26: Conformational parameter for beta-turn (computed from 29 proteins) 
Author(s): Chou P.Y., Fasman G.D. 
Reference: Adv. Enzym. 47:45-148(1978). 
   0.660    1.190    1.460    0.740    0.600    1.560    0.950    0.470    1.010    0.590 
   0.600    1.560    1.520    0.980    0.950    1.430    0.960    0.500    0.960    1.140 

27: Conformational parameter for alpha helix 
Author(s): Deleage G., Roux B. 
Reference: Protein Engineering 1:289-294(1987). 
   1.489    0.966    0.924    1.504    1.195    0.510    1.003    1.003    1.172    1.236 
   1.363    0.772    0.492    1.164    1.224    0.739    0.785    0.990    1.090    0.787 

28: Conformational parameter for beta-sheet
Author(s): Deleage G., Roux B. 
Reference: Protein Engineering 1:289-294(1987). 
   0.709    1.191    0.541    0.567    1.393    0.657    0.863    1.799    0.721    1.261 
   1.210    0.604    0.354    0.840    0.920    0.928    1.221    1.965    1.306    1.266 

29: Conformational parameter for beta-turn 
Author(s): Deleage G., Roux B. 
Reference: Protein Engineering 1:289-294(1987). 
   0.788    0.965    1.197    1.149    0.624    1.860    0.970    0.240    1.302    0.670 
   0.436    1.572    1.415    0.997    0.912    1.316    0.739    0.387    0.546    0.795 

30: Conformational parameter for coil 
Author(s): Deleage G., Roux B. 
Reference: Protein Engineering 1:289-294(1987). 
   0.824    0.953    1.197    0.761    0.797    1.251    1.068    0.886    0.897    0.810 
   0.810    1.167    1.540    0.947    0.893    1.130    1.148    0.772    0.941    1.109 

31: Normalized frequency for alpha helix 
Author(s): Levitt M. 
Reference: Biochemistry 17:4277-4285(1978). 
   1.290    1.110    1.040    1.440    1.070    0.560    1.220    0.970    1.230    1.300 
   1.470    0.900    0.520    1.270    0.960    0.820    0.820    0.910    0.990    0.720 

32: Normalized frequency for beta-sheet 
Author(s): Levitt M. 
Reference: Biochemistry 17:4277-4285(1978). 
   0.900    0.740    0.720    0.750    1.320    0.920    1.080    1.450    0.770    1.020 
   0.970    0.760    0.640    0.800    0.990    0.950    1.210    1.490    1.140    1.250 

33: Normalized frequency for beta-turn 
Author(s): Levitt M. 
Reference: Biochemistry 17:4277-4285(1978). 
   0.770    0.810    1.410    0.990    0.590    1.640    0.680    0.510    0.960    0.580 
   0.410    1.280    1.910    0.980    0.880    1.320    1.040    0.470    0.760    1.050 

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 MICELLANEOUS
     A        C        D        E        F        G        H        I        K        L
     M        N        P        Q        R        S        T        V        W        Y
34: Polarity 
Author(s): Zimmerman J.M., Eliezer N., Simha R. 
Reference: J. Theor. Biol. 21:170-201(1968). 
   0.000    1.480   49.700   49.900    0.350    0.000   51.600    0.130   49.500    0.130 
   1.430    3.380    1.580    3.530   52.000    1.670    1.660    0.130    2.100    1.610 

35: Polarity (p). 
Author(s): Grantham R. 
Reference: Science 185:862-864(1974). 
   8.100    5.500   13.000   12.300    5.200    9.000   10.400    5.200   11.300    4.900 
   5.700   11.600    8.000   10.500   10.500    9.200    8.600    5.900    5.400    6.200 

36: Refractivity 
Author(s): Jones. D.D. 
Reference: J. Theor. Biol. 50:167-184(1975). 
   4.340   35.770   13.280   17.560   29.400    0.000   21.810   18.780   21.290   19.060 
  21.640   12.000   10.930   17.260   26.660    6.350   11.010   13.920   42.530   31.530 

37: Average flexibility index 
Author(s): Bhaskaran R., Ponnuswamy P.K. 
Reference: Int. J. Pept. Protein. Res. 32:242-255(1988). 
   0.360    0.350    0.510    0.500    0.310    0.540    0.320    0.460    0.470    0.370 
   0.300    0.460    0.510    0.490    0.530    0.510    0.440    0.390    0.310    0.420 

38: Partial specific volume (ml/gm) 
Reference: Prog.Biophys.Mol.Biol.24:107-123(1972). 
   0.748    0.631    0.579    0.643    0.774    0.632    0.670    0.884    0.789    0.884 
   0.745    0.619    0.758    0.674    0.666    0.613    0.689    0.847    0.734    0.712 

39: Recognition factors
Author(s): Fraga S. 
Reference: Can. J. Chem. 60:2606-2610(1982). 
  78.000   89.000   81.000   78.000   81.000   84.000   84.000   88.000   87.000   85.000 
  80.000   94.000   91.000   87.000   95.000  107.000   93.000   89.000  104.000   84.000 

40: Atomic weight ratio of hetero elements in end group to C in side chain
Author(s): Grantham R. 
Reference: Science 185:862-864(1974). 
   0.000    2.750    1.380    0.920    0.000    0.740    0.580    0.000    0.330    0.000 
   0.000    1.330    0.390    0.890    0.650    1.420    0.710    0.000    0.130    0.200 

41: Antigenicity (value X 10) 
Author(s): Welling G.W., Weijer W.J., Van der Zee R., Welling-Wester S. 
Reference: FEBS Lett. 188:215-218(1985). 
   1.150   -1.200    0.650   -0.710   -1.410   -1.840    3.120   -2.920    2.060    0.750 
  -3.850   -0.770   -0.530   -0.110    0.580   -0.260   -0.450   -0.130   -1.140    0.130 
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 DATABASE RELATED
     A        C        D        E        F        G        H        I        K        L
     M        N        P        Q        R        S        T        V        W        Y
42: Number of codon(s) coding for each amino acid in universal genetic code 
   4.000    1.000    2.000    2.000    2.000    4.000    2.000    3.000    2.000    6.000 
   1.000    2.000    4.000    2.000    6.000    6.000    4.000    4.000    1.000    2.000 

43: Overall amino acid composition (%) 
Author(s): McCaldon P., Argos P. 
Reference: Proteins: Structure, Function and Genetics 4:99-122(1988). 
   8.300    1.700    5.300    6.200    3.900    7.200    2.200    5.200    5.700    9.000 
   2.400    4.400    5.100    4.000    5.700    6.900    5.800    6.600    1.300    3.200 

44: Amino acid composition (%) in the SWISS-PROT Protein Sequence data bank. 
Author(s): Bairoch A. 
Reference: Release notes for SWISS-PROT release 35 - September 1997. 
   7.560    1.680    5.290    6.340    4.080    6.830    2.230    5.770    5.950    9.390 
   2.350    4.500    4.910    4.010    5.150    7.160    5.700    6.540    1.230    3.180 

45: Relative mutability of amino acids (Ala=100). 
Author(s): Dayhoff M.O., Schwartz R.M., Orcutt B.C. 
Reference: In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (1978). 
 100.000   20.000  106.000  102.000   41.000   49.000   66.000   96.000   56.000   40.000 
  94.000  134.000   56.000   93.000   65.000  120.000   97.000   74.000   18.000   41.000 


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 QUALITATIVE
46: polar  CDEHKNQRST
47: polar extended CDEHKNQRST
48: hydrophobic ALVIMFWY
49: hydrophobic extended ACFGHIKLMRTVWY
50: cis-conformation PS
51: side chain: H-donnor CHKNQRSTWY
52: side chain: H-acceptor CDEHNQSTY
53: phenol-alcohol-thiol CSTY
54: phenol-alcohol STY
55: alcohol ST
56: methyl terminal AILMTV
57: thiol-thioether CM
58: aromatic strict FWY
59: aromatic extended FHRWY
60: charged KREDH
61: positive KRH
62: negative ED
--: huge W
--: very big FWY
--: big FRWY
--: medium EHIKLMQ
63: small ACDGNPSTV 64: very small ACSGP 65: tiny AG 66: turn-like ACDEGHKNQRST 67-86: A-C-D-E-F-G-H-I-K-L-M-N-P-Q-R-S-T-V-W-Y
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  Unfixed bugs

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  Fixed bugs

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Department of Biochemistry and Molecular Biophysics
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Saint Louis, MO, U.S.A.

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