Scales of Amino Acid Attributes
Description

Membrane protein structure, transmembrane, transmembrane structure, protein transmembrane structure, transmembrane structure prediction, protein transmembrane structure prediction, membrane protein, secondary structure, protein structure, structure prediction, protein structure prediction, protein secondary structure, protein secondary structure prediction, membrane protein structure prediction, membrane protein secondary structure prediction, preference functions, hydrophobicity analysis, sequence, protein sequence, amino acid scales, hydrophobicity scales, hydrophobicity plot, biochemistry, biophysics, biocomputing, Davor Juretic, Damir Zucic, Ana Jeroncic.

A total of 88 scales are available in the SPLIT algorithm as the scales with codes: 1,2,..,88.

The default scale is the Kyte and Doolittle scale (# 1) for calculation of preferences and Eisenberg scale (# 26) for calculation of hydrophobic moments.

Scales are used by the PREF-SPLIT suite of algorithms to a) extract preference functions (reference 1) from data base of protein secondary structures, b) evaluate and compare conformational preferences for each amino acid residue in a tested protein, and c) evaluate hydrophobic moments and hydrophobic moment threshold functions (reference 3).

Scales are listed in the order of decreasing performance in predicting transmembrane helices (this order depends on the performance parameters, proteins chosen to test performance, and algorithm version used in the test).

Two fields with the same list of 88 scales are in the form of two columns.

The choice of scale from the first column is used to evaluate preference functions, while the choice of scale from the second column (usually Eisenberg (26) or Cornette (27)) is used to evaluate hydrophobic moments in a tested sequence.

When SPLIT 3.5 run is performed one must first decide to use or not to use the Richardson's scale (code # 60) to refine the prediction for extramembrane ends of long transmembrane helices as described in the reference 3.

Thirteen of 88 scales result in extremely poor prediction of transmembrane helices. These are the scales with codes: 23,25,37,38,46,55,58,60,61,63,64,73,75. Of these 13 scales only the Richardson scale (code # 60) is useful to improve the prediction with SPLIT 3.5.

Of all 88 scales only the Richardson scale (60) has been used to extract preference functions from the data base of soluble protein structures, while all other scales have been used to extract preference functions from the data base of integral membrane proteins of alpha class and just enough soluble beta class proteins added (to extract preference functions for the beta strand conformation as well).

All scales are normalized by the program before being used to calculate preference functions or hydrophobic moments.

References:


1) Juretic, D., Lucic, B., Zucic, D. and Trinajstic, N. (1997). "Protein transmembrane structure: recognition and prediction by using hydrophobicity scales through preference functions."
Theoretical and Computational Chemistry, Vol 5. Theoretical Organic Chemistry, p. 405-445. Editor: Parkanyi, C., Elsevier Science, Amsterdam, 1998.
SPLIT 3.1 results are described in that paper. Scale number 100 from that paper is changed to # 88. Scale number 52 has slightly increased value for valine (from 0.559 to 0.859) as described in the third reference.

2) Juretic, D., Zucic, D., Lucic, B. and Trinajstic, N. "Preference functions for prediction of membrane-buried helices in integral membrane proteins."
Computers Chem. Vol. 22, No. 4, pp. 279-294, 1998.
SPLIT 3.1 results are described in that paper as well.

3) Juretic, D. and Lucin A. "The preference functions method for predicting helical turns with membrane propensity."
J. Chem. Inf. Comput. Sci. 38, pp. 575-585, 1998.
SPLIT 3.5 results are described in that paper.


Hydrophobicity scales (H), Physical scales (P), Chemical scales (C), Statistical preference scales (S), Optimal predictor scales (O), Biological scales (B) and Mathematical scales (M).

Kyte and Doolittle (1)= KYTDO

Kyte&Doolittle hydropathy values of amino acid residues. Selected (H) as published in: J. Kyte and R.F. Doolittle: "A Simple Method for Displaying the Hydropathic Character of a Protein". J. Mol. Biol. 157(1982)105-132.

Juretic (83) = MODKD Modified Kyte-Doolittle scale in an iterative procedure. Selected (H) as published in reference 1.
Iterative procedure described in: D. Juretic, B. Lucic and N. Trinajstic, "Predicting membrane protein secondary structure. Preference functions method for finding optimal conformational preferences" Croatica Chemica Acta 66 (1993), 201-208.

Edelman-25 (52) = EDE25

Optimal predictors (width 25).
Selected (O) values are the same as published valuers except for the Val value of 0.859 instead of 0.559 as in: J.Edelman: "Quadratic Minimization of Predictors for Protein Secondary Structure. Application to Transmembrane alpha-Helices". J.Mol.Biol. 232 (1993), 165-191.

Edelman-21 (53) = EDE21
Optimal predictors (width 21).
Selected (O) as published in Edelman 1993 paper.

Edelman-31 (51) = EDE31

Optimal predictors (width 31).
Selected (O) as published in Edelman 1993 paper.

Edelman-15 (54) = EDE15
Optimal predictors (width 15).
Selected (O) as published in Edelman 1993 paper.

Engelman (4) =ENGEL
Engelman hydrophobicity values.
Selected (H) with opposite sign from:
D.M. Engelman, T.A. Steitz and A. Goldman: "Identifying Nonpolar Transbilayer Helices in Amino Acid Sequences of Membrane Proteins". Ann.Rev.Biophys.Biophys.Chem. 15(1986), 321-353.

Eisenberg (26) = EISEN

Eisenberg normalized consensus hydrophobicity values. Average of 5 other scales.
Selected (H) normalized values as published in: D. Eisenberg, E. Schwarz, M. Komaromy and R. Wall: " Analysis of Membrane and Surface Protein Sequences with the Hydrophobic Moment Plot". J. Mol. Biol. 179 (1984), 125-142.

von Heijne and Blomberg (9) = VHEBL

Coil in water to helix in membrane values.
Selected (H) as published in: G. von Heijne and C. Blomberg Eur.J.Biochem. 97(1979)175-181.

Juretic (88) = CPREF

Scale of constant preference values extracted from the reference data set of 168 integral membrane proteins.
Selected (S) as published in the Juretic at al. reference 1 (see above), but the code number 88 instead of 100 is used by the server.

Juretic (86) = OSMP

Optimal scale (S) for memb. proteins with more than one transmembrane helical segment.
Obtained in an iterative procedure described in: D. Juretic, B. Lucic and N. Trinajstic, "Predicting membrane protein secondary structure. Preference functions method for finding optimal conformational preferences" Croatica Chemica Acta 66 (1993), 201-208.

Juretic (84) = MKD4

Scale (H) derived from # 1 (Kyte-Doolittle) in an iterative procedure as described for Juretic (86).

Juretic (82) = MKD2

Scale (H) derived from # 1 (Kyte-Doolittle) in an iterative procedure as described for Juretic (86).

Juretic (81) = MDK1

Scale (H) derived from # 1 (Kyte-Doolittle) in an iterative procedure as described for Juretic (86).

Juretic (80) = MDK0

Scale (H) derived from # 1 (Kyte-Doolittle) in an iterative procedure as described for Juretic (86).

Fauchere and Pliska (2) = FAUPL

Fauchere & Pliska scale of solution hydrophobicities for N-acetyl-amino-acid amides octanol/water distribution
Selected normalized (H) according to published values: J.-L. Fauchere and V. Pliska: "Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides". Eur.J.Med.Chem. - Chim. Ther. 18(1983)369-375

Chothia (29) = CHOTH

Proportion of residues that are 95% buried.
Selected normalized (H) according to the paper: C. Chothia: "The Nature of the Accessible and Buried Surfaces in Proteins". J. Mol. Biol. 105 (1976), 1-14.

Landolt-Marticorena (79) = MARTI

Positional preferences for occurrence of residues in the middle segment of single helix transmembrane spanning segments.
Selected (S) as published in:
C. Landolt-Marticorena, K.A. Williams, C.M. Deber, and R.A.F. Reithmeier: 'Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins'. J. Mol. Biol. 229 (1993), 602-608.

von Heijne (49) = HEIJN

Scale for transmembrane segments derived with the help of Engelman's scale (4) for bacterial inner membrane proteins: h=ln(fM/fA).
Selected (S) as published in:
G. von Heijne: "Membrane Protein Structure Prediction. Hydrophobicity Analysis and the Positive-inside Rule. J.Mol.Biol. 225 (1992),487-494.

Deber (44) = DEBER

M/A ratio in membrane transport proteins. Selected (S) as published with 1.0 subtracted from each value.
C.M. Deber, C.J. Brandl, R.B. Deber, L.C. Hsu and X.K. Young:" Amino Acid Composition of the Membrane and Aqueous Domains of Integral Membrane Proteins". Archives of Biochem. and Biophys. 251(1986) 68-76.

Kuhn and Leigh (43) = KUHLE

Membrane propensity scale.
Selected (S) as published in:
L.A. Kuhn and J.S. Leigh: "A statistical technique for predicting membrane protein structure". Biochim. Biophys. Acta 828(1985)351-361.

Cornette (27) = PRIFT

Optimal amphipathic helixes.
Selected normalized values (S) as published in:
J.L. Cornette, K.B. Cease, H. Margalit, J.L. Spouge, J.A. Berzofsky and C. DeLisi: "Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic Structures in Proteins". J.Mol.Biol. 196 (1987), 659-685.

Cornette (35)= NNEIG

Eigenvalues of nearest neighbor matrix. Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale).

Janin (5) = JANIN

DeltaG-transfer from buried interior to solvent accessible surface.
Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on: J. Janin, Nature 277 (1979), 491-492.

Ponnuswamy (3) = PONNU

Surrounding hydrophobicity scale.

Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on: P.K. Ponnuswamy, M. Prabhakaran and P. Manavalan Biochim. Biophys. Acta 623 (1980), 301-316.

Guy (7) = GUY-M

Average of four hydrophobicity scales.
Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on:
H.R. Guy: "Amino acid side-chain partition energies and distribution of residues in soluble proteins". Biophys.J. 47 (1985), 61-70.

Rose (30) = ROSEF

Mean fractional area loss.
Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on:
G.D. Rose, A.R. Geselowitz, G.J. Lesser, R.H. Lee and M.H. Zehfus: "Hydrophobicity of Amino Acid Residues in Globular Proteins". Science 229(1985)834-838.

Guy (31) = GUYFE

Transfer free energy for 6 layers.
Values for Trp, Tyr, Lys and Arg obtained by summing polar (positive) and apolar (negative) contribution. All values (H) normalized by Cornette (1987) and multiplied with -1. Original attributes published in the paper:
H.R. Guy: "Amino acid side-chain partition energies and distribution of residues in soluble proteins". Biophys.J. 47(1985)61-70.

Sweet and Eisenberg (32) = SWEET

Optimal matching hydrophobicity scale
Selected normalized values (H) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on:
R.M. Sweet and D. Eisenberg: "Correlation of Sequence Hydrophobicities Measures Similarity in Three-Dimensional Protein Structure". J.Mol.Biol. 171(1983)479-488.

Kuntz (33) = KUNTZ

Hydration (H2O that does not freeze)
Selected normalized values (P) as published in the Cornette 1987 paper (reference from Cornette (27) scale) based on:
I.D. Kuntz, J.Am.Chem.Soc. 93(1971)514-516.

Gibrat (12) = GIBRA

Distribution of residues toward protein interior. Scale (H) normalized as ax+b with a=0.02675, b=2a so that glycine is associated with 0.0.
For larger positive values residue is more often in the interior of a protein.
J.F. Gibrat: "Modelization by Computers of the 3-D Structure of Proteins". Ph.D. thesis. Univ. of Paris VI, Paris, France.
Scale collected from:
G.D. Fasman: "Prediction of Protein Structure and the Principles of Protein Conformation", Plenum, New York 1989, page 457, Table XVII.

Juretic (85) = OSMP1

Optimal scale for memb. proteins with one transmembrane helix.
Obtained in an iterative procedure described in:
D. Juretic, B. Lucic and N. Trinajstic, "Predicting membrane protein secondary structure. Preference functions method for finding optimal conformational preferences" Croatica Chemica Acta 66 (1993), 201-208.

Cid (13) = CIDAA

Hydrophobicity scale (H) for proteins of aa class, Ponnuswamy's 1980 procedure was used.
Selected normalized values based on reported values in:
H.Cid, M. Bunster, M. Canales and F. Gazitua: "Hydrophobicity and structural classes in proteins" Protein Engineering 5 (1992), 373-375.

Cid (16) = CIDAB

Hydrophobicity scale (H) for proteins of a/b class.
Published values normalized to average=0, sigma=1.
The same Cid reference as above.

Cid (14) = CIDBB

Hydrophobicity scale (H) for proteins of bb class.
Published values normalized to average=0, sigma=1.
The same Cid reference as above.

Cid (15) = CIDA+

Hydrophobicity scale (H) for proteins of a+b class.
Published values normalized to average=0, sigma=1.
The same Cid reference as above

Ponnuswamy and Gromiha (17) = PONG1

Globular protein surrounding hydrophobicity scale.
Selected published values (H) from:
P.K. Ponnuswamy and M.M. Gromiha: "Prediction of transmembrane helices from hydrophobic characteristics of proteins". Int. J. Peptide Protein Res. 42 (1993), 326-341.

Ponnuswamy and Gromiha (19) = PONG3

Membrane protein surrounding hydrophobicity (H) scale (combined membrane scale) from the Ponnuswamy and Gromiha 1993 reference (above).

Kidera (20) = KIDER

Hydrophobicity-related scale (H). All published values multiplied with -1.
A. Kidera, Y. Konishi, M. Oka, T. Ooi and A. Scheraga "Statistical Analysis of the Physical Properties of the 20 Naturally Occuring Amino Acids". J. Prot. Chem. 4 (1985), 23-55.

Roseman (21) = ROSEM

Calculated values (H) for hydrophathy based on the transfer of solutes from water to alkalane solvents. Free energy changes are corrected for self-solvation.
All published values are multiplied by -1 to associate positive numbers with Phe, Ile, Leu, Val.
M.A. Roseman: "Hydrophilicity of Polar Amino Acid Side-chains is Markedly Reduced by Flanking Peptide Bonds". J. Mol. Biol. 200 (1988), 513-522.

Jacobs and White (40) = JACWH

Jacobs & White weights from their IFH scale (H):
R. Jacobs and S.H. White: " The nature of the hydrophobic bonding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices." Biochemistry 28 (1989), 3421-3437.

Jacobs and White (87) = JACWH2

Jacobs & White IFH(0.5) scale (H).
Table V in the above reference.

Wertz and Scheraga (45) = WERSC

Scheraga ratio of in/out residues. Selected normalized values from Cornette 1987 reference are derived from:
D.H. Wertz and H.A. Scheraga Macromolecules 11(1978)9-15.

Juretic and Pesic (48) = JURPE

Statistical (S) scale of beta preferences derived from 8 membrane porins.
D. Juretic and R. Pesic: " A scale of beta- preferences for structure-activity predictions in membrane proteins". Croatica Chemica Acta 68 (1995) 215-232.

Chou (66) = CHOU6

Statistical preferences (S) for the alpha helix conformation in soluble alpha/beta class proteins. class proteins.
Values taken from:
P.Y. Chou: "Prediction of Protein Structural Classes from Amino Acid Compositions". p 549-586 in the Fasman's 1989 book:
G.D. Fasman: "Prediction of Protein Structure and the Principles of Protein Conformation", Plenum, New York 1989.

Chou (62)= CHOU2

Statistical preferences (S) for beta conformation in beta class proteins.
Values taken from the Fasman's 1989 book as for the Chou 66 scale (above).

Zamyatin (41) = ZAMYA

Partial specific volume = increase in volume of water after adding one gram of residue expressed in cubic centimeters per gram.
This physical property scale (P) can be found in:
T.E. Creighton: "Proteins. Structural and Molecular Properties". Freeman, New York 1992, p. 143, Table 4.3 A.A. Zamyatin, Ann. Rev. Biophys. Bioeng. 13 (1984), 145-165.

Miyazava and Jernigan (42) = MIJER

An average contact energy scale (P). Selected normalized values from Cornette 1987 reference are derived from:
S. Miyazava and R.L. Jernigan, Macromolecules 18(1985)534-552.

Mathusamy and Ponnuswamy (69) = MATPO

Mean rms fluctational displacements F1 (P).
R. Mathusamy and P.K. Ponnuswamy: "Variation of amino properties in protein secondary structures, alpha- helices and beta-strands." Int. J.Peptide Protein Res. 35 (1990), 378-395.

Woese (70) = WOESE

Polarity values (P).
All reported values subtracted from number 8 in order to obtain positive values for less polar residues.
M. Di Giulio, M.R. Capobianco and M, Medugno: "On the Optimization of the Physicochemical Distances between Amino Acids in the Evolution of Genetic Code". J. theor. Biol. 168 (1994), 43-51
C.R. Woese, D.H. Dugre, S.A. Dugre, M. Kondo and W.C. Saxinger: "On the fundamental nature and evolution of the genetic code". Cold Spring Harbor Symp. Quant. Biol. 31 (1966) 723-736.

Grantham (71) = GRANT

Polarity values (P).
Normalized values derived from:

R.Grantham: "Amino Acid Difference Formula to Help Explain Protein Evolution", Science, 185 (1974) 862-864.

Zimmerman (72) = ZIMMP

Polarity values (P).
Published values are divided with 10.
D.D. Jones: "Amino Acid Properties and Side-chain Orientation in Proteins". J. Theor. Biol. 50 (1975), 167-183.
Collected by:
J.M. Zimmerman, N. Eliezer and R. Simha: "The Characterization of Amino Acid Sequences in Proteins by Statistical Methods". J. Theor. Biol. 21 (1968) 170-201. Table 3 third column.

Wolfenden (22) = WOLFE

Wolfenden hydrophobicity scale (H) with proline.
R.M. Sweet and D. Eisenberg: "Correlation of Sequence Hydrophobicities Measures Similarity in Three-Dimensional Protein Structure". J.Mol.Biol. 171(1983)479-488.
R.V. Wolfenden, P.M. Cullis and C.C.F. Southgate Science, 206 (1979) 575-577.

Edelman and White (50) = EDEWH

Linear optimization weights.
Optimal predictor scale (O) from:
J. Edelman and S.H. White: "Linear Optimization of Predictors for Secondary Structure. Application to Transbilayer Segments of Membrane Proteins". J. Mol. Biol. 210 (1989), 195-209.

Chou and Fasman (57) = FASMT

Statistical turn preferences (S).
Values reported in:
P.Y. Chou and G.D. Fasman "Prediction of protein secondary structure" Adv. Enzymol. 47 (1978) 45-148.
M. Charton and B.I. Charton: "The dependence of the Chou-Fasman parameters on amino acid side chain structure". J. theor. Biol. 102(1983), 121-134.

Juretic (59) = JURET

Statistical preferences (S) for alpha and beta conformation averaged for each amino acid residue.
D. Juretic, N. Trinajstic and B. Lucic, "Protein secondary structure conformations and associated hydrophobicity scales". J. Math. Chem. 14 (1993), 35-45.
Calculated from:
G. Deleage and B. Roux: "An algorithm for protein secondary structure prediction based on class prediction". Protein Engineering 1 (1987), 289-294. Table I second and fourth column; values from each row averaged.
Preference for alpha and beta conformation reported in: P.Y. Chou and G.D. Fasman "Prediction of protein secondary structure" Adv. Enzymol. 47 (1978) 45-148.

Casari and Sippl (78) = CASSI

Structure-derived hydrophobicity scale (H)
G. Casari and M. Sippl: "Structure-derived Hydrophobic Potential. Hydrophobic Potential Derived from X-ray Structures of Globular Proteins is able to Identify Native Folds". J. Mol. Biol. 224 (1992), 725-732.

Eisenberg and McLachlan (10) = EIMCL

Solvation energy (P).
Normalized values from Cornette 1987 paper derived from: D. Eisenberg and A.D. McLachlan:

"Solvation energy in protein folding and binding". Nature 319(1986)199-203. Table 1, third column.

Krigbaum and Komoriya (8) = KRIGK

Ethanol to H2O interaction parameter (C).
Selected normalized values from Cornette 1987 paper are derived from:
W.R. Krigbaum and A. Komoriya Biochim. Biophys. Acta 576(1979)204-228.

Hopp and Woods (28) = HOPPW

Antigenic determinant scale (B).
Normalized values from Cornette 1987 paper derived from:
T.P. Hopp and K.R. Woods: "Prediction of protein antigenic determinants from amino acid sequences". Proc. Natl. Acad. Sci. USA 78 (1981), 3824-3828.

Levitt (11) = LEVIT

Hydrophobicity values (H)
Statistical scale of hydrophobicity based on information theory of the observed solvent accessibility of residues in proteins of known structure.
M. Levitt, J.Mol.Biol. 104(1976)59-107.

Meirovitch (39) = MEIRO

Average normalized distance of the alpha-carbon of amino acid X from the center of the protein. Normalization by the radius of gyration.
Normalized values (H) in Cornette 1987 paper derived from:
H. Meirovitch, S. Rackovsky and H.A. Scheraga, Macromolecules 13 (1980), 1398-1405.

Ponnuswamy and Gromiha (18) = PONG2

Membrane protein surrounding hydrophobicity (H) scale from the Ponnuswamy and Gromiha 1993 reference (above).

Urry (76) = URRY1

The temperature T1 of inverse temperature transition (P).
Selected values are 1-T1/100. Reported T1 values in:
D.W. Urry: "Free energy transduction in polypeptides and proteins based on inverse temperature transitions" Progress Bioph.& Mol. Biol. 57 (1992), 23-57. Table 1,. column 2.

Urry (77) = URRY2

The temperature T1 of inverse temperature transition (P). Selected values are T1/100.
Reported T1 vales from the reference cited above.

Karplus and Schulz (68) = KARPL

Karplus flexibility scale (P) from his FIGURE 1a in:
P.A. Karplus and G.E. Schulz: "Prediction of Chain Flexibility in Proteins". Naturwissenschaften 72 (1985), 212-213.

Meek (67) = MEEKR

Retention times at HPLC (C).
J.L. Meek, Proc. Natl. Acad. Sci., USA 77 (1980), 1632-1636. J.L. Meek

Chou and Fasman (56) = FASMB

Beta preferences (S).
Reported in the Chou & Fasman review (see above) from Adv. Enzymol. 47 (1978) 45-148.

Bull and Bresse (34) = BULDG

Surface tension of water (P).
H.B. Bull and K. Bresse Arch.Biochem.Biophys. 161(1973)665-670.

Cohen and Kuntz (36) = COHEN

Nonpolar area for residues in isolated beta sheets. Selected values (H) are published values/100.
Published values are from Fasman's 1989 book (see above) page 669, Table IX, column IV.
F.E. Cohen and I.D. Kuntz: "Tertiary Structure Prediction", p 647-705 from Fasman's 1989 book.

Jones (6) = JONES

Hydrophobicity scale (H)(NOZAKI-TANFORD-JONES).
New version normalized differently and with slight difference in the His value is not taken here but can be found in:
M. Mutter, F. Master & K.-H. Altman (1985) Biopolymers 24, 1057-1074.
Normalized values in Cornette 1987 paper derived from:
D.D. Jones: "Amino Acid Properties and Side-chain Orientation in Proteins: A Cross Correlation Approach". J.Theor.Biol. 50(1975)167-183.

Scheraga (47) = SCHER

Scheraga s values (P).
From: J. Wojcik, K.-H. Altmann and H.A. Scheraga, Biopolymers 30 (1990) 12.
We took these s values from:
K.T. O'Neil and W.F. DeGrado: "A Thermodynamic Scale for the Helix-Forming Tendencies of the Commonly Occurring Amino Acids", Science 250(1990), 646-651.

Chou (65) = CHOU5

Statistical (S) preferences for beta conformation in alpha+beta class proteins.
Values taken from:
P.Y. Chou: "Prediction of Protein Structural Classes from Amino Acid Compositions". p 549-586 in the Fasman's 1989 book:
G.D. Fasman: "Prediction of Protein Structure and the Principles of Protein Conformation", Plenum, New York 1989.

Fauchere (74) = FAUCH

Graph shape index (M).
J.-L. Fauchere, M. Charton, L.B. Kier, A. Verloop and V. Pliska: "Amino acid side chain parameters for correlation studies in biology and pharmacology". Int. J. Peptide Protein Res. 32 (1988), 269-278.

Rose (24) = ROSEB

Array (H) for Rose mean area buried on transfer from the standard state ( extended tripeptide ) to the folded protein ( proportional to the hydrophobic contribution to dG(conf)). All values expressed as nm squared.
G.D. Rose, A.R. Geselowitz, G.J. Lesser, R.H. Lee and M.H. Zehfus: "Hydrophobicity of Amino Acid Residues in Globular Proteins".Science 229 (1985), 834-838.

Chou (63) = CHOU3

Statistical (S) preferences for alpha conformation in alpha+beta class proteins.
Values taken from:
P.Y. Chou: "Prediction of Protein Structural Classes from Amino Acid Compositions". p 549-586 in the Fasman's 1989 book:
G.D. Fasman: "Prediction of Protein Structure and the Principles of Protein Conformation", Plenum, New York 1989.

Kim and Berg (37) = KIMBE

Thermodynamic beta-sheet propensities (S)
All published values were multiplied with -1 in order to associate larger positive values with beta forming residues.
The value for Pro was taken to be 0.23 according to:
C.K. Smith, J.M. Withka and L. Regan: "A thermodynamic Scale for the beta-Sheet Forming Tendencies of the Amino Acids". Biochemistry 33 (1994), 5510-5517.
C.A. Kim and J.M. Berg, Nature: "Thermodynamic beta-sheet propensities measured using a zinc-finger host peptide". Nature 362 (1993) 267-270.

Minor and Kim (38) = MINKI

Beta-sheet propensities (S)
D.L.Minor jr.,P.S.Kim, Nature, vol.367,no.6464 (1994) 660-665.

Chothia (23) = CHOTA

Chothia residue accessible surface area in tripeptide (H).
Selected H as published but surface area in nm squared.
C. Chothia: "The Nature of the Accessible and Buried Surfaces in Proteins". J. Mol. Biol. 105 (1976), 1-14.

Rose (25) = ROSEA

Array for Rose standard state accessibility (H).
Selected as published but area expressed in nm squared.
G.D. Rose, A.R. Geselowitz, G.J. Lesser, R.H. Lee and M.H. Zehfus: "Hydrophobicity of Amino Acid Residues in Globular Proteins". Science 229(1985)834-838. (second column in Table 1.).

O'Neil and DeGrado (46) = NEILD

Helix formation parameters (C) - the differences in the free energies of helix stabilization for each amino acid relative to Gly (in kcal/mol).
More negative values are more helix favoring. Ala is the most helix favoring residue ! One should multiply each value with -1 and try such scale for the prediction of transmembrane alpha helices.
K.T. O'Neil and W.F. DeGrado: "A Thermodynamic Scale for the Helix-Forming Tendencies of the Commonly Occurring Amino Acids", Science 250 (1990), 646-651.

Chou and Fasman (55) = FASMA

Statistical preferences (S) for the alpha helix conformation in soluble proteins.
Identical values reported in:
P.Y. Chou and G.D. Fasman "Prediction of protein secondary structure" Adv. Enzymol. 47 (1978) 45-148.
M. Charton and B.I. Charton: "The dependence of the Chou-Fasman parameters on amino acid side chain structure". J. theor. Biol. 102(1983), 121-134.

Richardson and Richardson (58) = RICRI

Middle alpha helix preferences (S): 5-point averages of values N4, N5, Mid, C5 and C4 in the Table I from:
Richardson & Richardson: Science 240(1988)1648. For full reference look at scale 60 comment.

Richardson and Richardson (60) = RICH1

Mid-alpha preference values (S) from:
J.S. Richardson and D.C. Richardson: "Amino Acid Preferences for Specific Locations at the Ends of alpha Helices. Science 240 (1988), 1648-1652.
Same P-mid values are used in the O'Neil & DeGrado 1990 reference.

Chou (61) = CHOU1

Statistical preferences (S) for the alpha helix conformation in alpha class soluble protein.
Values from Fasman's 1989 book:
G.D. Fasman: "Prediction of Protein Structure and the Principles of Protein Conformation", Plenum, New York 1989.
Page 568 from the chapter: P.Y. Chou: "Prediction of Protein Structural Classes from Amino Acid Compositions". p 549-586.

Chou (64) = CHOU4

Statistical preferences (S) for the alpha helix conformation in alpha/beta class soluble proteins)
Fasman's book (see above), page 568.

Kubota (75) = KUBOT

Relative mutability factor (B).
Reported values divided with 100.
Y. Kubota, H. Takahashi, K. Nishikawa and T. Ooi, J. Theor. Biol. 91 (1981), 347.

McMeekin (73) = MCMER

Refractivity values (P).
All values from Jones paper divided with 10.
D.D. Jones: "Amino Acid Properties and Side-chain Orientation in Proteins". J. Theor. Biol. 50 (1975), 167-183.
Collected by:
T.L. McMeekin, M.L. Groves and N.J. Hipp (1964) In "Amino Acids and Serum Proteins" (J.A. Stekol, ed) p. 54, Washington, D.C.: American Chemical Society.