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Table 1 The 31 informative physicochemical properties mined by IPMA.

From: Computational identification of ubiquitylation sites from protein sequences

AAindex identity Description MED
NADH010102 Hydropathy scale based on self-information values in the two-state model of 9% accessibility 31.79
BROC820102 Retention coefficient in HFBA 29.80
MEIH800102 Average reduced distance for side chain 28.48
LEVM780101 Normalized frequency of alpha-helix, with weights 25.17
GUYH850104 Apparent partition energies calculated from Janin index 23.84
CORJ870101 NNEIG index 23.18
RACS770102 Average reduced distance for side chain 22.52
GEOR030108 Linker propensity from helical (annotated by DSSP) dataset 22.52
HARY940101 Mean volumes of residues buried in protein interiors 21.85
GRAR740102 Polarity 19.87
GUYH850105 Apparent partition energies calculated from Chothia index 19.87
MEIH800103 Average side chain orientation angle 17.88
KRIW790102 Fraction of site occupied by water 17.88
LEVM780106 Normalized frequency of reverse turn, unweighted 14.57
BULH740102 Apparent partial specific volume 13.25
FAUJ880101 Graph shape index 11.92
PUNT030102 Knowledge-based membrane-propensity scale from 3D_Helix in MPtopo databases 10.60
HUTJ700103 Entropy of formation 9.93
EISD840101 Consensus normalized hydrophobicity scale 8.61
CEDJ970105 Composition of amino acids in nuclear proteins (percent) 7.28
ZIMJ680102 Bulkiness 7.28
CEDJ970103 Composition of amino acids in membrane proteins (percent) 5.96
CHOC760103 Proportion of residues 95% buried 5.30
CEDJ970102 Composition of amino acids in anchored proteins (percent) 5.30
ROSM880102 Side chain hydropathy, corrected for solvation 4.64
BROC820101 Retention coefficient in TFA 4.64
FAUJ830101 Hydrophobic parameter pi 1.99
NAKH920101 AA composition of CYT of single-spanning proteins 1.99
ZHOH040102 The relative stability scale extracted from mutation experiments 1.99
NAKH900101 AA composition of total proteins 1.32
QIAN880129 Weights for coil at the window position of -4 1.32