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python-biopython  1.60
ProtParamData.py
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00001 # This module contains indices to be used with ProtParam
00002 
00003 # Kyte & Doolittle index of hydrophobicity
00004 kd = {'A': 1.8,'R':-4.5,'N':-3.5,'D':-3.5,'C': 2.5,
00005       'Q':-3.5,'E':-3.5,'G':-0.4,'H':-3.2,'I': 4.5,
00006       'L': 3.8,'K':-3.9,'M': 1.9,'F': 2.8,'P':-1.6,
00007       'S':-0.8,'T':-0.7,'W':-0.9,'Y':-1.3,'V': 4.2 }
00008 
00009 # Flexibility
00010 # Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
00011 Flex= {'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,
00012        'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
00013        'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
00014        'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
00015        'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929}
00016 
00017 # Hydrophilicity
00018 # 1 Hopp & Wood
00019 # Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). 
00020 hw = {'A':-0.5,'R':3.0, 'N':0.2, 'D':3.0, 'C':-1.0,
00021       'Q':0.2, 'E':3.0, 'G':0.0, 'H':-0.5,'I':-1.8,
00022       'L':-1.8,'K':3.0, 'M':-1.3,'F':-2.5,'P':0.0,
00023       'S':0.3, 'T':-0.4,'W':-3.4,'Y':-2.3,'V':-1.5 }
00024 
00025 # Surface accessibility
00026 # 1 Emini Surface fractional probability
00027 em = {'A':0.815,'R':1.475,'N':1.296,'D':1.283,'C':0.394,
00028       'Q':1.348,'E':1.445,'G':0.714,'H':1.180,'I':0.603,
00029       'L':0.603,'K':1.545,'M':0.714,'F':0.695,'P':1.236,
00030       'S':1.115,'T':1.184,'W':0.808,'Y':1.089,'V':0.606 }
00031 
00032 # 2 Janin Interior to surface transfer energy scale
00033 ja = {'A': 0.28,'R':-1.14,'N':-0.55,'D':-0.52,'C': 0.97,
00034       'Q':-0.69,'E':-1.01,'G': 0.43,'H':-0.31,'I': 0.60,
00035       'L': 0.60,'K':-1.62,'M': 0.43,'F': 0.46,'P':-0.42,
00036       'S':-0.19,'T':-0.32,'W': 0.29,'Y':-0.15,'V': 0.60 }
00037 
00038 
00039 # A two dimentional dictionary for calculating the instability index.
00040 # Guruprasad K., Reddy B.V.B., Pandit M.W.    Protein Engineering 4:155-161(1990).
00041 # It is based on dipeptide values therefore the vale for the dipeptide DG is DIWV['D']['G'].
00042 DIWV = {'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49,
00043               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49,
00044               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00045               'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
00046               'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
00047         'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26,
00048               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60,
00049               'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0,
00050               'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0,
00051               'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0},
00052         'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26,
00053               'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54,
00054               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00055               'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0,
00056               'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
00057         'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00058               'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
00059               'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00060               'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54,
00061               'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
00062         'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0,
00063               'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0,
00064               'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49,
00065               'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
00066               'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49},
00067         'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34,
00068               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
00069               'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00070               'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
00071               'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601},
00072         'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0,
00073               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34,
00074               'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0,
00075               'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
00076               'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
00077         'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00078               'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0,
00079               'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68,
00080               'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
00081               'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94},
00082         'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00083               'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0,
00084               'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0,
00085               'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60,
00086               'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
00087         'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00088               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28,
00089               'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0,
00090               'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54,
00091               'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68},
00092         'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00093               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
00094               'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00095               'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26,
00096               'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0},
00097         'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0,
00098               'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0,
00099               'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00100               'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0,
00101               'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0},
00102         'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26,
00103               'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
00104               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00105               'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0,
00106               'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54},
00107         'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54,
00108               'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0,
00109               'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0,
00110               'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54,
00111               'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0},
00112         'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0,
00113               'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
00114               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00115               'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26,
00116               'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
00117         'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00118               'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26,
00119               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34,
00120               'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28,
00121               'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54},
00122         'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0,
00123               'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0,
00124               'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03,
00125               'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0,
00126               'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
00127         'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0,
00128               'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68,
00129               'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34,
00130               'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
00131               'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
00132         'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03,
00133               'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0,
00134               'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0,
00135               'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
00136               'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54},
00137         'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68,
00138               'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34,
00139               'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0,
00140               'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91,
00141               'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34},
00142         }