Package Bio :: Package SeqUtils :: Module ProtParamData
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Source Code for Module Bio.SeqUtils.ProtParamData

  1  """Indices to be used with ProtParam.""" 
  2   
  3   
  4  # Kyte & Doolittle index of hydrophobicity 
  5  # J. Mol. Biol. 157:105-132(1982). 
  6  kd = {'A': 1.8, 'R': -4.5, 'N': -3.5, 'D': -3.5, 'C': 2.5, 
  7        'Q': -3.5, 'E': -3.5, 'G': -0.4, 'H': -3.2, 'I': 4.5, 
  8        'L': 3.8, 'K': -3.9, 'M': 1.9, 'F': 2.8, 'P': -1.6, 
  9        'S': -0.8, 'T': -0.7, 'W': -0.9, 'Y': -1.3, 'V': 4.2} 
 10   
 11  # Flexibility 
 12  # Normalized flexibility parameters (B-values), average 
 13  # Vihinen M., Torkkila E., Riikonen P. Proteins. 19(2):141-9(1994). 
 14  Flex = {'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068, 
 15          'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950, 
 16          'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048, 
 17          'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008, 
 18          'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929} 
 19   
 20  # Hydrophilicity 
 21  # 1 Hopp & Wood 
 22  # Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981). 
 23  hw = {'A': -0.5, 'R': 3.0, 'N': 0.2, 'D': 3.0, 'C': -1.0, 
 24        'Q': 0.2, 'E': 3.0, 'G': 0.0, 'H': -0.5, 'I': -1.8, 
 25        'L': -1.8, 'K': 3.0, 'M': -1.3, 'F': -2.5, 'P': 0.0, 
 26        'S': 0.3, 'T': -0.4, 'W': -3.4, 'Y': -2.3, 'V': -1.5} 
 27   
 28  # Surface accessibility 
 29  # Vergoten G & Theophanides T, Biomolecular Structure and Dynamics, 
 30  # pg.138 (1997). 
 31  # 1 Emini Surface fractional probability 
 32  em = {'A': 0.815, 'R': 1.475, 'N': 1.296, 'D': 1.283, 'C': 0.394, 
 33        'Q': 1.348, 'E': 1.445, 'G': 0.714, 'H': 1.180, 'I': 0.603, 
 34        'L': 0.603, 'K': 1.545, 'M': 0.714, 'F': 0.695, 'P': 1.236, 
 35        'S': 1.115, 'T': 1.184, 'W': 0.808, 'Y': 1.089, 'V': 0.606} 
 36   
 37  # 2 Janin Interior to surface transfer energy scale 
 38  ja = {'A': 0.28, 'R': -1.14, 'N': -0.55, 'D': -0.52, 'C': 0.97, 
 39        'Q': -0.69, 'E': -1.01, 'G': 0.43, 'H': -0.31, 'I': 0.60, 
 40        'L': 0.60, 'K': -1.62, 'M': 0.43, 'F': 0.46, 'P': -0.42, 
 41        'S': -0.19, 'T': -0.32, 'W': 0.29, 'Y': -0.15, 'V': 0.60} 
 42   
 43   
 44  # A two dimensional dictionary for calculating the instability index. 
 45  # Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990). 
 46  # It is based on dipeptide values; therefore, the value for the dipeptide DG 
 47  # is DIWV['D']['G']. 
 48  DIWV = {'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49, 
 49                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49, 
 50                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
 51                'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 
 52                'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0}, 
 53          'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26, 
 54                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60, 
 55                'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0, 
 56                'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0, 
 57                'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0}, 
 58          'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26, 
 59                'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54, 
 60                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
 61                'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0, 
 62                'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0}, 
 63          'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
 64                'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0, 
 65                'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
 66                'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54, 
 67                'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0}, 
 68          'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0, 
 69                'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0, 
 70                'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49, 
 71                'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0, 
 72                'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49}, 
 73          'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34, 
 74                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 
 75                'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
 76                'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 
 77                'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601}, 
 78          'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0, 
 79                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34, 
 80                'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0, 
 81                'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0, 
 82                'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 
 83          'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
 84                'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0, 
 85                'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68, 
 86                'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0, 
 87                'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94}, 
 88          'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
 89                'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0, 
 90                'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0, 
 91                'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60, 
 92                'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 
 93          'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
 94                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28, 
 95                'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0, 
 96                'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54, 
 97                'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68}, 
 98          'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
 99                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 
100                'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
101                'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26, 
102                'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0}, 
103          'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0, 
104                'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0, 
105                'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
106                'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0, 
107                'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0}, 
108          'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26, 
109                'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0, 
110                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
111                'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0, 
112                'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54}, 
113          'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54, 
114                'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0, 
115                'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0, 
116                'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54, 
117                'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0}, 
118          'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0, 
119                'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0, 
120                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
121                'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26, 
122                'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0}, 
123          'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
124                'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26, 
125                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34, 
126                'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28, 
127                'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54}, 
128          'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0, 
129                'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0, 
130                'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03, 
131                'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0, 
132                'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0}, 
133          'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0, 
134                'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68, 
135                'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34, 
136                'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0, 
137                'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0}, 
138          'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03, 
139                'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0, 
140                'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0, 
141                'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0, 
142                'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54}, 
143          'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68, 
144                'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34, 
145                'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0, 
146                'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91, 
147                'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34}, 
148          } 
149