Package Bio :: Package SeqUtils :: Module ProtParamData
[hide private]
[frames] | no frames]

Source Code for Module Bio.SeqUtils.ProtParamData

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