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ProtParamData.py
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ProtParamData.py
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# This module contains indices to be used with ProtParam
# Kyte & Doolittle index of hydrophobicity
kd = {'A': 1.8, 'R':-4.5, 'N':-3.5, 'D':-3.5, 'C': 2.5,
'Q':-3.5, 'E':-3.5, 'G':-0.4, 'H':-3.2, 'I': 4.5,
'L': 3.8, 'K':-3.9, 'M': 1.9, 'F': 2.8, 'P':-1.6,
'S':-0.8, 'T':-0.7, 'W':-0.9, 'Y':-1.3, 'V': 4.2 }
# Flexibility
# Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
Flex= {'A': 0.984, 'C': 0.906, 'E': 1.094, 'D': 1.068,
'G': 1.031, 'F': 0.915, 'I': 0.927, 'H': 0.950,
'K': 1.102, 'M': 0.952, 'L': 0.935, 'N': 1.048,
'Q': 1.037, 'P': 1.049, 'S': 1.046, 'R': 1.008,
'T': 0.997, 'W': 0.904, 'V': 0.931, 'Y': 0.929}
# Hydrophilicity
# 1 Hopp & Wood
# Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828(1981).
hw = {'A':-0.5, 'R': 3.0, 'N': 0.2, 'D': 3.0, 'C':-1.0,
'Q': 0.2, 'E': 3.0, 'G': 0.0, 'H':-0.5, 'I':-1.8,
'L':-1.8, 'K': 3.0, 'M':-1.3, 'F':-2.5, 'P': 0.0,
'S': 0.3, 'T':-0.4, 'W':-3.4, 'Y':-2.3, 'V':-1.5 }
# Surface accessibility
# 1 Emini Surface fractional probability
em = {'A': 0.815, 'R': 1.475, 'N': 1.296, 'D': 1.283, 'C': 0.394,
'Q': 1.348, 'E': 1.445, 'G': 0.714, 'H': 1.180, 'I': 0.603,
'L': 0.603, 'K': 1.545, 'M': 0.714, 'F': 0.695, 'P': 1.236,
'S': 1.115, 'T': 1.184, 'W': 0.808, 'Y': 1.089, 'V': 0.606 }
# 2 Janin Interior to surface transfer energy scale
ja = {'A': 0.28, 'R':-1.14, 'N':-0.55, 'D':-0.52, 'C': 0.97,
'Q':-0.69, 'E':-1.01, 'G': 0.43, 'H':-0.31, 'I': 0.60,
'L': 0.60, 'K':-1.62, 'M': 0.43, 'F': 0.46, 'P':-0.42,
'S':-0.19, 'T':-0.32, 'W': 0.29, 'Y':-0.15, 'V': 0.60 }
# A two dimentional dictionary for calculating the instability index.
# Guruprasad K., Reddy B.V.B., Pandit M.W. Protein Engineering 4:155-161(1990).
# It is based on dipeptide values therefore the vale for the dipeptide DG is DIWV['D']['G'].
DIWV = {'A': {'A': 1.0, 'C': 44.94, 'E': 1.0, 'D': -7.49,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': -7.49,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
'C': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 20.26,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 33.60,
'K': 1.0, 'M': 33.60, 'L': 20.26, 'N': 1.0,
'Q': -6.54, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 33.60, 'W': 24.68, 'V': -6.54, 'Y': 1.0},
'E': {'A': 1.0, 'C': 44.94, 'E': 33.60, 'D': 20.26,
'G': 1.0, 'F': 1.0, 'I': 20.26, 'H': -6.54,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': 1.0,
'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
'D': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 1.0, 'S': 20.26, 'R': -6.54,
'T': -14.03, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
'G': {'A': -7.49, 'C': 1.0, 'E': -6.54, 'D': 1.0,
'G': 13.34, 'F': 1.0, 'I': -7.49, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': -7.49,
'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': 13.34, 'V': 1.0, 'Y': -7.49},
'F': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 13.34,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -14.03, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 33.601},
'I': {'A': 1.0, 'C': 1.0, 'E': 44.94, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 13.34,
'K': -7.49, 'M': 1.0, 'L': 20.26, 'N': 1.0,
'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
'H': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -9.37, 'F': -9.37, 'I': 44.94, 'H': 1.0,
'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 24.68,
'Q': 1.0, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': -6.54, 'W': -1.88, 'V': 1.0, 'Y': 44.94},
'K': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -7.49, 'F': 1.0, 'I': -7.49, 'H': 1.0,
'K': 1.0, 'M': 33.60, 'L': -7.49, 'N': 1.0,
'Q': 24.64, 'P': -6.54, 'S': 1.0, 'R': 33.60,
'T': 1.0, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
'M': {'A': 13.34, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 58.28,
'K': 1.0, 'M': -1.88, 'L': 1.0, 'N': 1.0,
'Q': -6.54, 'P': 44.94, 'S': 44.94, 'R': -6.54,
'T': -1.88, 'W': 1.0, 'V': 1.0, 'Y': 24.68},
'L': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -7.49, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 33.60, 'P': 20.26, 'S': 1.0, 'R': 20.26,
'T': 1.0, 'W': 24.68, 'V': 1.0, 'Y': 1.0},
'N': {'A': 1.0, 'C': -1.88, 'E': 1.0, 'D': 1.0,
'G': -14.03, 'F': -14.03, 'I': 44.94, 'H': 1.0,
'K': 24.68, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': -6.54, 'P': -1.88, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 1.0},
'Q': {'A': 1.0, 'C': -6.54, 'E': 20.26, 'D': 20.26,
'G': 1.0, 'F': -6.54, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 1.0,
'T': 1.0, 'W': 1.0, 'V': -6.54, 'Y': -6.54},
'P': {'A': 20.26, 'C': -6.54, 'E': 18.38, 'D': -6.54,
'G': 1.0, 'F': 20.26, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': -6.54, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 20.26, 'S': 20.26, 'R': -6.54,
'T': 1.0, 'W': -1.88, 'V': 20.26, 'Y': 1.0},
'S': {'A': 1.0, 'C': 33.60, 'E': 20.26, 'D': 1.0,
'G': 1.0, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 20.26, 'P': 44.94, 'S': 20.26, 'R': 20.26,
'T': 1.0, 'W': 1.0, 'V': 1.0, 'Y': 1.0},
'R': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 20.26,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': 13.34,
'Q': 20.26, 'P': 20.26, 'S': 44.94, 'R': 58.28,
'T': 1.0, 'W': 58.28, 'V': 1.0, 'Y': -6.54},
'T': {'A': 1.0, 'C': 1.0, 'E': 20.26, 'D': 1.0,
'G': -7.49, 'F': 13.34, 'I': 1.0, 'H': 1.0,
'K': 1.0, 'M': 1.0, 'L': 1.0, 'N': -14.03,
'Q': -6.54, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': 1.0, 'W': -14.03, 'V': 1.0, 'Y': 1.0},
'W': {'A': -14.03, 'C': 1.0, 'E': 1.0, 'D': 1.0,
'G': -9.37, 'F': 1.0, 'I': 1.0, 'H': 24.68,
'K': 1.0, 'M': 24.68, 'L': 13.34, 'N': 13.34,
'Q': 1.0, 'P': 1.0, 'S': 1.0, 'R': 1.0,
'T': -14.03, 'W': 1.0, 'V': -7.49, 'Y': 1.0},
'V': {'A': 1.0, 'C': 1.0, 'E': 1.0, 'D': -14.03,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 1.0,
'K': -1.88, 'M': 1.0, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 20.26, 'S': 1.0, 'R': 1.0,
'T': -7.49, 'W': 1.0, 'V': 1.0, 'Y': -6.54},
'Y': {'A': 24.68, 'C': 1.0, 'E': -6.54, 'D': 24.68,
'G': -7.49, 'F': 1.0, 'I': 1.0, 'H': 13.34,
'K': 1.0, 'M': 44.94, 'L': 1.0, 'N': 1.0,
'Q': 1.0, 'P': 13.34, 'S': 1.0, 'R': -15.91,
'T': -7.49, 'W': -9.37, 'V': 1.0, 'Y': 13.34},
}