The format for the residue-residue interaction matrix should be as follows. The exact order of the column and rows does not have to be the same as in this example, but each column and row should be labeled with the corresponding one-letter amino acid abbreviation.

Values for each residue-residue pair will be used to define a coloring scheme for viewing the helix-helix interface. For example, if you wish to highlight interactions between charged residues, you could construct a matrix such that the values for Asp-Lys, Asp-Arg, Asp-His, Glu-Lys, Glu-Arg, and Glu-His (and vice versa; i.e., Lys-Asp, Arg-Asp, ...) are +5.00 and all other values are 0.00.

  G A S C V T I P M D N L K E Q R H F Y W
G -1.83 -1.11 -0.96 -1.18 -0.78 -0.45 -1.04 -0.65 -0.71 -0.04 0.12 -0.55 0.20 0.82 0.00 0.32 -0.12 -0.50 -0.38 -0.42
A -1.11 -0.61 -0.33 -0.51 -0.46 -0.64 -0.32 -0.30 -0.56 0.19 0.14 -0.45 0.47 0.22 0.30 0.46 -0.02 -0.03 -0.22 0.13
S -0.96 -0.33 -0.17 -0.28 0.12 -0.22 0.64 -0.40 -0.34 0.82 -0.37 -0.06 0.82 0.72 0.24 0.46 -0.33 0.30 0.42 0.41
C -1.18 -0.51 -0.28 -1.66 -0.23 0.01 -0.10 -0.10 -0.48 0.07 0.18 -0.31 1.00 0.37 0.36 0.79 -0.22 0.03 0.40 0.47
V -0.78 -0.46 0.12 -0.23 -0.32 -0.01 -0.10 0.30 -0.50 0.49 0.16 -0.53 0.83 0.70 0.85 0.94 0.15 -0.09 0.04 0.50
T -0.45 -0.64 -0.22 0.01 -0.01 -0.42 -0.08 -0.40 0.07 0.28 -0.19 -0.14 0.67 0.99 0.79 0.59 0.29 0.18 0.10 0.18
I -1.04 -0.32 0.64 -0.10 -0.10 -0.08 -0.14 0.31 -0.12 0.27 0.33 -0.40 0.59 1.06 0.54 0.73 0.68 -0.16 0.10 0.43
P -0.65 -0.30 -0.40 -0.10 0.30 -0.40 0.31 -0.06 -0.07 0.11 -0.31 0.05 0.62 0.19 0.29 0.43 0.19 0.23 0.38 0.41
M -0.71 -0.56 -0.34 -0.48 -0.50 0.07 -0.12 -0.07 -1.14 0.09 0.25 -0.50 -0.14 0.67 -0.09 0.38 0.38 -0.18 -0.20 -0.39
D -0.04 0.19 0.82 0.07 0.49 0.28 0.27 0.11 0.09 -0.61 -0.28 0.45 0.25 1.04 0.80 -0.32 -0.40 0.55 -0.14 -0.19
N 0.12 0.14 -0.37 0.18 0.16 -0.19 0.33 -0.31 0.25 -0.28 -0.32 -0.08 0.17 0.15 -0.27 -0.25 -0.11 0.17 -0.25 0.09
L -0.55 -0.45 -0.06 -0.31 -0.53 -0.14 -0.40 0.05 -0.50 0.45 -0.08 -0.47 0.79 0.48 0.33 0.27 0.32 -0.32 -0.18 0.25
K 0.20 0.47 0.82 1.00 0.83 0.67 0.59 0.62 -0.14 0.25 0.17 0.79 1.33 0.14 -0.02 0.60 0.15 1.00 0.66 0.94
E 0.82 0.22 0.72 0.37 0.70 0.99 1.06 0.19 0.67 1.04 0.15 0.48 0.14 0.83 0.51 -0.14 0.40 0.52 0.16 1.44
Q 0.00 0.30 0.24 0.36 0.85 0.79 0.54 0.29 -0.09 0.80 -0.27 0.33 -0.02 0.51 1.18 0.67 0.17 0.52 0.58 0.79
R 0.32 0.46 0.46 0.79 0.94 0.59 0.73 0.43 0.38 -0.32 -0.25 0.27 0.60 -0.14 0.67 0.43 0.63 0.92 0.17 0.49
H -0.12 -0.02 -0.33 -0.22 0.15 0.29 0.68 0.19 0.38 -0.40 -0.11 0.32 0.15 0.40 0.17 0.63 -0.94 -0.14 -0.25 -0.29
F -0.50 -0.03 0.30 0.03 -0.09 0.18 -0.16 0.23 -0.18 0.55 0.17 -0.32 1.00 0.52 0.52 0.92 -0.14 -0.32 0.16 0.11
Y -0.38 -0.22 0.42 0.40 0.04 0.10 0.10 0.38 -0.20 -0.14 -0.25 -0.18 0.66 0.16 0.58 0.17 -0.25 0.16 0.25 0.02
W -0.42 0.13 0.41 0.47 0.50 0.18 0.43 0.41 -0.39 -0.19 0.09 0.25 0.94 1.44 0.79 0.49 -0.29 0.11 0.02 0.25

Last Updated 9/2004
By Anne E. Counterman