!!AA_SCORING_MATRIX_RECT 1.0

Alternate symbol comparison table for the comparison of protein
sequences.

Similirity matrix based upon the analysis of amino acid substitutions
after superposition of homologous protein structures (Risler, J. L.,
Delorme, M. O., Delacroix, H., and Henaut, A. [1988]. Amino Acid
Substitutions in Structurally Related Proteins. A Pattern Recognition
Approach. Determination of a New and Efficient Scoring Matrix. J. Mol.
Biol. 204, 1019-1029).  Only substitutions whose alpha carbon atoms are
no more than 1.2 angstroms apart after superposition of structures were
considered in constructing this matrix.

                     February 20, 1996 14:56   ..

{
GAP_CREATE 40
GAP_EXTEND 5
}

      A    B    C    D    E     F    G    H    I    K     L    M    N    P    Q     R    S    T    V    W     Y    Z 
A    22    8  -15    2   17     6    6   -6   17   14    13   10   13   -2   18    15   20   19   20   -9     2   18 
B     8   15  -17   15   12     1   -1   -8    5    6     3   -3   15  -11   11     6   13    6    6  -13    -3   12 
C   -15  -17   22  -17  -15   -16  -17  -18  -16  -16   -15  -16  -16  -18  -14   -15  -13  -14  -14  -18   -11  -15 
D     2   15  -17   22   10    -3   -4  -13    0    1    -2   -5    8  -12    6    -1    7    0    0  -14    -4    8 
E    17   12  -15   10   22     6    3   -6   15   14     9    6   14   -1   21    19   18   16   16  -10     2   22 

F     6    1  -16   -3    6    22   -4  -11   10    1    10   -2    4  -11    7     4    5    3    8   -9    20    7 
G     6   -1  -17   -4    3    -4   22  -12    0   -1    -2   -4    2  -12    2     1    7    2    1  -13    -2    3 
H    -6   -8  -18  -13   -6   -11  -12   22   -8  -10    -9  -12   -3  -16   -5    -4   -4   -9   -7  -17    -8   -6 
I    17    5  -16    0   15    10    0   -8   22   10    21    9    9   -6   14    14   16   16   22   -7     4   15 
K    14    6  -16    1   14     1   -1  -10   10   22     7    4   10   -7   17    21   14   12   12  -11     5   16 

L    13    3  -15   -2    9    10   -2   -9   21    7    22   18    8   -8   11    12   13   12   20   -8     5   10 
M    10   -3  -16   -5    6    -2   -4  -12    9    4    18   22    0  -12   12    11    6    8    8  -13    -2    9 
N    13   15  -16    8   14     4    2   -3    9   10     8    0   22  -10   16    12   19   11   11  -11    -1   15 
P    -2  -11  -18  -12   -1   -11  -12  -16   -6   -7    -8  -12  -10   22   -6    -3   -3   -5   -6  -16   -12   -4 
Q    18   11  -14    6   21     7    2   -5   14   17    11   12   16   -6   22    20   18   17   15  -10     5   22 

R    15    6  -15   -1   19     4    1   -4   14   21    12   11   12   -3   20    22   20   19   15   -8     8   20 
S    20   13  -13    7   18     5    7   -4   16   14    13    6   19   -3   18    20   22   21   18   -8     4   18 
T    19    6  -14    0   16     3    2   -9   16   12    12    8   11   -5   17    19   21   22   16  -10     3   17 
V    20    6  -14    0   16     8    1   -7   22   12    20    8   11   -6   15    15   18   16   22   -7     3   16 
W    -9  -13  -18  -14  -10    -9  -13  -17   -7  -11    -8  -13  -11  -16  -10    -8   -8  -10   -7   22    -6  -10 

Y     2   -3  -11   -4    2    20   -2   -8    4    5     5   -2   -1  -12    5     8    4    3    3   -6    22    4 
Z    18   12  -15    8   22     7    3   -6   15   16    10    9   15   -4   22    20   18   17   16  -10     4   22