A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | |
A | 2 | |||||||||||||||||||
R | -2 | 6 | ||||||||||||||||||
N | 0 | 0 | 2 | |||||||||||||||||
D | 0 | -1 | 2 | 4 | ||||||||||||||||
C | -2 | -4 | -4 | -5 | 4 | |||||||||||||||
Q | 0 | 1 | 1 | 2 | -5 | 4 | ||||||||||||||
E | 0 | -1 | 1 | 3 | -5 | 2 | 4 | |||||||||||||
G | 1 | -3 | 0 | 1 | -3 | -1 | 0 | 5 | ||||||||||||
H | -1 | 2 | 2 | 1 | -3 | 3 | 1 | -2 | 6 | |||||||||||
I | -1 | -2 | -2 | -2 | -2 | -2 | -2 | -3 | -2 | 5 | ||||||||||
L | -2 | -3 | -3 | -4 | -6 | -2 | -3 | -4 | -2 | 2 | 6 | |||||||||
K | -1 | 3 | 1 | 0 | -5 | 1 | 0 | -2 | 0 | -2 | -3 | 5 | ||||||||
M | -1 | 0 | -2 | -3 | -5 | -1 | -2 | -3 | -2 | 2 | 4 | 0 | 6 | |||||||
F | -4 | -4 | -4 | -6 | -4 | -5 | -5 | -5 | -2 | 1 | 2 | -5 | 0 | 9 | ||||||
P | 1 | 0 | -1 | -1 | -3 | 0 | -1 | -1 | 0 | -2 | -3 | -1 | -2 | -5 | 6 | |||||
S | 1 | 0 | 1 | 0 | 0 | -1 | 0 | 1 | -1 | -1 | -3 | 0 | -2 | -3 | 1 | 3 | ||||
T | 1 | -1 | 0 | 0 | -2 | -1 | 0 | 0 | -1 | 0 | -2 | 0 | -1 | -2 | 0 | 1 | 3 | |||
W | -6 | 2 | -4 | -7 | -8 | -5 | -7 | -7 | -3 | -5 | -2 | -3 | -4 | 0 | -6 | -2 | -5 | 17 | ||
Y | -3 | -4 | -2 | -4 | 0 | -4 | -4 | -5 | 0 | -1 | -1 | -4 | -2 | 7 | -5 | -3 | -3 | 0 | 10 | |
V | 0 | -2 | -2 | -2 | -2 | -2 | -2 | -1 | -2 | 4 | 2 | -2 | 2 | -1 | -1 | -1 | 0 | -6 | -2 | 4 |
The matrix is frequently used to score aligned peptide sequences to determine the similarity
of those sequences. The numbers given above were derived from comparing aligned sequences of proteins
with known homology and determining the "accepted point mutations" (PAM) observed. The frequencies of these
mutations are in this table as a "log odds-matrix" where: