Results and discussion in the present paper used the same amino acid codes as the above tools and data bank use, i.e. the IUPAC (International Union of Pure and Applied Chemistry) one letter amino acid codes, given in Table 1 below. For completeness, conservative replacements in column 3 of Table 1 are given. They relate largely to substitutions that can usefully be made in the design of synthetic peptides [4,5]. This is an application which is not specifically discussed in the present paper but which could be a basis for design of synthetic vaccines and preventative or therapeutic agents [4,5], in this case targeted at sialic acid glycan binding site of a virus. As discussed in the sequence of steps for the methodology above, the sialic acid glycan binding motifs are taken to be indicators of the sialic acid binding domain and not necessarily of the target sites per se, but they may be, and often are, potential target sites. The list of conservative replacements also remains useful for considering substitutions that are conservative in maintaining similar amino acid properties when detecting and comparing related sequences.
Table 1 One letter amino acid codes and sialic acid site binding region measures discussed in the text.
One letter code Amino acid Conservative replacements Preliminary sialic acid binding amino acid score SABS (see Results) SABR-P prediction method refined parameters (see Results)
A alanine A, E, S, T 1 1
C cysteine/cystine S, T, V 1 1
D aspartic acid E 1 1
E glutamic acid A, D 0 0
F phenylalanine M, W, Y 1 2
G glycine N, P 1 1
H histidine K, R 1 2
I isoleucine L, V 0 0
K lysine H, R 0 0
L leucine I, V 0 0
M methionine F, W, Y 0 0
N asparagine G, D, Q 1 1
P proline G 0 0
Q glutamine N, E 0 0
R arginine H, K 0 0
S serine A, T 1 1
T threonine A, I, S 1 1
V valine A, I, L 0 0
W tryptophan F, M, Y 2 4
Y tyrosine F. M, W 1 2