I need your feedback on this question. Specifically the rating of each position. A sequence of sequence alignment is shown. For positions 61-66 comment briefly, but specifically, on the the character of the amino acids present in that position. Rate each position on the tolerance of amino acid substitution.
1= No substitution tolerated
2= highly conservative substitutions are tolerated
3= moderately conservative substitutions are tolerated
4= nonconservative substitutions are occasionally tolerated
5= most substitutions appear to be allowed
61 62 63 64 65 66
V A S E R A
V Y N R K A
I L D Q K G
V Q S K R G
V K N R K G
I S S E H A
I M D Q K A
My thoughts:
Position 61: Valine and isoleucine residues reside at this position. They could be used for structural support (hydrophobic effect).
Position 62: This position has many different amino acids with different properties. It may indicate that that position on the polypeptide is not a big factor for its main function.
Position 63: This position contains uncharged polar residues. It may just contribute to H-bonds for structural support.
Position 64: This position has residues with sides chains that are ionizable. It may contribute to enzymatic activity.
Position 65: This position has side chains that are basic.
Position 66: Non-polar residues, contribution to hydrophobic effect.
Ratings:
Position 61: 2 Only valine and isoleucine.
Position 62: 5 Many different amino acids with different properties/characteristics
Position 63: 4 Mainly uncharged polar groups (S and N) with aspartic acid.
Position 64: 4 Mainly amino acids with charged side chains.
Position 65: 3 Only 1 histidine but arginine and lysine repeats.
Position 66: 2 Only alanine and glycine
I'm having trouble on positions 51, 53-56.
Any help would be great.
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Topic: Tolerance of amino acid substitution (Read 3263 times)