Click here to get a look at the residues that are less than 4 angstroms away from Lys H93. (Click here to eliminate the alpha carbon trace.)
Of the residues within 4 angstroms of Lys H93 only Serine 35 is hydrophilic. Click here to get a top view of LysH93 and Serine 35 in CPK color format.
With in the hydrophobic pocket only one charged residue is with in 8 angstroms, Glu H50 (Click here to highlight Glu 50 orange). We can change the Glu 50 to CPK color scheme and see that there is no interaction with Lys H93. This absence of charged residues in or around the hydrophobic pocket reassures the perturbed pKa for Lys H93.
To try to sum all this information up lets look at the hydrophobic pocket with both chains . To summarize the color scheme again, the light chain is blue, the heavy chain is green, the catalytic Lys H93 is red, hydrophobic residues in the binding pocket of the light chain are orange and those of the heavy chain are yellow.
From this view Lys H93 stands out nicely
in the hydrophobic pocket, and if we look from the top
, we can almost imagine the opening of the binding pocket. Lets complicate
things a little by space-filling the rest of the residues on both chains
. Now we can barely glimpse Lys H93,
but this view shows Lys H93's isolation and
ability to maintain it's special, catalytic neutrality.