output Coulomb interactions

[juranga004]

Hello,

I am currently trying to assign protonation states of a protein through the estimation of the pKa values. I am wondering about the output of the Coulomb interactions and I would appreciate it if someone could help me to figure this out. I am focusing on three residues whose output results are listed here:

ASP 17 0.88 100 % 3.84 580 1.73 0 -0.85 N+ 1 -0.54 THR 2 -0.36 K 638 ASP 17 -0.85 LYS 33 -0.12 SER 18 -0.39 ARG 19 ASP 17 0.00 XXX 0 X -0.52 ARG 19 -2.03 N+ 1 ASP 17 0.00 XXX 0 X -0.80 GLY 170 -2.03 LYS 33

LYS 33 6.46* 100 % -4.34 578 0.00 0 0.85 ASP 17 0.00 XXX 0 X -0.08 ARG 19 LYS 33 -0.63 LYS 33 0.00 XXX 0 X 0.06 ASP 32 LYS 33 0.00 XXX 0 X 0.00 XXX 0 X 0.08 ASP 166 LYS 33 0.00 XXX 0 X 0.00 XXX 0 X 2.03 ASP 17 LYS 33 0.00 XXX 0 X 0.00 XXX 0 X -2.02 LYS 33

N+ 1 7.59* 93 % -3.83 541 0.00 0 0.85 ASP 17 0.00 XXX 0 X -0.27 K 638 N+ 1 0.63 N+ 1 0.00 XXX 0 X -0.31 ARG 19 N+ 1 0.00 XXX 0 X 0.00 XXX 0 X 0.48 ASP 166 N+ 1 0.00 XXX 0 X 0.00 XXX 0 X 2.03 ASP 17

I would like to ask on the Coulomb values that are printed. For residue ASP 17, it can be seen that LYS 33 lowers its pKa value by 2.03 units. In the same way, for residue LYS 33, ASP 17 increases its pKa value by 2.03. They are the same but with opposite sign.

However, I am a bit surprised to observe that LYS 33 interacts with itself, decreasing its pKa by 2.02. Is this due to the coupling between the two residues? Shouldnt I instead of LYS 33 think of the N+ 1 residue? But then, why does not the interaction with the residue LYS 33 show up for N+ 1 with opposite sign?

I have generated this output executing:

propka31 -d output_2271.pdb > propka.out

Thank you very much for your time and attention

Best regards,

Jon Uranga

[sobolevnrm]

Can you provide the PDB file you used for this?

[juranga004]

This is the PDB file I have used in this case output_2271.txt

[sobolevnrm]

Thank you.