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Grimsley GR, Scholtz JM & Pace CN, 2009
Grimsley, Scholtz, and Pace report a nearly complete set of mean pK values culled from 541 pK values measured in 78 folded proteins in their 2009 paper (1). The vast majority of measurements were made directly using nuclear magnetic resonance. A small number of pK measurements were made by indirect methods.
Amino acid pK values from Grimsley GR, Scholtz JM & Pace CN, 2009 (1).
Group
pK   
CT
3.3
†‡
 
ASP
3.5
†¶
 
GLU
4.2
†§
 
HIS
6.6
†€
 
NT
7.7
†¥
 
CYS
6.8
†*
 
TYR
10.3
†•
 
LYS
10.5
†£
 
ARG
12.3
†¤
 
†  Data from Table I.
‡  The reported value for 22 c-terminal carboxylic acids is 3.3 ± 0.8.
¶  The reported value for 139 aspartic acid residues is 3.5 ± 1.2.
§  The reported value for 153 glutamic acid residues is 4.2 ± 0.9.
€  The reported value for 131 histidine residues is 6.6 ± 1.0.
¥  The reported value for 16 n-terminal amino groups is 7.7 ± 0.5.
*  The reported value for 25 cysteine residues is 6.8 ± 2.7.
•  The reported value for 20 tyrosine residues is 10.3 ± 1.2.
£  The reported value for 35 lysine residues is 10.5 ± 1.1.
¤  Due to the high pK value of the guanidino group of arginine, no measured values are available, and no value is reported. The authors used the value of 12.3 in a later review paper (2). This value is the pK value of the guanidino group in the free amino acid arginine from Cohen & Edsall (1943) corrected for the influence of the negative charge on the carboxylic acid (3).
References
(1)  Grimsley GR, Scholtz JM & Pace CN (2009) A summary of the measured pK values of the ionizable groups in folded proteins. Protein Sci 18:247-51.
(2)  Pace CN, Grimsley GR & Scholtz JM (2009) Protein ionizable groups: pK values and their contribution to protein stability and solubility. J Biol Chem 284:13285-9.
(3)  Cohen EJ, Edsall JT (1943) Proteins, Amino Acids and Peptides, Reinhold, New York