J. C. Dobrowolsk et al.
92
settings. For example, in partitioning methods, it is the choice of the phase to be
used, i.e. liquid, vapour, or micellar, as well as the components of the immiscible
solvent system (e.g. 1-octanol/water; cyclohexanol/water etc.) that are the most
important.
Even though hydrophobicity parameters are assigned to individual amino acids,
they are usually derived from peptide properties, and the hydrophobicity scales
are first and foremost used in a range of fields related to proteins. the standard
and most common application of such scales is in identifying surface-exposed
regions as well as transmembrane regions and for the prediction of protein secondary structure [50]. Another important application of these scales is in studying the
structural homology between proteins and as an aid in sequence alignment [51].
Finally, some were developed for peptide QSAR (Quantitative Structure–Activity Relationship) and QSPR (Quantitative Structure-Property-Relationships) purposes [52].
It is certain that hydrophobicity has an important role for single amino acids in
solution; however, the derived scales, although quite useful for the above mentioned
applications, give only a rough insight into the meaning of spectroscopy measurements of individual amino acids in aqueous solution.
Table 5.2 α-Amino acids ordered from hydrophilic to hydrophobic according to different scales
Levitt [42] Parker
et al. [43]
Radzicka &
Wolfenden
[44]
a
Kyte & doolittle [45]
Chothia
[46]
Janin [47] Rose et al.
[48]
moret &
Zebende
[49]
Arg
Asp
Arg
Arg
his
Lys
Lys
Lys
Lys
glu
Asp
Lys
Arg
Arg
glu
Arg
glu
Asn
glu
Asp
Lys
glu
Asp
Asp
Asp
Ser
Asn
glu
gln
gln
gln
glu
Ser
gln
Lys
Asn
Asn
Asp
Asn
Ser
gln
Lys
gln
gln
Asp
Asn
Arg
gln
Asn
gly
his
his
tyr
tyr
Pro
Asn
gly
thr
Ser
Pro
glu
Pro
Ser
Pro
thr
Arg
thr
tyr
Pro
thr
thr
thr
his
Pro
Pro
trp
Ser
his
gly
his
Ala
his
tyr
Ser
thr
Ser
Ala
gly
Cys
Ala
gly
thr
trp
trp
tyr
Ala
met
Cys
Cys
gly
gly
gly
his
trp
Pro
tyr
Ala
Ala
Ala
Ala
trp
Leu
val
val
trp
met
met
met
met
Phe
Ile
met
met
Cys
Leu
Phe
Leu
met
Leu
Ile
Phe
Phe
Phe
Leu
val
tyr
tyr
Phe
val
Leu
Cys
val
Ile
Ile
Phe
Leu
Leu
val
val
Ile
Phe
val
trp
trp
Ile
Ile
Cys
Cys
Cys
a
Isoleucine not included in the analysis
92
settings. For example, in partitioning methods, it is the choice of the phase to be
used, i.e. liquid, vapour, or micellar, as well as the components of the immiscible
solvent system (e.g. 1-octanol/water; cyclohexanol/water etc.) that are the most
important.
Even though hydrophobicity parameters are assigned to individual amino acids,
they are usually derived from peptide properties, and the hydrophobicity scales
are first and foremost used in a range of fields related to proteins. the standard
and most common application of such scales is in identifying surface-exposed
regions as well as transmembrane regions and for the prediction of protein secondary structure [50]. Another important application of these scales is in studying the
structural homology between proteins and as an aid in sequence alignment [51].
Finally, some were developed for peptide QSAR (Quantitative Structure–Activity Relationship) and QSPR (Quantitative Structure-Property-Relationships) purposes [52].
It is certain that hydrophobicity has an important role for single amino acids in
solution; however, the derived scales, although quite useful for the above mentioned
applications, give only a rough insight into the meaning of spectroscopy measurements of individual amino acids in aqueous solution.
Table 5.2 α-Amino acids ordered from hydrophilic to hydrophobic according to different scales
Levitt [42] Parker
et al. [43]
Radzicka &
Wolfenden
[44]
a
Kyte & doolittle [45]
Chothia
[46]
Janin [47] Rose et al.
[48]
moret &
Zebende
[49]
Arg
Asp
Arg
Arg
his
Lys
Lys
Lys
Lys
glu
Asp
Lys
Arg
Arg
glu
Arg
glu
Asn
glu
Asp
Lys
glu
Asp
Asp
Asp
Ser
Asn
glu
gln
gln
gln
glu
Ser
gln
Lys
Asn
Asn
Asp
Asn
Ser
gln
Lys
gln
gln
Asp
Asn
Arg
gln
Asn
gly
his
his
tyr
tyr
Pro
Asn
gly
thr
Ser
Pro
glu
Pro
Ser
Pro
thr
Arg
thr
tyr
Pro
thr
thr
thr
his
Pro
Pro
trp
Ser
his
gly
his
Ala
his
tyr
Ser
thr
Ser
Ala
gly
Cys
Ala
gly
thr
trp
trp
tyr
Ala
met
Cys
Cys
gly
gly
gly
his
trp
Pro
tyr
Ala
Ala
Ala
Ala
trp
Leu
val
val
trp
met
met
met
met
Phe
Ile
met
met
Cys
Leu
Phe
Leu
met
Leu
Ile
Phe
Phe
Phe
Leu
val
tyr
tyr
Phe
val
Leu
Cys
val
Ile
Ile
Phe
Leu
Leu
val
val
Ile
Phe
val
trp
trp
Ile
Ile
Cys
Cys
Cys
a
Isoleucine not included in the analysis