Representation of selected AAIndex properties. More...

#include <OpenMS/CHEMISTRY/AAIndex.h>

Static Public Member Functions
static DoubleReal	aliphatic (char aa)
	Returns if the residue is aliphatic (1.0 or 0.0).
static DoubleReal	acidic (char aa)
	Returns if the residue is acidic (1.0 or 0.0).
static DoubleReal	basic (char aa)
	Returns if the residue is basic (1.0 or 0.0).
static DoubleReal	polar (char aa)
	Returns if the residue is polar (1.0 or 0.0).
static DoubleReal	getKHAG800101 (char aa)
	The Kerr-constant increments (Khanarian-Moore, 1980).
static DoubleReal	getVASM830103 (char aa)
	Relative population of conformational state E (Vasquez et al., 1983).
static DoubleReal	getNADH010106 (char aa)
	Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001).
static DoubleReal	getNADH010107 (char aa)
	Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001).
static DoubleReal	getWILM950102 (char aa)
	Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2O (Wilce et al. 1995).
static DoubleReal	getROBB760107 (char aa)
	Information measure for extended without H-bond (Robson-Suzuki, 1976).
static DoubleReal	getOOBM850104 (char aa)
	Optimized average non-bonded energy per atom (Oobatake et al., 1985).
static DoubleReal	getFAUJ880111 (char aa)
	Positive charge (Fauchere et al., 1988).
static DoubleReal	getFINA770101 (char aa)
	Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977).
static DoubleReal	getARGP820102 (char aa)
	Signal sequence helical potential (Argos et al., 1982).
static DoubleReal	calculateGB (const AASequence &seq, DoubleReal T=500.0)
	Calculates an estimated gas-phase basicity for an amino acid sequence at a given temperature.
Static Protected Member Functions
static DoubleReal	GBsidechain_ (char aa)
	Calculates part of the gas-phase basicity.
static DoubleReal	GBleft_ (char aa)
	Calculates part of the gas-phase basicity.
static DoubleReal	GBdeltaright_ (char aa)
	Calculates part of the gas-phase basicity.
Private Member Functions
	AAIndex ()
	Constructor not implemented => private.

Detailed Description

Representation of selected AAIndex properties.

The literature that describe the indices can be found with:
Kawashima, S., Ogata, H., and Kanehisa, M. (1999).
AAindex: Amino Acid Index Database,
Nucleic Acids Res, 27(1), 368–369.

The provided values are:

GB500 Estimated gas-phase basicity at 500 K,
VASM830103 Relative population of conformational state E,
NADH010106 Hydropathy scale (36% accessibility),
FAUJ880111 Positive charge,
WILM950102 Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2 O,

OOBM850104 Optimized average non-bonded energy per atom,

KHAG800101 The Kerr-constant increments,
NADH010107 Hydropathy scale (50% accessibility),
ROBB760107 Information measure for extended without H-bond,
FINA770101 Helix-coil equilibrium constant,
ARGP820102 Signal sequence helical potential.

Upper-case one-letter-code can be used to access the properties of a single amino acid.

Constructor & Destructor Documentation

AAIndex ( ) [private]

Constructor not implemented => private.

Member Function Documentation

static DoubleReal acidic ( char aa ) [inline, static]

Returns if the residue is acidic (1.0 or 0.0).

static DoubleReal aliphatic ( char aa ) [inline, static]

Returns if the residue is aliphatic (1.0 or 0.0).

static DoubleReal basic ( char aa ) [inline, static]

Returns if the residue is basic (1.0 or 0.0).

static DoubleReal calculateGB	(	const AASequence &	seq,
		DoubleReal	T = `500.0`
	)			`[inline, static]`

Calculates an estimated gas-phase basicity for an amino acid sequence at a given temperature.

Energy level E at each protonation site i is -GB(i) fractional proton population of a microstate k is
P_k = exp (- E_k/(RT)) / ( sum_i exp (- E_i/(RT)))
The apparent proton association constant K_app: K_app = sum_i GB(i)/(RT)
Then the apparent GB is GB_app^ion = R * T * ln(K_app)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

References OpenMS::Constants::GAS_CONSTANT, Residue::getOneLetterCode(), OpenMS::Constants::R, and AASequence::size().

static DoubleReal GBdeltaright_ ( char aa ) [inline, static, protected]

Calculates part of the gas-phase basicity.

For a detailed description see calculateGB(const AASequence&, DoubleReal) .

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal GBleft_ ( char aa ) [inline, static, protected]

Calculates part of the gas-phase basicity.

For a detailed description see calculateGB(const AASequence&, DoubleReal) .

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal GBsidechain_ ( char aa ) [inline, static, protected]

Calculates part of the gas-phase basicity.

For a detailed description see calculateGB(const AASequence&, DoubleReal) .

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getARGP820102 ( char aa ) [inline, static]

Signal sequence helical potential (Argos et al., 1982).

LIT:0901079b PMID:7151796
Argos, P., Rao, J.K.M. and Hargrave, P.A.
Structural prediction of membrane-bound proteins
Eur. J. Biochem. 128, 565-575 (1982)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getFAUJ880111 ( char aa ) [inline, static]

Positive charge (Fauchere et al., 1988).

LIT:1414114 PMID:3209351
Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
Amino acid side chain parameters for correlation studies in biology and pharmacology
Int. J. Peptide Protein Res. 32, 269-278 (1988)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getFINA770101 ( char aa ) [inline, static]

Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977).

LIT:2004052b PMID:843599
Finkelstein, A.V. and Ptitsyn, O.B.
Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments
Biopolymers 16, 497-524 (1977) (Pro 0.096)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getKHAG800101 ( char aa ) [inline, static]

The Kerr-constant increments (Khanarian-Moore, 1980).

LIT:0611050b
Khanarian, G. and Moore, W.J.
The Kerr effect of amino acids in water
Aust. J. Chem. 33, 1727-1741 (1980) (Cys Lys Tyr !)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getNADH010106 ( char aa ) [inline, static]

Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001).

PMID:11170200
Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
Prediction of protein surface accessibility with information theory
Proteins. 42, 452-459 (2001)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getNADH010107 ( char aa ) [inline, static]

Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001).

PMID:11170200
Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
Prediction of protein surface accessibility with information theory
Proteins. 42, 452-459 (2001)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getOOBM850104 ( char aa ) [inline, static]

Optimized average non-bonded energy per atom (Oobatake et al., 1985).

LIT:1207075b
Oobatake, M., Kubota, Y. and Ooi, T.
Optimization of amino acid parameters for correspondence of sequence to tertiary structures of proteuins
Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getROBB760107 ( char aa ) [inline, static]

Information measure for extended without H-bond (Robson-Suzuki, 1976).

PMID:1003471
Robson, B. and Suzuki, E.
Conformational properties of amino acid residues in globular proteins
J. Mol. Biol. 107, 327-356 (1976)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getVASM830103 ( char aa ) [inline, static]

Relative population of conformational state E (Vasquez et al., 1983).

LIT:0908110
Vasquez, M., Nemethy, G. and Scheraga, H.A.
Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue alpha-aminobutyric acid
Macromolecules 16, 1043-1049 (1983) (Pro !)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal getWILM950102 ( char aa ) [inline, static]

Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2O (Wilce et al. 1995).

Wilce, M.C., Aguilar, M.I. and Hearn, M.T.
Physicochemical basis of amino acid hydrophobicity scales: evaluation of four new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of peptides
Anal Chem. 67, 1210-1219 (1995)

Exceptions:

InvalidValue

is thrown if an undefined one-letter-code is used

static DoubleReal polar ( char aa ) [inline, static]

Returns if the residue is polar (1.0 or 0.0).

AAIndex Class Reference [Chemistry]

Static Public Member Functions

Static Protected Member Functions

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

AAIndex Class Reference
[Chemistry]