| OpenMS 2.5.0

Static Public Member Functions | Static Protected Member Functions | Private Member Functions | List of all members
AAIndex Class Reference
Chemistry

Representation of selected AAIndex properties. More...

`#include <OpenMS/CHEMISTRY/AAIndex.h>`

## Static Public Member Functions

static double | aliphatic (char aa)
| Returns if the residue is aliphatic (1.0 or 0.0) More...
static double | acidic (char aa)
| Returns if the residue is acidic (1.0 or 0.0) More...
static double | basic (char aa)
| Returns if the residue is basic (1.0 or 0.0) More...
static double | polar (char aa)
| Returns if the residue is polar (1.0 or 0.0) More...
static double | getKHAG800101 (char aa)
| The Kerr-constant increments (Khanarian-Moore, 1980) More...
static double | getVASM830103 (char aa)
| Relative population of conformational state E (Vasquez et al., 1983) More...
static double | getNADH010106 (char aa)
| Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001) More...
static double | getNADH010107 (char aa)
| Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001) More...
static double | getWILM950102 (char aa)
| Hydrophobicity coefficient in RP-HPLC, C8 with 0.1TFA/MeCN/H2O (Wilce et al. 1995) More...
static double | getROBB760107 (char aa)
| Information measure for extended without H-bond (Robson-Suzuki, 1976) More...
static double | getOOBM850104 (char aa)
| Optimized average non-bonded energy per atom (Oobatake et al., 1985) More...
static double | getFAUJ880111 (char aa)
| Positive charge (Fauchere et al., 1988) More...
static double | getFINA770101 (char aa)
| Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977) More...
static double | getARGP820102 (char aa)
| Signal sequence helical potential (Argos et al., 1982) More...
static double | calculateGB (const AASequence &seq, double T=500.0)
| Calculates an estimated gas-phase basicity for an amino acid sequence at a given temperature. More...

## Static Protected Member Functions

static double | GBsidechain_ (char aa)
| Calculates part of the gas-phase basicity. More...
static double | GBleft_ (char aa)
| Calculates part of the gas-phase basicity. More...
static double | GBdeltaright_ (char aa)
| Calculates part of the gas-phase basicity. More...

## Private Member Functions

| AAIndex ()
| Constructor not implemented => private. More...

## 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()

AAIndex | ( |  | ) |

private

Constructor not implemented => private.

## Member Function Documentation

## ◆ acidic()

static double acidic | ( | char | aa | ) |

inline static

Returns if the residue is acidic (1.0 or 0.0)

## ◆ aliphatic()

static double aliphatic | ( | char | aa | ) |

inline static

Returns if the residue is aliphatic (1.0 or 0.0)

## ◆ basic()

static double basic | ( | char | aa | ) |

inline static

Returns if the residue is basic (1.0 or 0.0)

## ◆ calculateGB()

static double calculateGB | ( | const AASequence & | seq,
|  | double | 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().

## ◆ GBdeltaright_()

static double GBdeltaright_ | ( | char | aa | ) |

inline static protected

Calculates part of the gas-phase basicity.

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

Exceptions

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

## ◆ GBleft_()

static double GBleft_ | ( | char | aa | ) |

inline static protected

Calculates part of the gas-phase basicity.

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

Exceptions

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

## ◆ GBsidechain_()

static double GBsidechain_ | ( | char | aa | ) |

inline static protected

Calculates part of the gas-phase basicity.

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

Exceptions

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

## ◆ getARGP820102()

static double 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

## ◆ getFAUJ880111()

static double 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

## ◆ getFINA770101()

static double 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

## ◆ getKHAG800101()

static double 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

## ◆ getNADH010106()

static double 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

## ◆ getNADH010107()

static double 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

## ◆ getOOBM850104()

static double 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 proteins
Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)

Exceptions

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

## ◆ getROBB760107()

static double 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

## ◆ getVASM830103()

static double 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

## ◆ getWILM950102()

static double 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

## ◆ polar()

static double polar | ( | char | aa | ) |

inline static

Returns if the residue is polar (1.0 or 0.0)