pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Class Phenylalanine

java.lang.Object
  pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
      pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine

All Implemented Interfaces:

AminoacidProperties

public class Phenylalanine
extends Aminoacid
implements AminoacidProperties

A phenylalanine molecule.

See Also:

Aminoacid, AminoacidProperties

Field Summary

private Atom	Cb
private Atom	Cd1
private Atom	Cd2
private Atom	Ce1
private Atom	Ce2
private Atom	Cg
private Atom	Cz

Fields inherited from class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

absdeviation, avgdihedralangle, C, Ca, deviation, lnradiusofcurvature, N, O, pdbindex, phi, psi

Constructor Summary

Phenylalanine(java.lang.String residuenum, java.util.Map AtomCoords)
Creates a new instance of the Methionine aminoacid.

Method Summary

java.lang.String	getAbbrev()
java.util.List	getAtoms() return all atoms in concrete aminoacid molecule
java.util.List	getBonds() return all COVALENT non-SS bonds in concrete aminoacid molecule
float[]	getCoordsOfCbeta()
float[]	getCoordsOfCdelta1()
float[]	getCoordsOfCdelta2()
float[]	getCoordsOfCepsilon()
float[]	getCoordsOfCepsilon1()
float[]	getCoordsOfCepsilon2()
float[]	getCoordsOfCgamma()
float	getHydropathy()
float	getMass()
byte	getNumOfNonHAtoms()
float	getPI()
char	getSymbol()
boolean	isAcidic()
boolean	isAliphatic()
boolean	isAromatic()
boolean	isBasic()
boolean	isBuried()
boolean	isCyclic()
boolean	isHydrophobic()

Methods inherited from class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid

getAbsDeviation, getAvgDihedralAngle, getBackboneAtoms, getBackboneAtomsWithoutOcarbonyl, getBackboneBonds, getCcarbonyl, getCoordsOfCalpha, getCoordsOfCcarbonyl, getCoordsOfNamid, getCoordsOfOcarbonyl, getDeviation, getLnRadiusOfCurvature, getNamid, getPhiAngle, getPsiAngle, getResiduePdbIndex, setAbsDeviation, setAvgDihedralAngle, setDeviation, setLnRadiusOfCurvature, setPhiAngle, setPsiAngle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

Cb

private Atom Cb

Cg

private Atom Cg

Cd1

private Atom Cd1

Cd2

private Atom Cd2

Ce1

private Atom Ce1

Ce2

private Atom Ce2

Cz

private Atom Cz

Constructor Detail

Phenylalanine

public Phenylalanine(java.lang.String residuenum,
                     java.util.Map AtomCoords)

Creates a new instance of the Methionine aminoacid.

Parameters:

residuenum - sequential residue number - due to the PdbFile index

AtomCoords - a HashMap with atoms' coordinates

Method Detail

getAtoms

public java.util.List getAtoms()

Description copied from interface: AminoacidProperties

return all atoms in concrete aminoacid molecule

Specified by:

getAtoms in interface AminoacidProperties

getBonds

public java.util.List getBonds()

Description copied from interface: AminoacidProperties

return all COVALENT non-SS bonds in concrete aminoacid molecule

Specified by:

getBonds in interface AminoacidProperties

getSymbol

public char getSymbol()

Specified by:

getSymbol in interface AminoacidProperties

Returns:

one-letter conventional symbol

getAbbrev

public java.lang.String getAbbrev()

Specified by:

getAbbrev in interface AminoacidProperties

Specified by:

getAbbrev in class Aminoacid

Returns:

three-letter abbreviation for the kind of aminoacid

getNumOfNonHAtoms

public byte getNumOfNonHAtoms()

Specified by:

getNumOfNonHAtoms in interface AminoacidProperties

Returns:

number of atoms excluding hydrogens

getPI

public float getPI()

Specified by:

getPI in interface AminoacidProperties

Returns:

isoelectric point of the aminoacid

getMass

public float getMass()

Specified by:

getMass in interface AminoacidProperties

Returns:

molecular mass of a single aminoacid molecule

getHydropathy

public float getHydropathy()

Specified by:

getHydropathy in interface AminoacidProperties

Returns:

hydropathy index
hydropathy index - a scale combining hydrophobicity and hyrophilicity of R groups; used to estimate general "polarity" of aminoacid:
when < 0, aacid is rather hydrophobic;
when > 0, aacid is rather polar.
Kyte J, Doolitle RF (1982) A Simple Method For Displaying the hydropahitic character of a protein, J Mol Biol, 157, 105-132

isBuried

public boolean isBuried()

Specified by:

isBuried in interface AminoacidProperties

Returns:

true, if the aminoacid tends to avoid surfacial localization in the peptide

isHydrophobic

public boolean isHydrophobic()

Specified by:

isHydrophobic in interface AminoacidProperties

Returns:

true, if the aminoacid is rather hydrophobic than polar

isAliphatic

public boolean isAliphatic()

Specified by:

isAliphatic in interface AminoacidProperties

Returns:

true, if the amioacid's backbone is purely C- & H-based

isAromatic

public boolean isAromatic()

Specified by:

isAromatic in interface AminoacidProperties

Returns:

true, if the aminoacid comprise the aromatic ring

isCyclic

public boolean isCyclic()

Specified by:

isCyclic in interface AminoacidProperties

Returns:

true, if the aminoacid has a closed ring of atoms

isAcidic

public boolean isAcidic()

Specified by:

isAcidic in interface AminoacidProperties

Returns:

true, if the aminoacid is of rather acidic character

isBasic

public boolean isBasic()

Specified by:

isBasic in interface AminoacidProperties

Returns:

true, if the aminoacid is of rather basic character

getCoordsOfCbeta

public float[] getCoordsOfCbeta()

Returns:

coordinates of C_beta

getCoordsOfCgamma

public float[] getCoordsOfCgamma()

Returns:

coordinates of C_gamma

getCoordsOfCdelta1

public float[] getCoordsOfCdelta1()

Returns:

coordinates of C_delta1

getCoordsOfCdelta2

public float[] getCoordsOfCdelta2()

Returns:

coordinates of C_delta2

getCoordsOfCepsilon1

public float[] getCoordsOfCepsilon1()

Returns:

coordinates of C_epsilon1

getCoordsOfCepsilon2

public float[] getCoordsOfCepsilon2()

Returns:

coordinates of C_epsilon2

getCoordsOfCepsilon

public float[] getCoordsOfCepsilon()

Returns:

coordinates of C_zeta