pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Class Arginine
java.lang.Object
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Arginine
- All Implemented Interfaces:
- AminoacidProperties
public class Arginine
- extends Aminoacid
- implements AminoacidProperties
An arginine molecule.
- See Also:
Aminoacid
,
AminoacidProperties
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 |
Arginine(java.lang.String residuenum,
java.util.Map AtomCoords)
Creates a new instance of the Histidine aminoacid. |
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 |
Cb
private Atom Cb
Cg
private Atom Cg
Cd
private Atom Cd
Ne
private Atom Ne
Cz
private Atom Cz
Nh1
private Atom Nh1
Nh2
private Atom Nh2
Arginine
public Arginine(java.lang.String residuenum,
java.util.Map AtomCoords)
- Creates a new instance of the Histidine aminoacid.
- Parameters:
residuenum
- sequential residue number - due to the PdbFile indexAtomCoords
- a HashMap with atoms' coordinates
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 Cbeta
getCoordsOfCgamma
public float[] getCoordsOfCgamma()
- Returns:
- coordinates of Cgamma
getCoordsOfCdelta
public float[] getCoordsOfCdelta()
- Returns:
- coordinates of Cdelta
getCoordsOfNepsilon
public float[] getCoordsOfNepsilon()
- Returns:
- coordinates of Nepsilon
getCoordsOfCzeta
public float[] getCoordsOfCzeta()
- Returns:
- coordinates of Czeta
getCoordsOfNeta1
public float[] getCoordsOfNeta1()
- Returns:
- coordinates of Neta1
getCoordsOfNeta2
public float[] getCoordsOfNeta2()
- Returns:
- coordinates of Neta2