pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Class Cysteine
java.lang.Object
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Cysteine
- All Implemented Interfaces:
- AminoacidProperties
public class Cysteine
- extends Aminoacid
- implements AminoacidProperties
A cysteine 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 |
Cysteine(java.lang.String residuenum,
java.util.Map AtomCoords)
Creates a new instance of the Cysteine 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
Sg
private Atom Sg
Cysteine
public Cysteine(java.lang.String residuenum,
java.util.Map AtomCoords)
- Creates a new instance of the Cysteine 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
getCoordsOfSgamma
public float[] getCoordsOfSgamma()
- Returns:
- coordinates of Sgamma