Package org.biojava.nbio.aaproperties

Class AminoAcidProperties

java.lang.Object
org.biojava.nbio.aaproperties.AminoAcidProperties
public class AminoAcidProperties extends Object
This class provides the protein properties at the level of individual amino acids.
Author:
Yana Valasatava

  • Constructor Summary

    Constructors
    Constructor
    Description
    AminoAcidProperties()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    static final int
    getChargeOfAminoAcid(char aa)
    Returns the charge of amino acid.
    static final int
    getPolarityOfAminoAcid(char aa)
    There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
    static final boolean
    isCharged(char aa)
    At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
    static final boolean
    isPolar(char aa)
    There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

  • Method Details

    • isCharged

      public static final boolean isCharged(char aa)
      At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
      Parameters:
      aa - The one-letter amino acid code
      Returns:
      true if amino acid is charged

    • getChargeOfAminoAcid

      public static final int getChargeOfAminoAcid(char aa)
      Returns the charge of amino acid. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains), and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
      Parameters:
      aa - The one-letter amino acid code
      Returns:
      the charge of amino acid (1 if positively charged, -1 if negatively charged, 0 if not charged)

    • isPolar

      public static final boolean isPolar(char aa)
      There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
      Parameters:
      aa - The one-letter amino acid code
      Returns:
      true if amino acid is polar

    • getPolarityOfAminoAcid

      public static final int getPolarityOfAminoAcid(char aa)
      There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
      Parameters:
      aa - The one-letter amino acid code
      Returns:
      the polarity of amino acid (1 if polar, 0 if not polar)