Class AminoAcidProperties


  • public class AminoAcidProperties
    extends java.lang.Object
    This class provides the protein properties at the level of individual amino acids.
    Author:
    Yana Valasatava
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static int getChargeOfAminoAcid​(char aa)
      Returns the charge of amino acid.
      static int getPolarityOfAminoAcid​(char aa)
      There are 10 amino acids: D, E, H, K, R, N, Q, S, T, Y, that are polar.
      static 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 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 Detail

      • AminoAcidProperties

        public AminoAcidProperties()
    • Method Detail

      • 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)