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 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)