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Residue attributes#

Residue attributes are defined in the residue attribute space (short names: res, r), that matches only residue noder.

Attributes inherited from the node attribute space:

Attribute name Short name Possible values Examples
hasMaterial hm true, false r.hm
not r.hm
hidden h true, false r.h
not r.h
name n strings in quotes r.n "A"
r.n "L*"
ownsMaterial om true, false r.om
selected true, false r.selected
not r.selected
selectionFlag sf true, false r.sf false
r.sf
visibilityFlag vf true, false r.vf false
r.vf
visible v true, false r.v
not r.v

Attributes inherited from the structuralGroup attribute space:

Attribute name Short name Possible values Examples
formalCharge fc integers r.fc > 1
r.fc 6:8
numberOfAtoms nat integers r.nat < 1000
r.nat 100:200
numberOfCarbons nC integers r.nC < 10
r.nC 10:20
numberOfHydrogens nH integers r.nH < 10
r.nH 10:20
numberOfNitrogens nN integers r.nN < 10
r.nN 10:20
numberOfOxygens nO integers r.nO < 10
r.nO 10:20
numberOfSulfurs nS integers r.nS < 10
r.nS 10:20
numberOfCoarseGrainedAtoms ncga integers r.ncga < 1000
r.ncga 100:200
partialCharge pc floats r.pc > 1.5
r.pc 1.5:2.0

The following residue attributes depend on the structure of the residue or the whole system:

Attribute name Short name Possible values Examples
completeAminoAcidBackbone caab true, false r.caab
residueSequenceNumber id integers r.id == 42
r.id 42:50, 60:70
secondaryStructure ss alpha (a, helix, h),
beta (b, strand, s),
unstructured (u, loop, l)		 r.ss alpha
r.ss a, b
standardResidueName srn true, false r.srn
nonStandardResidueName nsrn true, false r.nsrn
terminal ter true, false r.ter
type t See residue type r.t ALA
r.t ALA, LYS, VAL

The following residue attributes depend only on the residue type (i.e. they are equal for residues of the same residue type):

Attribute name Short name Possible values Examples
aminoAcid aa true, false r.aa
nucleicAcid na true, false r.na
hydrophobicity floats r.hydrophobicity < 0
dna true, false r.dna
rna true, false r.rna
charge c negative (neg),
neutral (neu),
positive (pos),
undefined (un)		 r.c neutral
r.c neutral, positive
polarity p acidicPolar (acidic),
basicPolar (basic),
nonpolar,
polar,
undefined (un)		 r.p polar
r.p basic, polar
isoelectricPointPH pI floats r.pI < 6.0
r.pI 5:6
pKa1 pKa1 floats r.pKa1 < 2.0
r.pKa1 1.5:2.5
pKa2 pKa2 floats r.pKa2 < 9.0
r.pKa2 7.5:9.0

aminoAcid#

The residue.aminoAcid attribute (short name: r.aa) matches amino acid residues.

Possible values: true, false.

Examples:

  • node.type atom in residue.aminoAcid (short version: n.t a in r.aa): matches atoms in amino acid residues

charge#

The residue.charge attribute (short name: r.c) matches amino acid residues with specific charge:

Attribute name Short name Meaning
negative neg matches amino acid residues with negative side chain charge
neutral neu matches amino acid residues with neutral side chain charge
positive pos matches amino acid residues with positive side chain charge
undefined un matches residues with undefined side chain charge

Examples:

  • residue.charge negative (short version: r.c neg): matches amino acid residues with negative side chain charge
  • residue.charge neutral, positive (short version: r.c neu, pos): matches amino acid residues with neutral or positive side chain charge

completeAminoAcidBackbone#

The residue.completeAminoAcidBackbone attribute (short name: r.caab) matches residues that have complete amino acid backboner.

Possible values: true, false.

Examples:

  • residue.completeAminoAcidBackbone (short version: r.hcaab): matches residues that have complete amino acid backbones

dna#

The residue.dna attribute (short name: r.dna) matches DNA residues.

Possible values: true, false.

formalCharge#

The residue.formalCharge attribute (short name: r.fc) matches residues with specific total formal charge.

Possible values: integerr.

Examples:

  • residue.fc 1 (short version: r.fc 1): matches residues with formal charge equal to 1
  • residue.fc 6:8 (short version: r.fc 6:8): matches residues with formal charge between 6 and 8

hasMaterial#

Inherited from node.hasMaterial.

hidden#

Inherited from node.hidden.

hydrophobicity#

The residue.hydrophobicity attribute matches amino acid residues with the given hydrophobicity (based on the hydrophobicity scale from Kyte, Doolittle, 1982).

Possible values: floating-point values.

Examples:

  • residue.hydrophobicity -60:-20 (short version: r.hydrophobicity < 0): matches amino acid residues with hydrophobicity in the range from -60 to -20

name#

Inherited from node.name.

nucleicAcid#

The residue.nucleicAcid attribute (short name: r.na) matches nucleic acid residues.

Possible values: true, false.

Examples:

  • node.type atom in residue.nucleicAcid (short version: n.t a in r.na): matches atoms in nucleic acid residues

numberOfAtoms#

Inherited from structuralGroup.numberOfAtoms.

numberOfCarbons#

Inherited from structuralGroup.numberOfCarbons.

numberOfCoarseGrainedAtoms#

Inherited from structuralGroup.numberOfCoarseGrainedAtoms.

numberOfHydrogens#

Inherited from structuralGroup.numberOfHydrogens.

numberOfNitrogens#

Inherited from structuralGroup.numberOfNitrogens.

numberOfOxygens#

Inherited from structuralGroup.numberOfOxygens.

numberOfSulfurs#

Inherited from structuralGroup.numberOfSulfurs.

Dissociation constants#

The residue.pKa1, residue.pKa2, and residue.isoelectricPointPH (short name: r.pI) attributes matches amino acid residues with certain dissociation constants:

  • pKa1 - the negative of the logarithm of the dissociation constant for the carboxyl functional group, -COOH
  • pKa2 - the negative of the logarithm of the dissociation constant for the amino functional group, -NH3
  • pI - the pH at the isoelectric point

Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

Possible values: floating-point values.

Examples:

  • residue.pKa1 < 2.0 (short version: r.pKa1 < 2.0): matches amino acid residues with pKa1 values less than 2
  • residue.pKa2 < 9.5 (short version: r.pKa2 < 9.5): matches amino acid residues with pKa2 values less than 9.5
  • residue.isoelectricPointPH < 6.0 (short version: r.pI < 6.0): matches amino acid residues with pI values less than 6
  • residue.pKa1 1.5:2.0 (short version: r.pKa1 1.5:2.0): matches amino acid residues with pKa1 values between 1.5 and 2

ownsMaterial#

Inherited from node.ownsMaterial.

partialCharge#

Inherited from structuralGroup.partialCharge.

polarity#

The residue.polarity attribute (short name: r.p) matches amino acid residues with specific polarity:

Attribute name Short name Meaning
acidicPolar acidic matches amino acid residues with an acidic side chain
basicPolar basic matches amino acid residues with a basic side chain
nonpolar - matches amino acid residues with a nonpolar side chain
polar - matches amino acid residues with a polar side chain
undefined un matches residues with undefined side chain polarity

Examples:

  • residue.polarity polar (short version: r.p polar): matches amino acid residues with a polar side chain
  • residue.polarity acidicPolar, basicPolar (short version: r.p acidic, basic): matches amino acid residues with an acidic or basic side chain

residueSequenceNumber#

The residue.residueSequenceNumber attribute (short name: r.id) matches residues with specific residue sequence number (structure ID).

Possible values: integerr.

Examples:

  • residue.residueSequenceNumber == 42 (short version: r.id == 42): matches residues with residue sequence number equal to 42
  • residue.residueSequenceNumber 1:10, 20:30 (short version: r.id 1:10, 20:30): matches residues with residue sequence number between 1 and 10 and between 20 and 30

rna#

The residue.rna attribute (short name: r.rna) matches RNA residues.

Possible values: true, false.

secondaryStructure#

The residue.secondaryStructure attribute (short name: r.ss) matches residues with specific secondary structurer:

Attribute name Aliases Meaning
alpha a, helix, h alpha helix
beta b, strand, s beta strand
unstructured u, loop, l unstructured region (loop)

Examples:

  • residue.secondaryStructure helix (short version: r.ss h): matches residues in alpha helices
  • residue.secondaryStructure alpha, beta (short version: r.ss a, b): matches residues in alpha helices and in beta sheets

standardResidueName#

The residue.standardResidueName attribute (short name: r.srn) matches residues that have the standard PDB residue namer.

Possible values: true, false.

Examples:

  • residue.standardResidueName (short version: r.srn): matches residues that have the standard PDB residue names

nonStandardResidueName#

The residue.nonStandardResidueName attribute (short name: r.nsrn) matches residues that do not have the standard PDB residue namer.

Possible values: true, false.

Examples:

  • residue.nonStandardResidueName (short version: r.nsrn): matches residues that do not have the standard PDB residue names

selected#

Inherited from node.selected, but without the short name s.

selectionFlag#

Inherited from node.selectionFlag.

terminal#

The residue.terminal attribute (short name: r.ter) matches residues that are terminal.

Possible values: true, false.

Examples:

  • residue.terminal (short version: r.ter): matches residues that are terminal
  • "CA" in residue.terminal (short version: "CA" in r.ter): matches alpha carbons (by name) in all terminal residues

type#

The residue.type attribute (short name: r.t) matches residues with specific typer.

Possible values:

  • A, C, G, U, I
  • DA, DC, DG, DT, DI
  • ALA, ARG, ASP, ASN, VAL, HIS, GLY, GLU, GLN, ILE, LEU, LYS, MET, PRO, SER, TYR, THR, TRP, PHE, CYS, ASX, GLX, XLE, XAA, SEC, PYL

Examples:

  • residue.type ALA (short version: r.t ALA): matches alanines
  • residue.type HIS (short version: r.t HIS): matches histidines
  • residue.type LYS, PRO (short version: r.t LYS, PRO): matches lysines and prolines
  • "CA" in residue.type VAL (short version: "CA" in r.t VAL): matches alpha carbons (by name) in all valines

visibilityFlag#

Inherited from node.visibilityFlag.

visible#

Inherited from node.visible.