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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 real 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
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 residuer.

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.

Possible values:

  • negative (short name: neg) - matches amino acid residues with negative side chain charge
  • neutral (short name: neu) - matches amino acid residues with neutral side chain charge
  • positive (short name: pos) - matches amino acid residues with positive side chain charge
  • undefined (short name: 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 residuer.

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.

name#

Inherited from node.name.

nucleicAcid#

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

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 valuer.

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.

Possible values:

  • acidicPolar (also acidic) - matches amino acid residues with an acidic side chain
  • basicPolar (also 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 (short name: 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 residuer.

Possible values: true, false.

secondaryStructure#

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

Possible values:

  • alpha (short name: a) or helix (short name: h) - alpha helix
  • beta (short name: b) or strand (short name: s)- beta strand
  • unstructured (short name: u) or loop (short name: 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.