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Residue attributes#

Residue attributes are defined in the residue attribute space (short names: res, r). Residue attributes may only match residue nodes.

Below are the tables of residue attributes are available in NSL.

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

Attribute name Short name Possible values Examples
completeAminoAcidBackbone caab true, false r.caab
formalCharge fc integers r.fc > 1
r.fc 6:8
numberOfAtoms nat integers r.nat < 1000
r.nat 100:200
numberOfCoarseGrainedAtoms ncga integers r.ncga < 1000
r.ncga 100:200
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 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.

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 backbones.

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: integers.

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

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#

The residue.numberOfAtoms attribute (short name: r.nat) matches residues with specific number of atoms.

Possible values: integers.

Examples:

  • residue.nat > 100 (short version: r.nat > 100): matches residues with the number of atoms more than 100
  • residue.nat 100:200 (short version: r.nat 100:200): matches residues with the number of atoms between 100 and 200

numberOfCoarseGrainedAtoms#

The residue.numberOfCoarseGrainedAtoms attribute (short name: r.ncga) matches residues with specific number of coarse-grained atoms.

Possible values: integers.

Examples:

  • residue.ncga > 100 (short version: r.ncga > 100): matches residues with the number of coarse-grained atoms more than 100
  • residue.ncga 100:200 (short version: r.ncga 100:200): matches residues with the number of coarse-grained atoms between 100 and 200

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

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: integers.

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 structures.

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 names.

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 names.

Possible values: true, false.

Examples:

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

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 types.

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