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Residue attributes#

Residue attributes are defined in the residue attribute space (short name r). Residue attributes may only match residue nodes.

The following residue attributes are available in NSL:

Attribute name Short name Possible values Examples
aminoAcid aa r.aa
charge c negative,
neutral,
positive
r.c neutral
completeAminoAcidBackbone caab r.caab
nucleicAcid na r.na
pKa1 pKa1 r.pKa1 < 2.0
pKa2 pKa2 r.pKa2 < 9.0
isoelectricPointPH pI r.pI < 6.0
polarity p acidicPolar,
basicPolar,
nonpolar,
polar
r.p polar
residueSequenceNumber id r.id == 42
secondaryStructure ss alpha (helix),
beta (strand),
unstructured (loop)
r.ss alpha
standardResidueName srn r.srn
nonStandardResidueName nsrn r.nsrn
terminal ter r.ter
type t See residue type r.t ALA

aminoAcid#

The residue.aminoAcid attribute (short name r.aa) matches residues that are amino acids.

Possible values: boolean.

Examples:

  • residue.aminoAcid (short version: r.aa): matches all residues that are amino acids
  • 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
  • neutral
  • positive

Examples:

  • residue.charge negative (short version: r.c negative): matches all amino acid residues with negative side chain charge
  • residue.charge neutral (short version: r.c neutral): matches all amino acid residues with neutral side chain charge
  • residue.charge positive (short version: r.c positive): matches all amino acid residues with positive side chain charge

completeAminoAcidBackbone#

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

Possible values: boolean.

Examples:

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

nucleicAcid#

The residue.nucleicAcid attribute (short name na) matches residues that are nucleic acids.

Possible values: boolean.

Examples:

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

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

polarity#

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

Possible values:

  • acidicPolar (also acidic)
  • basicPolar (also basic)
  • nonpolar
  • polar

Examples:

  • residue.polarity acidicPolar (short version: r.p acidic): matches all amino acid residues with an acidic side chain
  • residue.polarity basicPolar (short version: r.p basic): matches all amino acid residues with a basic side chain
  • residue.polarity nonpolar (short version: r.p nonpolar): matches all amino acid residues with a nonpolar side chain
  • residue.polarity polar (short version: r.p polar): matches all amino acid residues with a polar side chain
  • residue.polarity acidicPolar or residue.polarity basicPolar (short version: r.p acidic or r.p basic): matches all 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 and residue.residueSequenceNumber < 10 (short version: r.id > 1 and r.id < 10): matches all residues with residue sequence number between 1 and 10

secondaryStructure#

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

Possible values:

  • alpha (short name a) - alpha helix
  • beta (short name b) - beta strand
  • unstructured (short name u) - unstructured region (loop)
  • helix (short name h) (same matches as alpha) - alpha helix
  • strand (short name s) (same matches as beta) - beta strand
  • loop (short name l) (same matches as unstructured) - unstructured region (loop)

Examples:

  • residue.secondaryStructure helix (short version: r.ss h): matches all residues in alpha helices
  • residue.secondaryStructure beta or residue.secondaryStructure unstructured (short version: r.ss b or r.ss u): matches all residues in beta sheets and in loops

standardResidueName#

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

Possible values: boolean.

Examples:

  • residue.standardResidueName (short version: r.srn): matches all 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: boolean.

Examples:

  • residue.nonStandardResidueName (short version: r.nsrn): matches all 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: boolean.

Examples:

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