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:
aa
)c
)caab
)na
)pKa1
, pKa2
, and isoelectricPointPH
(short name pI
), see Dissociation constantsp
)id
)ss
)srn
)nsrn
)ter
)t
)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 |
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 acidsnode.type atom in residue.aminoAcid
(short version: n.t a in r.aa
): matches atoms in amino acid residuesThe 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 chargeresidue.charge neutral
(short version: r.c neutral
): matches all amino acid residues with neutral side chain chargeresidue.charge positive
(short version: r.c positive
): matches all amino acid residues with positive side chain chargeThe 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 backbonesThe 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 acidsnode.type atom in residue.nucleicAcid
(short version: n.t a in r.na
): matches atoms in nucleic acid residuesThe 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 2residue.pKa2 < 9.5
(short version: r.pKa2 < 9.5
): matches amino acid residues with pKa2 values less than 9.5residue.isoelectricPointPH < 6.0
(short version: r.pI < 6.0
): matches amino acid residues with pI values less than 6The 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 chainresidue.polarity basicPolar
(short version: r.p basic
): matches all amino acid residues with a basic side chainresidue.polarity nonpolar
(short version: r.p nonpolar
): matches all amino acid residues with a nonpolar side chainresidue.polarity polar
(short version: r.p polar
): matches all amino acid residues with a polar side chainresidue.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 chainThe 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 42residue.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 10The residue.secondaryStructure
attribute (short name r.ss
) matches residues with specific secondary structures.
Possible values:
alpha
(short name a
) - alpha helixbeta
(short name b
) - beta strandunstructured
(short name u
) - unstructured region (loop)helix
(short name h
) (same matches as alpha
) - alpha helixstrand
(short name s
) (same matches as beta
) - beta strandloop
(short name l
) (same matches as unstructured
) - unstructured region (loop)Examples:
residue.secondaryStructure helix
(short version: r.ss h
): matches all residues in alpha helicesresidue.secondaryStructure beta or residue.secondaryStructure unstructured
(short version: r.ss b or r.ss u
): matches all residues in beta sheets and in loopsThe 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 namesThe 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 namesThe 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 residuesThe 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 alaninesresidue.type HIS
(short version: r.t HIS
): matches all histidinesresidue.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