NSL examples#
Below you can see a table of problem-oriented selection tasks with the corresponding NSL expressions.
| Task | NSL expression |
|---|---|
| Receptor residues within 6 Å of any ligand, excluding Gly/Ala (mutagenesis focus) | ((n.t r and not (r.t GLY,ALA)) in n.c rec) w 6A of n.c lig |
| Backbone nitrogen atoms contacting ligands within 3 Å | (a.s N in n.t bb) w 3A of n.c lig |
| Ligand heavy atoms (non-hydrogen) for contact analysis | (n.t a in n.c lig) and not a.s H |
| Water within 4 Å of any ligand (displaceable waters) | n.c wat w 4A of n.c lig |
| Binding-pocket atoms: atoms in residues within 5 Å of a ligand | n.t a in (n.t r w 5A of n.c lig) |
| Water oxygens bridging receptor and ligand (=3 Å to both) | (a.s O in n.c wat) and (n.t a w 3A of n.c rec) and (n.t a w 3A of n.c lig) |
| Positively or negatively charged residues within 8 Å of ligand | (r.c positive or r.c negative) and (n.t r w 8A of n.c lig) |
| Receptor atoms within 5 Å of ligand but >3 Å from any water oxygen | (n.t a in n.c rec) and (n.t a w 5A of n.c lig) and (n.t a b 3A of (a.s O in n.c wat)) |
| Aromatic residues near ligand (p-stack candidates) within 5 Å | (r.t PHE,TYR,TRP,HIS) and (n.t r w 5A of n.c lig) |
| Potential salt-bridge partners: positive residues within 3 Å of negative residues | r.c positive w 3A of r.c negative |
| Polar heavy atoms (O/N) in receptor within 3 Å of ligand | (a.s O,N in n.c rec) w 3A of n.c lig |
| Atoms in protein chain "A" within 5 Å of protein chain "B" (protein-protein interface), non-H | (((n.t a in c.n "A") in n.c rec) and not a.s H) w 5A of (((n.t a in c.n "B") in n.c rec) and not a.s H) |
| Backbone atoms not contacting ligand (>6 Å away) | (n.t a in n.t bb) b 6A of n.c lig |
| Residues coordinating metals: residues within 2.5 Å of metal ions | n.t r w 2.5A of (a.transitionMetal or a.alkaliMetal) |
| Glycine alpha carbons within 5 Å of ligands | "CA" in r.t GLY w 5A of n.c lig |
| Helical residues contacting ligand (=5 Å) | r.ss a w 5A of n.c lig |
| Chain "B" residues contacting glycans (=5 Å) | (n.t r in c.n "B") w 5A of n.c gly |
| Negative receptor residues close to positive receptor residues (=4 Å) | (r.c negative in n.c rec) w 4A of (r.c positive in n.c rec) |
| Ligand atoms within 3 Å of catalytic triad residues HIS, ASP, SER | (n.t a in n.c lig) w 3A of ("HIS *" or "ASP *" or "SER *") |
| Pocket atoms defined by residues 30-50 in chain "A" | n.t a in (r.id 30:50 in c.n "A") |
| Residues within 5 Å of ligand with pI < 6 (acidic environment) | (n.t r w 5A of n.c lig) and (r.pI < 6.0) |
| Atoms in ligand within 2 Å of receptor atoms (tight contacts) | (n.t a in n.c lig) w 2A of n.c rec |
| Side chains within 6 Å of ligand, excluding Gly/Ala side chains | (n.t sc w 6A of n.c lig) and not (n.t sc in (r.t GLY or r.t ALA)) |
| Receptor atoms with occupancy > 0.9 near ligand (=4 Å) | ((n.t a in n.c rec) and (a.oc > 0.9)) w 4A of n.c lig |
| Residues in receptor with =4 nitrogens within 6 Å of ligand | ((n.t r in n.c rec) and (r.nN 4)) w 6A of n.c lig |
| Ligand halogen atoms (F/Cl/Br) contacting receptor (=3 Å) | (a.s F,Cl,Br in n.c lig) w 3A of n.c rec |
| Disulfide sulfur atoms (S-S) within 5 Å of ligand | ((a.s S in r.t CYS) l (a.s S in r.t CYS)) w 5A of n.c lig |
| Backbone atoms in helices that also contact ligand (=4 Å) | (n.t a in (n.t bb in r.ss a)) w 4A of n.c lig |
| Receptor residues with at least one sulfur atom within 5 Å of ligand | ((n.t r in n.c rec) and (n.t r having a.s S)) w 5A of n.c lig |
| sp2 atoms within 3 Å of ligand | a.hy sp2 w 3A of n.c lig |
| Acidic residues near metal ions (=3 Å) | r.p acidic w 3A of (a.transitionMetal or a.alkaliMetal) |
| Atoms with x >= 2y within 4 Å of ligand (geometry filter) | (a.x >= 2*a.y) and (n.t a w 4A of n.c lig) |
| Residues 50-80 in chain "B" contacting ligand (=4 Å) | (r.id 50:80 in c.n "B") w 4A of n.c lig |
| Binding-site atoms in receptor with vdw radius 1.4-1.8 Å | (a.vdwr 1.4A:1.8A in n.c rec) w 5A of n.c lig |
| Non-receptor residues (small peptides/ligands) =3 Å from ions | (n.t r out of n.c rec) w 3A of n.c ion |
| Glycan atoms contacting receptor (=4 Å) | (n.t a in n.c gly) w 4A of n.c rec |
| Aromatic residues near ligand (=5 Å) but >3 Å from any water | (r.t PHE,TYR,TRP,HIS w 5A of n.c lig) and (n.t r b 3A of n.c wat) |
| Positive residues within 5 Å of acidic residues (protein interior networks) | r.c positive w 5A of r.p acidic |
| Atoms with alternate locations A or B near ligand (=3 Å) | a.alt A,B w 3A of n.c lig |
| Receptor atoms with low occupancy (< 0.3) near ligand (=4 Å) | ((n.t a in n.c rec) and (a.oc < 0.3)) w 4A of n.c lig |
| Side chains in chain "A" within 5 Å of glycans | (n.t sc in c.n "A") w 5A of n.c gly |
| Ligand-adjacent residues not contacting metals (>3 Å from metals) | (n.t r w 5A of n.c lig) and (n.t r b 3A of (a.transitionMetal or a.alkaliMetal)) |
| Nitrogen sp2 atoms within 3 Å of ligand | (a.s N and a.hy sp2) w 3A of n.c lig |
| Atoms from residues 25,30,35 near ligand (=4 Å) | (n.t a in r.id 25,30,35) w 4A of n.c lig |
| Non-hydrogen receptor atoms in chain "A" contacting ligand (=4 Å) | (n.t a in c.n "A") and (n.t a in n.c rec) and not a.s H and (n.t a w 4A of n.c lig) |
| Backbone alpha carbons (CA) in terminal residues near ligand (=5 Å) | "CA" in r.ter w 5A of n.c lig |
| Side chains with sulfur within 3 Å of ligand (Cys/Met contacts) | (n.t sc having a.s S) w 3A of n.c lig |
| Residues in loops contacting ligand (=6 Å) | (r.ss l) w 6A of n.c lig |
| Ligand atoms within 2 Å of receptor O/N polar atoms | (n.t a in n.c lig) w 2A of (a.s O,N in n.c rec) |
| Salt-bridge candidates bridging ligand and receptor: positive receptor residues within 4 Å of ligand and also within 4 Å of negative receptor residues | ((r.c positive in n.c rec) and (n.t r w 4A of n.c lig)) and (n.t r w 4A of (r.c negative in n.c rec)) |
| Steric clashes: ligand heavy atoms within 2.2 Å of receptor heavy atoms | ((n.t a in n.c lig) and not a.s H) w 2.2A of ((n.t a in n.c rec) and not a.s H) |
| Bridging waters between chains "A" and "B": water =3.2 Å from both chains | (n.c wat w 3.2A of c.n "A") and (n.c wat w 3.2A of c.n "B") |
| Side chains with =2 nitrogens inside 4 Å of ligand (chemistry hotspots) | (sc.nN 2) w 4A of n.c lig |
| Binding site aromatics excluding histidine (=5 Å of ligand) | r.t PHE,TYR,TRP w 5A of n.c lig |
| Ligand atoms near positive receptor residues (=3 Å) | (n.t a in n.c lig) w 3A of (r.c positive in n.c rec) |
| High-B receptor atoms near ligand: a.tf > 20 within 6 Å | ((a.tf > 20) in n.c rec) w 6A of n.c lig |
| Alpha carbons of receptor residues contacting ligand (=5 Å) | "CA" in ((n.t r in n.c rec) w 5A of n.c lig) |
| Protein-lipid contact atoms from chain "A" (=4 Å) | (n.t a in c.n "A") w 4A of n.c lip |
| Loop residues near ligand (=5 Å) with pI < 6 | ((r.ss l) and (r.pI < 6.0)) w 5A of n.c lig |
| Halogenated ligand contacts not wetted: Cl/Br/I within 3 Å of receptor and >3 Å from any water oxygen | ((a.s Cl,Br,I in n.c lig) w 3A of n.c rec) and (n.t a b 3A of (a.s O in n.c wat)) |
| Side chains containing sulfur within 3.5 Å of ligand | ((n.t sc having a.s S) w 3.5A of n.c lig) |
| Chain "B" residues with IDs 12-16 contacting glycans (=5 Å) | (r.id 12:16 in c.n "B") w 5A of n.c gly |
| Ligand atoms within 2.5 Å of aromatic residues (p interactions) | (n.t a in n.c lig) w 2.5A of r.t PHE,TYR,TRP,HIS |
| Polar receptor hydrogens within 2.2 Å of ligand | (a.hp in n.c rec) w 2.2A of n.c lig |
| Alternate-location A receptor atoms contacting ligand (=3 Å) | (a.alt A in n.c rec) w 3A of n.c lig |
| Receptor residues having an atom with exactly two bonded oxygens within 4 Å of ligand | ((n.t r in n.c rec) having a.nbo 2) and (n.t r w 4A of n.c lig) |
| Positive receptor residues near DNA residues (=6 Å) | (r.c positive in n.c rec) w 6A of r.dna |
| sp3 carbon atoms of ligand within 3 Å of receptor | ((a.s C and a.hy sp3) in n.c lig) w 3A of n.c rec |
| Pocket rim residues: within 12 Å but beyond 7 Å from ligand | (n.t r w 12A of n.c lig) and (n.t r b 7A of n.c lig) |
| Backbone atoms contacting ligand (=4 Å) | a.aabb w 4A of n.c lig |
| Binding-site residues that are not glycosylation (=5 Å of ligand, excluding glycans) | ((n.t r in n.c rec) w 5A of n.c lig) and (n.t r out of n.c gly) |
| Non-water atoms within 5 Å of ligand | ((n.t a out of n.c wat) w 5A of n.c lig) and (n.t a out of n.c lig) |
| Ligand atoms near backbone nitrogens (=3 Å) | (n.t a in n.c lig) w 3A of (a.s N in n.t bb) |
| Aromatic-bearing receptor residues near ligand (=4 Å) | ((n.t r having a.ar) in n.c rec) w 4A of n.c lig |
| Protein-protein interface residues between chains "A" and "B" (=4 Å) | (n.t r in n.c rec) and (((n.t r in c.n "A") w 4A of (n.t r in c.n "B")) or ((n.t r in c.n "B") w 4A of (n.t r in c.n "A"))) |
| Potential metal-binding triads: residues with at least one N within 2.5 Å of transition metals | (n.t r having a.s N) and (n.t r w 2.5A of a.transitionMetal) |
| Ligand atoms near nucleic-acid backbones (=4 Å) | (n.t a in n.c lig) w 4A of a.nabb |
| Hydrophobic shell: receptor residues with nonpolar side chains =5 Å from ligand | (r.p nonpolar in n.c rec) w 5A of n.c lig |
| Removable waters: water =2.2 Å from ligand heavy atoms | n.c wat w 2.2A of ((n.t a in n.c lig) and not a.s H) |
| High-electronegativity receptor atoms (>3.0) within 3 Å of ligand | (a.en > 3 in n.c rec) w 3A of n.c lig |
| Positive receptor residues near ligand phosphate atoms (=4 Å) | (r.c positive in n.c rec) w 4A of (a.s P,O in n.c lig) |
| Residues lining a named pocket group "Pocket" (=4 Å) | n.t r w 4A of (n.t a in "Pocket") |
| Glycan atoms contacting receptor (=3 Å) but not ligand (>3 Å) | ((n.t a in n.c gly) w 3A of n.c rec) and (n.t a b 3A of n.c lig) |
| Chain "A" receptor atoms near ligand (=4 Å) with occupancy < 0.5 | ((a.oc < 0.5 in n.c rec) in c.n "A") w 4A of n.c lig |
| Chain "B" amino-acid residues near ligand (=5 Å) excluding cysteines | ((r.aa and not r.t CYS) in c.n "B") w 5A of n.c lig |
| Atoms with exactly three bonded hydrogens within 2.5 Å of ligand | a.nbh 3 w 2.5A of n.c lig |
| Receptor residues having a polar hydrogen within 2 Å of ligand | (n.t r in n.c rec) having (a.hp w 2A of n.c lig) |
| Ligand atoms within 3 Å of backbone carbonyl oxygens | (n.t a in n.c lig) w 3A of (a.aabb and a.s O) |
| Non-standard residues near ligand (=6 Å) | r.nsrn w 6A of n.c lig |
| Nucleic-acid atoms contacting ligand (=4 Å) | (n.t a in r.na) w 4A of n.c lig |
| Ion atoms contacting receptor (=3 Å) | (n.t a in n.c ion) w 3A of n.c rec |
| Positive receptor residues near ligand (=4 Å) but far from water (>5 Å) | ((r.c positive in n.c rec) w 4A of n.c lig) and (n.t r b 5A of n.c wat) |
| Alpha carbons from residues 1-10 and 40-50 within 6 Å of ligand | ("CA" in r.id 1:10,40:50) w 6A of n.c lig |
| Receptor atoms with vdw radius 1.6-1.9 Å within 3.5 Å of ligand | ((a.vdwr 1.6A:1.9A) in n.c rec) w 3.5A of n.c lig |
| Beta-strand residues near ligand (=5 Å) with at least one oxygen | (r.ss b having a.s O) w 5A of n.c lig |
| Ligand atoms not contacting the receptor (>6 Å from any receptor atom) | (n.t a in n.c lig) b 6A of n.c rec |
| Receptor atoms near ligand (=4 Å) excluding chain "C" | (n.t a in n.c rec w 4A of n.c lig) and (n.t a out of c.n "C") |
| Non-terminal, nonpolar receptor residues within 4 Å of ligand (stabilizing shell) | ((r.p nonpolar and not r.ter) in n.c rec) w 4A of n.c lig |
| Chain "A"-"B" interface atoms that are sp2 hybridized (=4 Å across chains) | (((n.t a in c.n "A") w 4A of c.n "B") or ((n.t a in c.n "B") w 4A of c.n "A")) and (a.hy sp2) |