Contacts of the helix formed by residues 4324 - 4350 (chain B) in PDB entry 5NUG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO4324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4199B LEU* 5.2 7.2 - - + -
4318B PRO* 3.9 8.9 - - - +
4323B LEU* 1.3 99.7 - - + +
4325B ASN* 1.3 64.1 + - - +
4326B ASN* 3.3 5.2 - - + +
4327B ALA* 3.5 27.5 + - + +
4567B GLY* 5.3 9.0 - - - -
4578B SER 5.0 0.2 - - - +
4579B ASN* 4.6 12.1 - - - +
4580B ALA 5.6 1.1 - - - +
4638B ARG* 3.5 50.0 - - + +
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Residues in contact with ASN4325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4287B LYS 4.3 3.4 + - - -
4288B VAL* 5.4 9.8 - - - +
4289B ASP 5.7 1.2 + - - -
4317B THR* 3.7 24.0 + - - +
4318B PRO* 3.9 13.2 - - + +
4319B SER* 3.3 34.6 + - - +
4323B LEU 3.8 2.6 - - - +
4324B PRO* 1.3 72.6 - - - +
4326B ASN* 1.3 69.0 + - - +
4327B ALA 3.4 0.3 + - - -
4328B GLU* 3.7 2.6 + - - +
4329B ARG* 3.7 15.1 + - - +
4579B ASN* 5.1 14.1 + - + +
4638B ARG* 5.8 0.2 + - - -
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Residues in contact with ASN4326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4324B PRO* 3.3 2.3 - - + +
4325B ASN* 1.3 82.2 - - - +
4327B ALA* 1.3 63.4 + - - +
4329B ARG* 3.4 44.4 + - - +
4330B VAL* 4.1 7.3 + - - +
4579B ASN* 3.4 38.9 + - - +
4580B ALA* 4.6 5.3 - - - +
4581B ILE* 4.4 20.5 - - + +
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Residues in contact with ALA4327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4196B TYR* 5.6 8.3 - - + -
4199B LEU* 3.6 30.3 - - + -
4318B PRO* 5.9 1.3 - - + -
4323B LEU* 5.7 3.4 - - + -
4324B PRO* 3.5 25.3 + - + +
4325B ASN 3.2 0.8 - - - -
4326B ASN* 1.3 79.6 - - - +
4328B GLU* 1.3 61.7 + - - +
4329B ARG 3.3 0.7 + - - -
4330B VAL* 3.8 13.0 + - - +
4331B LEU* 4.2 3.6 + - - +
4581B ILE* 5.8 3.1 - - - -
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Residues in contact with GLU4328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4196B TYR* 3.4 39.5 - - + +
4318B PRO* 3.6 25.4 - - + -
4324B PRO 4.4 0.4 + - - -
4325B ASN 3.7 3.1 + - - +
4327B ALA* 1.3 78.5 - - - +
4329B ARG* 1.3 58.8 + - - +
4330B VAL 3.3 0.2 - - - -
4331B LEU* 3.2 9.2 + - - +
4332B LEU* 2.9 39.9 + - + +
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Residues in contact with ARG4329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3997B ARG* 5.1 12.9 - - - +
3998B PRO* 6.0 2.2 - - - -
3999B ASP* 3.6 32.1 - - + +
4325B ASN 3.7 6.1 + - - +
4326B ASN* 3.4 42.4 + - - +
4327B ALA 3.2 0.4 - - - -
4328B GLU* 1.3 77.0 - - - +
4330B VAL* 1.3 71.8 + - - +
4332B LEU* 3.2 13.5 + - - +
4333B THR* 2.9 37.0 + - - -
4581B ILE* 4.0 24.5 - - - +
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Residues in contact with VAL4330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4326B ASN 4.4 7.6 - - - +
4327B ALA 3.8 8.0 + - - +
4329B ARG* 1.3 95.9 - - - +
4331B LEU* 1.3 52.7 + - - +
4333B THR* 3.2 10.2 + - - -
4334B THR* 2.7 42.5 + - - +
4581B ILE* 4.9 12.8 - - + -
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Residues in contact with LEU4331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3878B GLN* 5.8 3.6 - - - +
4195B ARG* 4.1 20.9 - - + +
4196B TYR* 4.1 29.4 - - + -
4327B ALA 4.2 2.8 + - - +
4328B GLU* 3.2 14.5 + - - +
4330B VAL* 1.3 80.4 - - - +
4332B LEU* 1.3 57.9 + - + +
4334B THR* 3.2 14.3 + - + +
4335B GLN* 2.9 49.7 + - + +
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Residues in contact with LEU4332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3998B PRO 5.0 0.2 - - - +
3999B ASP* 3.4 20.7 - - - +
4000B ARG* 4.0 33.9 - - - +
4001B LEU* 5.7 0.2 - - - +
4002B LEU* 4.2 25.6 - - + +
4196B TYR* 6.0 3.4 - - + -
4318B PRO* 6.0 2.7 - - + -
4328B GLU* 2.9 31.8 + - + +
4329B ARG* 3.2 10.5 + - - +
4331B LEU* 1.3 76.8 - - + +
4333B THR* 1.3 57.1 + - - +
4335B GLN* 3.2 15.4 + - - +
4336B GLY* 2.9 25.8 + - - -
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Residues in contact with THR4333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3998B PRO* 3.9 35.4 - - + +
3999B ASP* 3.3 16.5 + - - +
4329B ARG* 2.9 21.7 + - - -
4330B VAL* 3.2 12.2 + - - -
4332B LEU* 1.3 74.6 - - - +
4334B THR* 1.3 58.3 + - - +
4336B GLY* 3.2 2.4 + - - -
4337B VAL* 2.9 42.8 + - + +
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Residues in contact with THR4334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4330B VAL* 2.7 29.3 + - - +
4331B LEU* 3.3 15.0 - - + +
4333B THR* 1.3 78.2 - - - +
4335B GLN* 1.3 57.6 + - - +
4337B VAL* 3.2 8.1 + - + +
4338B ASP* 2.9 46.4 + - - +
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Residues in contact with GLN4335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3877B HIS 5.6 0.2 - - - +
3878B GLN* 4.2 45.4 - - + +
3881B ILE* 5.6 0.7 - - - +
4002B LEU* 3.2 28.6 - - + +
4331B LEU* 2.9 39.2 + - + +
4332B LEU* 3.4 17.7 - - - +
4334B THR* 1.3 77.9 - - - +
4336B GLY* 1.3 55.8 + - - +
4338B ASP* 3.2 11.2 + - - +
4339B MET* 2.9 28.9 + - - +
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Residues in contact with GLY4336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3998B PRO 5.4 0.2 - - - -
4001B LEU* 3.7 27.6 - - - +
4002B LEU* 3.9 14.1 - - - +
4332B LEU 2.9 13.8 + - - -
4333B THR* 3.6 4.3 - - - -
4335B GLN* 1.3 74.9 - - - +
4337B VAL* 1.3 57.9 + - - +
4339B MET* 3.2 4.7 + - - +
4340B ILE* 2.9 32.3 + - - +
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Residues in contact with VAL4337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3998B PRO* 6.3 0.7 - - + -
4333B THR* 2.9 28.7 + - + +
4334B THR* 3.2 12.3 + - + +
4336B GLY* 1.3 75.2 - - - +
4338B ASP* 1.3 61.4 + - - +
4340B ILE* 3.2 10.4 + - + +
4341B SER* 2.9 38.1 + - - +
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Residues in contact with ASP4338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3821B ILE* 5.5 0.7 - - - +
3878B GLN* 4.9 8.0 - - - +
3879B ASP* 6.1 0.4 - - - +
4334B THR* 2.9 31.2 + - - +
4335B GLN* 3.2 11.8 + - - +
4337B VAL* 1.3 79.8 - - - +
4339B MET* 1.3 58.4 + - - +
4341B SER* 3.2 9.9 + - - -
4342B LYS* 2.9 27.8 + - - +
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Residues in contact with MET4339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3878B GLN 5.3 4.9 - - - +
3881B ILE* 3.4 40.4 - - + -
3882B THR* 3.4 29.8 - - + +
3885B MET* 3.4 24.2 - - + +
3908B PHE* 5.7 2.2 - - - -
4001B LEU* 4.9 9.9 - - - -
4002B LEU* 3.4 26.5 - - + -
4005B ALA* 4.5 10.8 - - + -
4335B GLN 2.9 12.7 + - - +
4336B GLY 3.3 9.9 - - - +
4338B ASP* 1.3 75.5 - - - +
4340B ILE* 1.3 61.8 + - + +
4342B LYS* 3.2 5.1 + - - +
4343B MET* 2.9 32.7 + - - +
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Residues in contact with ILE4340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3908B PHE* 3.4 37.0 - - + +
3909B LEU* 3.5 27.1 - - + +
3912B ASN* 5.2 5.6 - - + -
3994B GLN* 3.2 29.8 - - - +
4001B LEU* 4.1 10.1 - - + -
4336B GLY 2.9 18.5 + - - +
4337B VAL* 3.2 12.5 + - + +
4339B MET* 1.3 80.3 - - + +
4341B SER* 1.3 58.0 + - - +
4343B MET* 3.2 8.0 + - + +
4344B LEU* 2.9 28.6 + - + +
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Residues in contact with SER4341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4337B VAL* 2.9 23.6 + - - +
4338B ASP* 3.4 12.9 - - - -
4340B ILE* 1.3 79.1 - - - +
4342B LYS* 1.3 60.9 + - - +
4344B LEU* 3.2 14.2 + - - +
4345B LYS* 3.0 43.2 + - - +
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Residues in contact with LYS4342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3818B LEU* 3.4 20.8 - - - +
3821B ILE* 2.5 46.0 - - + +
3875B MET* 3.9 3.4 - - - +
3879B ASP* 3.2 20.2 + - + +
3882B THR* 2.4 42.1 + - + +
3883B PHE 3.9 2.8 - - - +
3886B LEU* 4.6 4.9 - - - -
4338B ASP 2.9 13.3 + - - +
4339B MET* 3.4 10.3 - - - +
4341B SER* 1.3 77.2 - - - +
4343B MET* 1.3 62.1 - - - +
4345B LYS* 3.2 13.0 + - + +
4346B MET* 3.1 51.3 + - + +
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Residues in contact with MET4343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3882B THR* 4.1 9.2 - - - +
3885B MET* 3.6 45.8 - - + -
3886B LEU* 3.5 42.6 - - + +
3889B ARG* 4.7 3.3 + - - +
3905B PHE* 4.1 21.1 - - + -
3909B LEU* 3.6 28.4 - - + +
4339B MET* 2.9 18.6 + - + +
4340B ILE* 3.5 9.6 - - + +
4342B LYS* 1.3 76.4 - - - +
4344B LEU* 1.3 57.7 + - - +
4346B MET* 3.2 6.6 + - - +
4347B GLN* 2.9 28.2 + - - +
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Residues in contact with LEU4344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3906B GLN* 6.0 0.2 - - - +
3909B LEU* 4.3 11.8 - - + +
3910B ARG* 3.6 50.3 - - + +
4340B ILE* 2.9 14.5 + - + +
4341B SER* 3.2 14.3 + - - +
4343B MET* 1.3 76.5 - - - +
4345B LYS* 1.3 57.9 + - + +
4347B GLN* 3.2 10.1 + - + +
4348B MET* 2.9 30.3 + - + +
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Residues in contact with LYS4345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3820B GLN* 3.8 37.6 - - + +
3821B ILE* 6.2 3.8 - - + -
4341B SER* 3.0 40.3 + - - +
4342B LYS* 3.3 13.0 - - + +
4344B LEU* 1.3 78.2 - - + +
4346B MET* 1.3 66.1 + - - +
4348B MET* 3.2 17.4 + - - +
4349B LEU* 3.3 18.6 + - - +
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Residues in contact with MET4346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3814B THR* 4.6 4.0 - - + +
3817B SER* 3.6 30.4 + - - +
3818B LEU* 3.7 35.0 - - + +
3820B GLN* 5.1 2.9 - - - -
3821B ILE* 4.7 4.5 - - + -
3886B LEU* 4.0 34.1 - - + -
3889B ARG* 5.6 4.4 + - - +
4342B LYS* 3.1 46.8 + - + +
4343B MET* 3.4 8.3 - - - +
4345B LYS* 1.3 83.9 - - - +
4347B GLN* 1.3 61.8 + - - +
4349B LEU* 3.4 6.9 + - - +
4350B GLU* 3.3 18.8 + - - +
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Residues in contact with GLN4347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3889B ARG* 2.7 31.5 + - - +
3905B PHE* 5.6 1.1 - - - -
3906B GLN* 3.3 35.3 + - - +
3909B LEU* 3.4 30.5 - - + -
3910B ARG* 6.4 0.2 - - - +
4343B MET 2.9 7.8 + - - +
4344B LEU* 3.2 15.9 + - + +
4346B MET* 1.3 76.5 - - - +
4348B MET* 1.3 63.3 + - - +
4350B GLU* 3.2 26.7 + - - +
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Residues in contact with MET4348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3164B ARG* 5.5 4.7 + - - -
3910B ARG* 6.0 4.5 - - - +
4344B LEU* 2.9 16.8 + - + +
4345B LYS* 3.2 13.7 + - - +
4347B GLN* 1.3 78.5 - - - +
4349B LEU* 1.3 64.7 + - + +
4350B GLU 4.0 3.6 - - - -
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Residues in contact with LEU4349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3164B ARG* 5.9 12.8 - - + +
3523B GLN* 5.0 7.1 + - - +
3817B SER* 2.1 43.3 - - - +
3820B GLN* 4.4 20.2 - - + +
4345B LYS 3.3 12.5 + - - +
4346B MET* 3.6 8.5 - - - +
4347B GLN 3.2 0.4 - - - -
4348B MET* 1.3 82.1 - - + +
4350B GLU* 1.3 62.6 + - - +
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Residues in contact with GLU4350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3523B GLN* 4.7 12.1 + - - +
3705B ARG* 4.8 16.5 + - - +
3889B ARG* 5.1 7.9 - - - +
4346B MET 3.3 8.9 + - - +
4347B GLN* 3.2 29.5 + - - +
4348B MET 4.0 3.8 - - - -
4349B LEU* 1.3 84.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il