Contacts of the helix formed by residues 390 - 417 (chain A) in PDB entry 6J8H
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 SER 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU 3.9 11.2 - - - -
358A MET* 3.1 25.3 + - - +
360A GLN* 2.0 37.2 + - - -
385A VAL 3.2 5.0 + - - -
386A ILE* 3.2 15.0 + - - -
389A GLY* 1.3 76.5 - - - +
391A PHE* 1.3 69.9 + - - +
392A TYR 3.3 0.9 - - - -
394A ILE* 3.3 28.2 + - - +
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Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLN* 3.9 22.9 - - - -
386A ILE* 3.0 15.2 + - + -
387A PHE* 3.4 46.9 - + - +
390A SER* 1.3 78.0 - - - +
392A TYR* 1.3 63.2 + - - +
394A ILE* 4.3 0.8 - - + +
395A ASN* 3.4 29.6 + - - +
1692A PHE* 6.5 0.2 - + - -
1695A THR* 5.2 5.6 - - + -
1696A THR* 3.5 30.5 - - + -
1751A VAL* 4.4 35.0 - - + -
1754A MET* 3.7 23.1 - - + -
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.9 5.3 - - + +
387A PHE 3.8 3.2 + - - +
388A LEU* 2.9 41.0 + - + +
390A SER 3.3 0.2 - - - -
391A PHE* 1.3 78.6 - - - +
393A LEU* 1.3 75.7 + - + +
395A ASN* 3.3 3.2 + - - +
396A LEU* 3.1 54.6 + - + +
1633A LEU 3.1 25.6 + - - -
1634A LEU* 4.8 4.2 - - + -
1636A ALA* 4.6 1.6 - - + +
1637A LEU* 3.2 41.6 + - + +
1640A SER* 5.5 1.1 - - - -
1644A LEU* 5.7 0.9 - - + -
1754A MET* 4.3 11.7 - - + -
1758A VAL* 4.5 25.6 - - + -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 5.1 1.5 - - + +
251A LEU* 4.3 25.4 - - + -
252A THR* 4.2 31.1 + - + +
255A CYS* 3.9 30.3 - - + -
256A LEU* 4.6 11.9 - - + -
259A PHE* 6.1 0.2 - - + -
358A MET* 4.7 11.0 - - + -
388A LEU* 4.5 1.8 - - + +
389A GLY* 2.9 31.7 + - - +
390A SER 4.6 0.2 - - - +
392A TYR* 1.3 91.7 - - + +
394A ILE* 1.3 63.6 + - - +
396A LEU* 3.2 16.9 + - + +
397A ILE* 3.3 18.5 + - + +
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A MET* 3.4 43.7 - - + +
359A THR* 4.4 10.3 - - - +
360A GLN* 5.2 3.1 - - + +
390A SER* 3.3 20.9 + - - +
391A PHE* 4.4 2.0 - - - +
393A LEU* 1.3 75.6 - - - +
395A ASN* 1.3 69.4 + - - +
397A ILE* 3.2 11.1 + - + +
398A LEU* 3.2 35.0 + - + +
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Residues in contact with ASN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PHE* 3.4 21.3 + - - +
392A TYR* 3.3 6.5 + - - +
393A LEU 3.2 0.6 - - - -
394A ILE* 1.3 83.8 - - - +
396A LEU* 1.3 61.5 + - - +
398A LEU* 3.2 11.1 + - - +
399A ALA* 3.0 24.1 + - - +
1754A MET* 3.5 16.5 - - - +
1755A TYR* 3.1 44.2 + - - +
1758A VAL* 3.8 20.0 - - + +
1759A ILE* 4.0 6.0 - - + +
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Residues in contact with LEU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 4.7 9.6 - - + -
251A LEU* 3.9 11.7 - - + -
392A TYR* 3.1 53.1 + - + +
393A LEU* 3.2 13.4 + - + +
395A ASN* 1.3 78.2 - - - +
397A ILE* 1.3 62.2 + - - +
399A ALA* 3.3 2.0 + - - +
400A VAL* 3.1 31.5 + - + +
1633A LEU* 3.9 41.5 - - + +
1636A ALA* 5.6 4.3 - - + -
1758A VAL* 4.8 4.7 - - + -
1762A ASN* 4.2 23.6 - - + +
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Residues in contact with ILE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.6 12.8 - - + -
248A VAL* 3.6 25.6 - - + -
249A MET* 4.9 13.7 - - + -
252A THR* 4.8 8.7 - - + +
358A MET* 4.4 21.3 - - + -
393A LEU* 3.3 12.5 + - + +
394A ILE* 3.2 10.5 + - + +
395A ASN 3.2 0.4 - - - -
396A LEU* 1.3 77.8 - - - +
398A LEU* 1.3 63.2 + - + +
400A VAL* 3.5 3.1 + - - +
401A VAL* 2.9 43.9 + - + +
960A LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ILE* 3.2 27.5 + - + +
395A ASN* 3.2 18.7 + - - +
397A ILE* 1.3 82.1 - - + +
399A ALA* 1.3 56.3 + - - +
401A VAL* 3.9 4.6 - - - +
402A ALA* 2.8 33.7 + - + +
960A LEU* 3.6 31.2 - - + -
964A LEU* 4.8 8.3 - - + +
1755A TYR* 3.8 35.4 - - + +
1759A ILE* 5.1 5.6 - - + -
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN 3.0 15.2 + - - +
396A LEU* 3.8 3.1 - - - +
398A LEU* 1.3 77.6 - - - +
400A VAL* 1.3 50.9 + - - +
402A ALA* 3.8 4.2 - - - +
403A MET* 2.6 38.1 + - - +
1758A VAL* 5.7 0.4 - - + -
1759A ILE* 3.7 21.5 - - + +
1762A ASN* 2.3 42.4 - - + +
1763A PHE* 4.0 9.2 - - + -
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER 5.8 0.2 - - - +
244A LYS* 3.8 27.6 - - + +
245A LEU* 3.4 27.1 - - + -
248A VAL* 3.4 20.2 - - + -
396A LEU* 3.1 18.1 + - - +
399A ALA* 1.3 74.3 - - - +
401A VAL* 1.3 59.5 + - - +
403A MET* 3.9 4.6 - - - +
404A ALA* 2.8 29.1 + - - +
1633A LEU* 5.1 9.6 - - + -
1762A ASN* 4.6 9.4 - - - +
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 5.4 9.6 + - - +
245A LEU* 4.2 20.0 - - + -
397A ILE* 2.9 32.3 + - + +
398A LEU 3.9 2.2 - - - +
400A VAL* 1.3 75.9 - - - +
402A ALA* 1.3 59.3 + - - +
404A ALA* 3.4 4.4 + - - +
405A TYR* 2.9 29.9 + - + +
957A LEU* 5.1 9.0 - - + -
960A LEU* 3.7 29.8 - - + -
961A ASN* 3.5 26.7 - - - +
964A LEU* 5.0 3.1 - - + -
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LEU 2.8 20.2 + - - +
399A ALA* 3.8 3.6 - - - +
401A VAL* 1.3 75.3 - - - +
403A MET* 1.3 65.1 + - - +
405A TYR* 3.3 6.0 + - - +
406A LYS* 3.2 31.9 + - - +
964A LEU* 3.9 29.6 - - + +
968A LEU* 4.5 10.4 - - + +
1759A ILE* 6.3 1.3 - - + -
1763A PHE* 5.0 4.3 - - + -
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Residues in contact with MET 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 4.7 15.0 - - - +
399A ALA 2.6 25.0 + - - +
400A VAL* 3.9 5.6 - - - +
402A ALA* 1.3 71.8 - - - +
404A ALA* 1.3 62.0 + - - +
406A LYS* 3.4 17.5 + - - +
407A GLU* 3.5 13.5 + - + +
1762A ASN* 5.6 2.0 - - - +
1763A PHE* 3.9 39.9 - - + -
1766A ALA* 5.5 12.3 - - + -
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Residues in contact with ALA 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 4.8 12.3 - - - +
244A LYS* 3.2 47.5 - - + +
400A VAL 2.8 19.5 + - - +
401A VAL* 3.8 5.2 - - - +
403A MET* 1.3 74.2 - - - +
405A TYR* 1.3 65.6 + - - +
407A GLU* 3.1 21.1 - - - +
408A GLN* 3.5 10.9 + - - +
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A SER* 5.3 8.5 + - - +
401A VAL* 2.9 20.3 + - + +
402A ALA* 3.7 7.0 - - - +
403A MET 3.3 0.2 - - - -
404A ALA* 1.3 78.9 - - - +
406A LYS* 1.3 61.7 + - + +
408A GLN* 3.5 4.2 + - - +
409A ASN* 2.8 66.6 + - + -
866A LEU* 5.4 4.3 - - - +
869A LEU* 5.9 1.3 - - + -
961A ASN* 5.0 14.8 - - - +
964A LEU* 5.4 3.1 - - + -
965A ALA* 3.3 50.0 + - + +
968A LEU* 4.2 26.9 - - + -
969A SER* 4.6 5.2 - - - -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ALA* 3.2 14.5 + - - +
403A MET* 3.7 13.9 - - - +
404A ALA 3.3 0.4 - - - -
405A TYR* 1.3 84.1 - - + +
407A GLU* 1.3 56.8 + - - +
409A ASN* 4.4 3.6 - - - +
410A GLN* 2.7 40.5 + - + +
968A LEU* 3.9 37.8 - - + +
1763A PHE* 3.6 36.2 - - - -
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 2.9 37.9 + - - +
403A MET* 3.5 13.8 + - + +
404A ALA 3.1 16.0 + - - +
406A LYS* 1.3 77.8 - - - +
408A GLN* 1.3 76.1 + - + +
410A GLN* 4.6 2.8 + - - +
411A ALA* 2.6 39.5 + - - +
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Residues in contact with GLN 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.9 21.0 + - - +
240A GLN* 3.3 41.6 - - - +
241A SER* 4.2 11.5 + - - +
404A ALA* 3.5 14.2 + - - +
405A TYR* 4.1 3.9 - - - +
406A LYS 3.4 0.2 - - - -
407A GLU* 1.3 87.7 + - + +
409A ASN* 1.3 67.2 + - - +
411A ALA* 4.1 4.2 - - - +
412A ASN* 3.1 27.0 + - - +
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Residues in contact with ASN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 2.8 62.6 + - + +
406A LYS* 4.0 4.6 - - - +
408A GLN* 1.3 73.3 - - - +
410A GLN* 1.3 69.5 + - - +
412A ASN* 2.5 25.2 + - - +
413A ILE* 3.2 15.7 + - - +
969A SER* 5.4 6.7 - - - +
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Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 2.7 29.3 + - + +
407A GLU* 4.2 3.2 + - - +
409A ASN* 1.3 78.1 + - - +
411A ALA* 1.3 69.5 + - - +
413A ILE* 2.7 33.5 - - + +
414A GLU* 3.0 20.0 + - - +
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU* 2.6 26.1 + - + +
408A GLN* 4.1 4.9 - - - +
410A GLN* 1.3 80.6 - - - +
412A ASN* 1.3 63.7 + - - +
414A GLU* 3.1 24.9 - - + +
415A GLU* 3.6 4.7 + - - +
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Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLN 3.1 14.6 + - - +
409A ASN* 2.5 32.0 + - - +
411A ALA* 1.3 77.1 - - - +
413A ILE* 1.3 61.9 + - - +
415A GLU* 2.7 38.1 - - + +
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ASN* 3.2 12.3 + - - +
410A GLN* 2.7 43.5 - - + +
412A ASN* 1.3 87.0 + - - +
414A GLU* 1.3 63.3 + - + +
415A GLU* 4.8 0.4 - - - -
416A ALA* 3.3 16.5 + - + +
417A LYS* 3.6 17.1 + - - +
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Residues in contact with GLU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLN* 3.0 21.1 + - - +
411A ALA* 3.1 21.5 - - - +
413A ILE* 1.3 82.0 - - + +
415A GLU* 1.3 72.6 + - + +
417A LYS 3.1 26.0 - - - +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ALA 4.2 3.4 - - - +
412A ASN* 2.7 30.6 + - + +
414A GLU* 1.3 86.9 - - + +
416A ALA* 1.3 101.3 + - - +
417A LYS* 4.3 1.2 - - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASN 4.7 0.2 - - - +
413A ILE* 3.3 11.4 + - + +
414A GLU 3.3 0.8 - - - -
415A GLU* 1.3 101.5 + - - +
417A LYS* 1.3 77.3 + - + +
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Residues in contact with LYS 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 3.6 12.2 + - - +
414A GLU* 3.1 22.7 + - - +
415A GLU 4.6 1.4 - - - +
416A ALA* 1.3 94.8 - - + +
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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