Contacts of the helix formed by residues 394 - 424 (chain F) in PDB entry 6X34
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 GLN 394 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F HIS* 5.6 0.9 - - - -
219F VAL* 4.4 2.7 - - - +
221F ARG* 5.4 5.3 - - - +
393F CYS* 1.3 90.1 - - - +
395F GLN* 1.3 63.4 + - - +
396F GLU* 3.7 21.8 - - + +
397F GLU* 3.3 41.1 + - - +
398F SER* 3.7 4.2 + - - -
477F LEU* 6.0 1.0 - - - +
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Residues in contact with GLN 395 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218F HIS* 5.5 6.7 + - + +
219F VAL* 5.6 0.7 - - - -
394F GLN* 1.3 71.4 - - - +
396F GLU* 1.3 59.4 + - - +
398F SER* 2.6 24.5 + - - +
399F GLN* 2.9 17.9 + - - +
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Residues in contact with GLU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F GLN* 3.2 15.5 - - + +
395F GLN* 1.3 78.4 - - - +
397F GLU* 1.3 56.6 + - - +
399F GLN* 3.4 6.7 + - - +
400F ALA* 2.9 29.7 + - - +
451F TYR* 5.3 4.7 + - - +
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Residues in contact with GLU 397 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221F ARG* 5.5 6.3 - - - +
259F LEU* 5.7 5.2 - - + -
393F CYS* 4.7 13.7 - - + -
394F GLN* 3.3 33.3 + - - +
395F GLN 3.2 0.4 - - - -
396F GLU* 1.3 80.1 - - - +
398F SER* 1.3 57.3 + - - +
400F ALA* 3.3 6.1 + - - +
401F ALA* 2.9 29.7 + - - +
477F LEU* 4.8 17.5 - - + +
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Residues in contact with SER 398 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F VAL* 3.6 36.6 - - - +
285F VAL* 5.2 2.6 - - - +
394F GLN 3.7 2.0 + - - -
395F GLN* 2.6 32.9 + - - +
397F GLU* 1.3 76.9 - - - +
399F GLN* 1.3 55.6 + - - +
401F ALA* 3.3 7.2 + - - +
402F ARG* 2.9 29.3 + - - +
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Residues in contact with GLN 399 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 5.3 2.4 - - + -
113F HIS* 4.1 23.1 - - - +
395F GLN 2.9 17.4 + - - +
396F GLU* 3.7 7.9 - - - +
398F SER* 1.3 77.6 + - - +
400F ALA* 1.3 57.1 + - - +
402F ARG* 3.3 7.2 + - - +
403F MET* 2.9 38.8 + - + +
451F TYR* 5.8 2.9 - - - +
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Residues in contact with ALA 400 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396F GLU 2.9 17.8 + - - +
397F GLU* 3.7 7.2 - - - +
399F GLN* 1.3 75.4 - - - +
401F ALA* 1.3 58.5 + - - +
403F MET* 3.3 11.9 + - - +
404F ILE* 2.9 38.8 + - + +
451F TYR* 5.1 10.9 + - + +
474F ARG* 5.9 7.2 - - + -
477F LEU* 4.7 17.9 - - + -
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Residues in contact with ALA 401 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ALA* 5.4 5.8 - - + +
259F LEU* 5.2 7.4 - - + -
285F VAL* 3.8 33.5 - - + +
286F THR* 5.0 2.2 - - + -
397F GLU 2.9 17.4 + - - +
398F SER* 3.6 8.1 - - - +
400F ALA* 1.3 74.8 - - - +
402F ARG* 1.3 60.0 + - - +
404F ILE* 3.0 17.8 - - + +
405F TYR* 2.9 30.0 + - - +
477F LEU* 6.1 0.4 - - - +
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Residues in contact with ARG 402 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 6.1 1.3 - - + -
64F ILE* 5.9 7.9 - - + -
113F HIS* 5.2 13.0 - - + -
285F VAL* 4.4 8.4 - - + +
398F SER 2.9 16.4 + - - +
399F GLN* 3.6 7.0 - - - +
401F ALA* 1.3 76.4 - - - +
403F MET* 1.3 59.5 + - + +
405F TYR* 3.3 9.2 + - - +
406F SER* 2.9 29.7 + - - -
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Residues in contact with MET 403 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.6 54.5 - - + -
399F GLN* 2.9 24.7 + - - +
400F ALA* 3.5 9.4 - - - +
401F ALA 3.2 0.2 - - - -
402F ARG* 1.3 76.2 - - - +
404F ILE* 1.3 59.2 + - + +
406F SER* 2.6 21.2 + - - -
407F THR* 2.9 20.5 + - - +
448F LEU* 5.3 8.5 - - + -
451F TYR* 3.6 50.9 - - + -
452F PHE* 4.6 9.9 - - + -
478F PHE* 6.0 2.7 - - + -
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Residues in contact with ILE 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F ALA* 4.1 22.7 - - + -
286F THR* 4.3 18.4 - - + -
400F ALA* 2.9 20.2 + - + +
401F ALA* 3.0 30.5 - - - +
403F MET* 1.3 76.4 - - + +
405F TYR* 1.3 57.9 + - + +
407F THR* 3.3 9.5 - - + +
408F ALA* 2.9 33.3 + - - +
477F LEU* 4.8 10.1 - - + +
478F PHE* 4.4 26.9 - - + -
481F GLU* 4.5 19.3 - - + -
483F MET* 4.8 9.8 - - - +
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Residues in contact with TYR 405 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285F VAL* 3.2 23.6 - - + +
286F THR 3.3 22.4 - - - +
287F THR 3.8 17.9 - - - -
288F GLY* 4.1 11.9 - - - -
401F ALA 2.9 13.2 + - - +
402F ARG* 3.6 8.3 - - - +
404F ILE* 1.3 79.5 - - - +
406F SER* 1.3 63.4 + - - +
408F ALA* 3.7 3.8 - - + +
409F GLY* 2.9 28.6 + - - -
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Residues in contact with SER 406 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F GLU* 5.7 6.7 - - - -
42F PHE* 4.5 23.3 + - - +
402F ARG 2.9 14.5 + - - -
403F MET* 2.6 26.2 + - - -
405F TYR* 1.3 82.9 - - - +
407F THR* 1.3 56.5 + - - +
409F GLY* 3.3 2.3 + - - -
410F LEU* 3.0 27.9 + - - +
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Residues in contact with THR 407 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F MET 2.9 22.1 + - - +
404F ILE* 3.3 14.1 - - - +
406F SER* 1.3 77.5 + - - +
408F ALA* 1.3 60.6 + - - +
410F LEU* 3.4 7.0 + - - +
411F TYR* 2.9 56.4 + - - -
444F SER* 5.8 7.8 - - - -
445F LEU* 5.7 0.2 - - - +
448F LEU* 6.1 4.5 - - - -
478F PHE* 5.0 6.5 - - + -
483F MET* 3.7 20.5 - - + +
----------------------------------------------------------
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Residues in contact with ALA 408 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F THR 5.6 3.1 - - - +
404F ILE 2.9 20.5 + - - +
405F TYR* 3.7 5.6 - - + +
407F THR* 1.3 75.8 - - + +
409F GLY* 1.3 57.7 + - - +
411F TYR* 3.2 6.6 + - - +
412F ASN* 2.6 44.0 + - - +
483F MET* 5.5 5.4 - - + -
486F LEU* 4.4 13.2 - - + -
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Residues in contact with GLY 409 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F TYR* 2.9 17.7 + - - -
406F SER 3.7 2.7 - - - -
408F ALA* 1.3 76.4 - - - +
410F LEU* 1.3 61.5 + - - +
412F ASN* 3.3 9.4 + - - +
413F HIS* 3.0 24.3 + - - +
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Residues in contact with LEU 410 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F SER 3.0 16.9 + - - +
407F THR* 3.7 8.7 - - - +
409F GLY* 1.3 75.3 - - - +
411F TYR* 1.3 64.3 + - + +
413F HIS* 3.3 7.6 + - - +
414F PHE* 2.9 27.4 + - - +
441F VAL* 5.7 8.7 - - + +
444F SER* 4.8 16.4 - - - +
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Residues in contact with TYR 411 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407F THR* 2.9 40.2 + - - +
408F ALA 3.2 1.1 + - - +
410F LEU* 1.3 78.4 - - + +
412F ASN* 1.3 61.2 + - - +
414F PHE* 3.3 6.9 + + + +
415F ILE* 2.9 32.7 + - - +
441F VAL* 4.9 11.2 - - + -
444F SER* 5.6 1.8 - - - -
445F LEU* 3.2 33.9 - - + +
448F LEU* 6.0 0.5 - - - +
483F MET* 3.7 11.4 - - + -
486F LEU* 3.5 41.1 - - + -
487F VAL* 3.7 24.4 - - + +
490F CYS* 4.6 12.2 - - - -
522F LEU* 5.4 8.0 - - + +
525F ILE* 3.7 20.1 - - - +
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Residues in contact with ASN 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408F ALA* 2.6 31.9 + - - +
409F GLY* 3.8 7.6 + - - +
411F TYR* 1.3 71.8 - - - +
413F HIS* 1.3 61.8 + - - +
415F ILE* 3.3 8.0 + - - +
416F LYS* 2.9 30.0 + - - +
486F LEU* 3.9 19.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 413 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F GLY 3.0 14.2 + - - +
410F LEU* 3.6 11.0 - - - +
411F TYR 3.3 0.2 - - - -
412F ASN* 1.3 77.6 - - - +
414F PHE* 1.3 55.2 + - - +
416F LYS* 3.3 9.3 + - + +
417F GLY* 2.9 27.4 + - - -
436F LEU* 5.8 2.1 - - + +
437F PRO* 3.8 36.4 - - + +
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Residues in contact with PHE 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410F LEU 2.9 17.3 + - - +
411F TYR* 3.3 11.0 + + + +
413F HIS* 1.3 76.4 - - - +
415F ILE* 1.3 58.2 + - - +
417F GLY* 3.3 2.1 + - - -
418F LEU* 2.9 38.5 + - + +
436F LEU* 3.8 39.7 - - + +
437F PRO* 6.2 2.5 - - + -
441F VAL* 4.3 35.0 - - + -
490F CYS* 4.6 27.1 - - + -
494F LEU* 4.4 32.3 - - + -
518F ILE* 4.6 15.7 - - + -
522F LEU* 6.0 3.4 - - + -
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Residues in contact with ILE 415 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411F TYR 2.9 15.6 + - - +
412F ASN* 3.8 7.6 - - - +
414F PHE* 1.3 73.5 - - + +
416F LYS* 1.3 60.5 + - - +
418F LEU* 3.3 5.7 + - - +
419F ASP* 2.9 32.5 + - + +
486F LEU* 3.5 34.3 - - + +
489F ASN* 3.5 32.5 - - + +
490F CYS* 3.8 20.2 - - + -
493F ARG* 5.2 6.8 + - + +
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Residues in contact with LYS 416 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412F ASN 2.9 16.8 + - - +
413F HIS* 3.6 11.9 - - + +
415F ILE* 1.3 79.5 - - - +
417F GLY* 1.3 56.8 + - - +
419F ASP* 3.3 6.1 + - - +
420F SER* 2.8 31.2 + - - -
----------------------------------------------------------
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Residues in contact with GLY 417 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F HIS* 2.9 17.4 + - - -
414F PHE 3.3 3.1 + - - -
415F ILE 3.3 0.2 - - - -
416F LYS* 1.3 77.2 - - - +
418F LEU* 1.3 55.3 + - - +
420F SER* 2.8 19.6 + - - -
421F PHE* 2.9 20.8 + - - +
434F THR* 5.0 10.6 - - - +
436F LEU* 4.7 21.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 418 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F PHE* 2.9 30.0 + - + +
415F ILE* 3.8 6.7 - - - +
417F GLY* 1.3 75.7 - - - +
419F ASP* 1.3 57.6 + - - +
421F PHE* 3.9 4.7 - - - +
422F SER* 2.8 35.1 + - - -
436F LEU* 4.9 6.3 - - + +
493F ARG* 4.7 24.5 - - + +
494F LEU* 6.3 2.7 - - + -
503F PHE* 6.5 1.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 419 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F ILE* 2.9 20.1 + - + +
416F LYS* 3.8 5.2 - - - +
418F LEU* 1.3 76.7 - - - +
420F SER* 1.3 62.9 + - - +
422F SER* 3.9 6.6 + - - -
423F GLY* 3.1 21.0 + - - -
493F ARG* 4.1 18.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 420 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416F LYS 2.8 20.2 + - - -
417F GLY* 2.8 17.7 + - - -
419F ASP* 1.3 75.9 - - - +
421F PHE* 1.3 58.6 + - - +
423F GLY* 4.7 0.4 - - - -
424F LYS* 3.8 18.0 + - - +
432F ALA 4.8 2.6 - - - +
433F GLY* 4.9 3.7 - - - -
434F THR* 4.0 18.8 - - - +
----------------------------------------------------------
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Residues in contact with PHE 421 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417F GLY 2.9 18.0 + - - +
418F LEU* 3.9 5.4 - - - +
420F SER* 1.3 76.8 - - - +
422F SER* 1.3 64.9 + - - +
423F GLY 3.3 0.2 - - - -
424F LYS* 3.3 20.9 + - - +
433F GLY* 5.1 11.4 - - - -
434F THR 5.5 5.6 - - - +
436F LEU* 5.8 5.6 - - + -
497F TYR* 4.4 4.2 + - - +
503F PHE* 5.6 4.0 - - + -
506F PHE* 5.1 1.7 - - - +
507F ALA* 3.9 33.2 + - + +
----------------------------------------------------------
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Residues in contact with SER 422 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418F LEU* 2.8 22.5 + - - -
419F ASP* 3.9 7.1 + - - -
421F PHE* 1.3 70.0 - - - +
423F GLY* 1.3 67.7 + - - +
424F LYS 3.4 6.2 + - - +
493F ARG* 4.9 12.4 + - - -
496F VAL* 5.7 4.7 - - - -
497F TYR* 3.6 29.3 + - - -
----------------------------------------------------------
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Residues in contact with GLY 423 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F ASP 3.1 15.7 + - - -
420F SER 4.7 0.4 - - - -
421F PHE 3.3 0.2 - - - -
422F SER* 1.3 83.8 + - - +
424F LYS* 1.3 59.2 + - - +
425F PRO* 3.6 7.3 - - - +
----------------------------------------------------------
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Residues in contact with LYS 424 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420F SER 3.8 15.4 + - - +
421F PHE* 3.3 17.6 + - - +
422F SER 3.3 5.5 - - - +
423F GLY* 1.3 77.0 - - - +
425F PRO* 1.3 76.0 - - + +
431F PRO 5.5 0.9 - - - +
432F ALA* 3.3 29.6 - - + +
506F PHE* 5.0 6.1 - - - +
----------------------------------------------------------
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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