Contacts of the helix formed by residues 418 - 449 (chain M) in PDB entry 2W4G
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 THR 418 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368M GLN* 6.2 0.7 - - + -
373M GLU* 3.8 23.2 + - + +
375M ALA* 3.6 3.6 - - - -
417M GLN* 1.3 73.8 - - - +
419M VAL* 1.3 81.8 + - + +
420M SER* 3.8 10.8 - - - +
421M GLN* 2.9 38.3 + - - -
422M VAL* 3.0 17.0 + - - +
544M LYS* 3.6 34.4 - - + +
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Residues in contact with VAL 419 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366M PHE* 4.2 19.5 - - + +
367M LYS* 4.2 3.8 - - - -
368M GLN* 3.8 43.5 - - + +
373M GLU 5.2 0.2 - - - +
374M GLN 4.5 1.1 - - - +
375M ALA* 3.7 13.9 - - + +
418M THR* 1.3 79.7 - - + +
420M SER* 1.3 65.4 + - - +
422M VAL* 2.9 15.4 + - - +
423M HIS* 3.2 35.2 + - + +
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Residues in contact with SER 420 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418M THR* 3.2 9.2 - - - +
419M VAL* 1.3 79.7 - - - +
421M GLN* 1.3 60.4 + - - +
423M HIS* 4.4 7.0 - - - +
424M ASN* 3.4 32.4 + - - +
543M PRO 4.0 6.9 - - - +
544M LYS* 5.3 6.3 - - - -
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Residues in contact with GLN 421 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416M GLY 3.9 2.4 - - - +
417M GLN* 3.2 21.1 + - - +
418M THR* 2.9 45.8 + - - +
420M SER* 1.3 74.7 - - - +
422M VAL* 1.3 61.8 + - - +
424M ASN* 3.6 4.4 + - - +
425M SER* 2.9 28.6 + - - -
543M PRO* 0.9 153.8 - - + +
544M LYS* 2.6 3.9 - - - +
600M LYS* 4.5 3.5 + - - +
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Residues in contact with VAL 422 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366M PHE* 3.6 38.8 - - + -
375M ALA* 3.6 21.5 - - + -
401M LEU* 4.0 29.6 - - + +
402M CYS* 4.7 4.7 - - - -
417M GLN* 4.2 9.4 - - + -
418M THR 3.1 15.7 - - - +
419M VAL 2.9 4.4 + - - +
421M GLN* 1.3 74.6 - - - +
423M HIS* 1.3 60.6 + - - +
424M ASN 2.9 1.3 - - - -
425M SER* 2.6 28.2 + - - +
426M VAL* 2.8 19.8 + - + +
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Residues in contact with HIS 423 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314M TYR* 4.6 2.8 + - - -
364M LEU 3.8 15.2 + - - -
365M LYS* 3.9 16.1 - - - +
366M PHE* 3.6 44.9 + + + -
419M VAL* 3.2 31.0 + - + +
420M SER* 4.4 6.5 - - - +
422M VAL* 1.3 77.3 - - - +
424M ASN* 1.3 68.0 + - - +
426M VAL* 3.7 7.1 + - - +
427M GLY* 3.3 17.3 + - - -
597M GLU* 4.3 6.0 - - - +
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Residues in contact with ASN 424 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420M SER* 3.4 21.0 + - - +
421M GLN 4.0 0.7 - - - +
422M VAL 2.9 0.6 - - - -
423M HIS* 1.3 83.4 - - - +
425M SER* 1.3 64.2 + - - +
427M GLY* 3.3 2.4 + - - -
428M ALA 3.0 16.3 + - - -
543M PRO 5.6 0.5 - - - +
545M ALA 4.9 8.0 - - - +
596M LEU* 5.6 3.8 - - - +
597M GLU* 3.5 36.1 + - + +
600M LYS* 3.0 48.9 + - + +
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Residues in contact with SER 425 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401M LEU* 4.5 10.7 + - - +
417M GLN* 4.0 14.5 + - - -
421M GLN 2.9 14.9 + - - -
422M VAL* 2.6 26.9 + - - +
424M ASN* 1.3 70.5 - - - +
426M VAL* 1.3 64.8 + - - -
428M ALA* 2.9 17.8 + - - +
429M LEU* 2.9 20.0 + - - +
600M LYS* 4.0 5.6 - - - +
604M ASN* 4.7 18.2 + - - -
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Residues in contact with VAL 426 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314M TYR* 3.8 6.1 - - - +
361M TYR* 3.7 47.2 - - + +
364M LEU* 4.8 6.7 - - + +
366M PHE* 4.3 10.5 - - + -
401M LEU* 4.1 18.8 - - + -
422M VAL* 2.8 35.2 + - + +
423M HIS* 3.7 7.9 - - - +
425M SER* 1.3 76.1 + - - +
427M GLY* 1.3 52.9 + - - +
429M LEU* 2.7 15.3 + - - +
430M ALA* 2.9 9.9 + - - +
601M ASP 2.4 22.3 - - - +
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Residues in contact with GLY 427 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276M THR* 4.6 5.6 - - - -
314M TYR* 3.3 19.7 + - - -
423M HIS 3.3 9.0 + - - -
424M ASN 3.6 4.3 - - - -
425M SER 3.2 0.4 - - - -
426M VAL* 1.3 75.0 - - - +
428M ALA 1.3 30.3 - - - +
430M ALA* 4.2 3.1 - - - -
431M LYS* 3.9 1.1 - - - -
597M GLU* 5.0 8.3 - - - -
600M LYS* 4.3 0.4 - - - -
601M ASP* 0.7 160.7 - - - +
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Residues in contact with ALA 428 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424M ASN 3.0 4.6 + - - +
425M SER* 2.9 12.9 + - - +
427M GLY* 1.3 66.9 - - - +
429M LEU* 1.3 55.6 + - + +
432M ALA* 2.9 13.6 + - - +
600M LYS* 0.7 118.5 - - + +
601M ASP* 1.8 29.0 + - - +
602M PRO 4.1 14.6 - - - +
603M LEU* 4.1 9.6 - - + +
649M VAL* 4.8 0.3 - - - +
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Residues in contact with LEU 429 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M TYR* 4.3 7.0 - - + -
401M LEU* 4.0 26.2 - - + -
425M SER* 2.9 19.0 + - - +
426M VAL* 2.7 9.8 + - - +
428M ALA* 1.3 70.4 - - + +
430M ALA* 1.4 55.8 - - - +
432M ALA* 2.7 5.3 + - + -
433M VAL* 2.6 40.9 + - + +
601M ASP 1.8 9.5 + - - -
603M LEU* 4.2 15.7 - - + -
604M ASN* 4.6 12.8 - - + +
607M VAL* 4.2 15.5 - - + -
608M ILE* 4.2 25.1 - - + -
611M TYR* 3.6 26.9 - - + +
623M PHE* 5.4 0.2 - - + -
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Residues in contact with ALA 430 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M VAL* 4.5 3.8 - - + -
276M THR* 4.8 0.7 - - - +
314M TYR* 3.8 29.4 - - + -
358M VAL* 4.0 23.5 - - + +
361M TYR* 4.3 14.3 - - + -
426M VAL 2.9 9.1 + - - +
427M GLY 3.5 4.5 - - - +
429M LEU* 1.4 68.9 - - - +
431M LYS* 1.3 55.5 - - - +
433M VAL* 3.5 3.5 + - - +
434M TYR* 3.1 21.3 + - - +
601M ASP* 1.8 29.3 + - - +
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Residues in contact with LYS 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M LYS* 3.4 26.3 - - + +
273M SER* 4.7 0.2 - - - +
275M VAL* 4.4 4.4 - - + +
276M THR* 3.6 12.3 - - - +
427M GLY 3.0 0.7 - - - +
430M ALA* 1.3 51.9 - - - +
432M ALA* 1.3 60.2 + - - +
434M TYR* 3.4 6.0 + - - +
435M GLU* 3.0 25.1 + - - +
597M GLU 1.7 29.7 + - - +
598M LYS* 1.2 105.5 - - - +
599M ASN* 2.3 0.9 - - - +
600M LYS 2.9 0.6 - - - +
601M ASP* 0.6 263.0 + - + +
649M VAL* 3.5 11.9 - - + -
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Residues in contact with ALA 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428M ALA 3.2 11.7 - - - +
429M LEU* 2.7 14.1 + - + +
431M LYS* 1.3 68.3 - - - +
433M VAL* 1.3 63.2 + - - +
435M GLU* 3.5 5.4 - - - +
436M LYS* 3.2 36.3 + - - +
601M ASP* 2.4 12.9 + - - +
603M LEU* 3.9 26.2 - - + -
623M PHE* 4.2 9.4 - - + -
647M GLN* 4.5 1.6 - - + +
648M THR 5.4 1.3 - - - +
649M VAL* 4.5 5.8 - - + +
652M LEU* 5.2 1.1 - - - -
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Residues in contact with VAL 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M LEU* 4.8 10.5 - - + +
358M VAL* 4.7 10.8 - - + -
361M TYR* 5.6 0.7 - - + -
390M MET* 4.2 20.0 - - + -
429M LEU 2.6 26.7 + - - +
430M ALA* 3.8 5.2 - - - +
432M ALA* 1.3 70.8 - - - +
434M TYR* 1.3 67.9 + - - +
436M LYS* 3.7 2.4 - - - +
437M MET* 3.1 24.1 + - + +
611M TYR* 3.7 34.3 - - + +
619M LEU* 4.5 14.8 - - + -
622M LEU* 4.3 5.8 - - + +
623M PHE* 3.8 13.5 - - + -
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Residues in contact with TYR 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232M PHE* 2.8 58.2 + + + -
270M LEU* 4.3 6.5 - - + -
272M LYS* 6.3 0.7 - - - -
275M VAL* 3.9 30.3 - - + -
285M TYR* 3.7 20.3 - + - +
287M ILE* 4.0 3.2 - - + +
288M PHE* 3.9 23.6 - + - -
355M THR* 5.0 4.0 - - + -
358M VAL* 4.8 10.9 - - + +
430M ALA 3.1 15.8 + - - +
431M LYS 3.5 4.9 - - - +
433M VAL* 1.3 78.0 - - - +
435M GLU* 1.4 72.9 + - - +
437M MET* 3.1 21.0 - - + +
438M PHE* 2.9 21.6 + - + +
601M ASP* 4.3 0.4 - - - +
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Residues in contact with GLU 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272M LYS* 3.1 35.1 - - + +
431M LYS 3.0 9.4 + - - +
432M ALA* 3.5 6.9 - - - +
434M TYR* 1.4 81.0 - - - +
436M LYS* 1.3 57.3 + - - +
438M PHE* 2.5 38.6 + - + +
439M LEU* 2.8 26.2 + - + +
649M VAL* 4.4 0.2 - - - -
652M LEU* 2.1 49.3 - - + +
653M PHE* 4.1 7.8 + - - +
656M ASN* 4.3 2.6 - - - +
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Residues in contact with LYS 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432M ALA* 3.2 23.3 + - - +
433M VAL* 3.7 5.4 - - - +
435M GLU* 1.3 77.9 - - - +
437M MET* 1.3 52.3 + - - +
439M LEU* 2.8 16.8 + - + +
440M TRP* 2.7 34.3 + - - +
603M LEU* 4.3 1.2 - - - +
622M LEU* 3.5 37.0 - - + +
623M PHE* 4.0 19.1 - - + -
625M THR* 6.2 2.7 - - - -
626M TYR* 5.4 0.2 - - - -
647M GLN* 2.4 46.1 + - - +
652M LEU* 3.1 39.3 - - + +
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Residues in contact with MET 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232M PHE* 4.0 21.1 - - + -
351M ILE* 3.9 14.1 - - + +
354M LEU* 3.8 31.4 - - + -
355M THR* 2.9 33.7 - - - +
433M VAL* 3.1 12.7 + - - +
434M TYR* 3.1 26.0 - - + +
436M LYS* 1.3 78.4 - - - +
438M PHE* 1.3 65.9 + - - +
440M TRP* 2.9 19.2 + - + +
441M MET* 2.8 32.7 + - + +
622M LEU* 4.0 14.6 - - + +
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Residues in contact with PHE 438 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229M LEU* 3.9 18.6 - - + -
232M PHE* 3.8 18.8 - - + -
233M GLY 3.8 3.6 - - - -
246M PHE* 4.5 1.8 - - + -
267M THR* 1.3 88.6 - - + -
268M TYR* 3.6 5.6 - - - -
269M LEU 5.4 1.1 - - - -
270M LEU* 3.7 38.4 - - + -
434M TYR* 2.9 15.1 + + + +
435M GLU* 2.5 20.3 + - - +
437M MET* 1.3 77.7 - - - +
439M LEU* 1.3 72.8 + - + -
441M MET* 3.4 14.3 + - + +
442M VAL* 3.2 19.9 + - - +
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Residues in contact with LEU 439 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266M GLU* 5.2 7.9 - - + +
267M THR 3.7 14.4 - - - +
268M TYR* 5.6 0.7 - - - -
269M LEU 6.2 0.4 - - - +
435M GLU* 3.4 36.8 - - + +
436M LYS* 2.8 15.7 + - + +
438M PHE* 1.3 95.1 - - + +
440M TRP* 1.3 62.9 + - - +
442M VAL* 3.1 10.2 + - - +
443M ILE* 3.0 28.0 + - + +
652M LEU* 4.2 10.8 - - + -
656M ASN* 3.0 34.3 - - - +
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Residues in contact with TRP 440 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M PHE* 4.2 6.5 - + - -
347M GLU* 3.5 47.1 + - + -
351M ILE* 4.0 26.9 - - + -
436M LYS 2.7 13.4 + - - +
437M MET* 3.1 24.5 - - + +
439M LEU* 1.3 74.5 - - - +
441M MET* 1.3 64.4 + - + +
443M ILE* 2.8 21.8 + - + +
444M ARG* 2.7 53.6 + - + +
618M THR* 3.6 34.5 - - + -
621M LEU* 5.2 14.2 - - + +
622M LEU* 4.2 20.3 - - + +
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Residues in contact with MET 441 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228M LEU* 4.3 15.9 - - + -
229M LEU* 5.1 4.5 - - + -
232M PHE* 3.8 44.4 - - + -
343M PHE* 3.7 20.1 - - + -
351M ILE* 3.6 32.3 - - + -
437M MET* 2.8 24.6 + - + +
438M PHE* 3.5 34.5 - - + +
440M TRP* 1.3 74.5 - - + +
442M VAL* 1.3 66.3 + - + +
444M ARG* 3.2 1.0 + - - -
445M ILE* 2.8 30.5 + - + +
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Residues in contact with VAL 442 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229M LEU* 4.1 9.4 - - + -
265M ILE* 2.2 47.6 - - + +
266M GLU* 2.4 29.6 - - + +
267M THR* 2.4 48.0 - - - +
438M PHE 3.4 9.0 - - - +
439M LEU 3.1 9.6 + - - +
441M MET* 1.3 77.8 - - - +
443M ILE* 1.3 64.0 + - - +
445M ILE* 2.9 19.7 + - - +
446M ASN 2.9 11.4 + - - -
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Residues in contact with ILE 443 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M ILE 4.0 4.9 - - - +
266M GLU* 5.0 12.1 - - + +
439M LEU* 3.0 21.9 + - + +
440M TRP* 2.8 22.1 + - + +
442M VAL* 1.3 80.0 - - + +
444M ARG* 1.3 69.5 + - + +
445M ILE 3.1 0.2 + - - -
446M ASN* 3.1 10.7 + - + +
447M GLN* 2.8 42.9 + - - +
659M LYS* 5.4 6.7 - - - +
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Residues in contact with ARG 444 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342M GLY 3.3 24.7 + - - -
343M PHE* 3.5 26.5 - - + +
344M SER* 4.5 0.8 - - - +
347M GLU* 3.4 32.5 + - - -
440M TRP* 2.7 46.3 + - + +
441M MET 3.7 0.2 - - - +
443M ILE* 1.3 77.5 - - + +
445M ILE* 1.3 66.4 + - - +
447M GLN* 3.0 48.9 + - - +
448M GLN* 3.2 29.9 + - - +
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Residues in contact with ILE 445 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225M ALA* 4.4 9.4 - - + +
228M LEU* 3.9 16.4 - - + -
229M LEU* 3.9 35.7 - - + -
265M ILE* 3.2 29.2 - - + -
341M LEU* 3.9 20.6 - - + -
343M PHE* 4.3 14.8 - - + -
441M MET 2.8 25.9 + - - +
442M VAL* 3.0 9.4 - - - +
444M ARG* 1.3 75.4 - - - +
446M ASN* 1.3 63.7 + - - +
448M GLN* 2.7 20.6 + - - +
449M LEU* 3.0 16.6 + - + +
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Residues in contact with ASN 446 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263M ALA 2.6 20.8 - - - +
264M ASP* 1.2 59.5 + - - +
265M ILE 0.7 95.0 + - - +
266M GLU* 4.4 7.3 + - - +
442M VAL 2.9 5.3 + - - -
443M ILE* 3.2 16.9 - - + +
445M ILE* 1.3 77.0 - - - +
447M GLN* 1.3 62.4 + - + +
449M LEU* 3.1 12.7 + - - -
450M ASP* 3.9 1.6 + - - -
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Residues in contact with GLN 447 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443M ILE* 2.8 37.5 + - - +
444M ARG* 3.2 45.1 + - - +
445M ILE 2.8 0.8 + - - -
446M ASN* 1.3 73.5 - - + +
448M GLN* 1.3 52.0 - - - +
450M ASP* 1.7 68.2 + - + +
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Residues in contact with GLN 448 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221M GLN* 4.0 16.9 - - - +
340M ILE 5.1 0.2 - - - +
341M LEU* 2.6 33.5 + - + +
342M GLY* 3.5 12.8 - - - +
444M ARG* 3.2 42.4 + - - +
445M ILE* 2.7 11.7 + - - +
447M GLN* 1.3 70.2 - - - +
449M LEU* 1.3 69.0 + - + +
450M ASP 2.8 17.4 + - - +
451M THR* 5.4 3.1 - - - +
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Residues in contact with LEU 449 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218M LEU* 4.5 21.1 - - + +
221M GLN* 3.6 33.7 - - + +
222M ILE* 4.7 15.0 - - + +
250M ILE* 5.7 1.1 - - + -
262M SER* 3.1 7.0 - - - -
263M ALA* 2.2 61.4 + - + +
265M ILE* 3.1 41.5 - - + -
341M LEU* 4.5 3.8 - - + -
445M ILE* 3.0 16.7 + - + +
446M ASN 3.1 14.8 + - - +
448M GLN* 1.3 90.8 - - + +
450M ASP* 3.5 8.1 - - - -
451M THR* 5.6 2.2 - - - -
----------------------------------------------------------
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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