Contacts of the helix formed by residues 448 - 481 (chain M) in PDB entry 2DFS
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 448 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446M ILE* 5.4 5.4 - - - -
447M ASN* 1.3 73.5 - - - +
449M PHE* 1.3 69.0 + - - +
450M GLU* 3.4 2.9 - - - -
451M GLN* 2.8 16.9 + - - +
452M PHE* 3.1 21.0 + - - +
559M TYR* 3.7 3.3 - - - -
560M GLN* 4.4 1.8 - - - -
562M GLU 4.0 15.2 + - - -
563M GLY 4.9 0.3 - - - -
564M PHE* 3.7 17.0 - - - -
567M LYS* 2.9 32.7 + - - +
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Residues in contact with PHE 449 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M SER* 4.8 4.3 - - - -
448M SER* 1.3 76.3 + - - +
450M GLU* 1.3 71.3 + - - +
452M PHE* 3.2 4.1 + + - +
453M CYS* 3.0 54.6 + - - -
506M LEU* 4.7 5.4 - - + -
509M LEU* 3.9 19.5 - - + -
564M PHE* 3.6 41.6 - + + -
567M LYS* 3.8 27.8 - - + -
568M ASN* 3.5 30.1 - - + -
636M VAL* 3.8 23.1 - - + -
637M GLY* 3.8 16.4 - - - -
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Residues in contact with GLU 450 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M ARG* 4.6 0.2 - - - +
245M GLU* 3.5 31.5 - - + +
247M SER* 2.7 36.7 + - - +
248M ARG* 5.3 5.4 - - + +
251M PHE* 5.1 3.3 - - - -
448M SER* 3.4 2.6 - - - -
449M PHE* 1.3 79.5 + - + +
451M GLN* 1.3 74.0 + - - +
453M CYS* 3.4 6.3 + - - +
454M ILE* 3.1 29.1 + - - +
567M LYS* 2.6 44.1 + - - +
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Residues in contact with GLN 451 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M ARG* 4.2 2.0 - - - +
442M GLU* 2.9 45.6 + - + +
444M PHE* 3.4 24.5 - - + -
446M ILE 4.3 1.6 - - - +
447M ASN* 3.6 23.7 - - - +
448M SER* 2.8 37.4 + - - +
449M PHE 3.4 0.4 - - - -
450M GLU* 1.3 82.7 - - - +
452M PHE* 1.4 59.5 + - - +
454M ILE* 3.3 8.1 + - - +
455M ASN* 3.0 34.7 + - - -
559M TYR* 4.0 10.3 - - + -
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Residues in contact with PHE 452 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448M SER 3.1 13.9 + - - +
449M PHE* 3.4 11.4 - + - +
451M GLN* 1.4 73.8 - - - +
453M CYS* 1.3 61.6 + - - +
455M ASN* 3.6 1.2 + - - +
456M TYR* 3.0 31.5 + - + +
499M ILE* 3.8 41.5 - - + +
505M VAL* 3.6 24.9 - - + -
506M LEU* 3.8 26.5 - - + -
548M PHE* 3.9 22.9 - + - -
550M ILE* 4.3 13.2 - - + -
552M HIS* 5.2 2.2 - - - -
559M TYR* 3.5 33.3 + + + -
564M PHE* 4.1 15.0 - + + -
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Residues in contact with CYS 453 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449M PHE* 3.0 52.3 + - - +
450M GLU* 3.6 7.2 - - - +
452M PHE* 1.3 77.5 - - - +
454M ILE* 1.3 64.6 + - + +
456M TYR* 3.5 6.8 + - - +
457M ALA 3.1 18.0 + - - -
506M LEU* 5.5 4.7 - - - -
636M VAL* 5.8 0.9 - - - -
637M GLY* 5.5 0.7 - - - -
640M PHE* 3.1 53.2 - - + -
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Residues in contact with ILE 454 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219M ARG* 3.5 19.1 - - - +
245M GLU* 4.4 5.8 - - + +
439M TYR* 3.7 39.9 - - + +
440M GLY 3.2 26.7 - - - +
442M GLU* 3.3 44.4 - - + +
450M GLU 3.1 17.4 + - - +
451M GLN* 3.3 6.5 + - - +
453M CYS* 1.3 74.6 - - + +
455M ASN* 1.3 63.1 + - - +
457M ALA* 3.3 5.0 + - - +
458M ASN* 2.8 27.7 + - - -
640M PHE* 5.6 0.4 - - + -
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Residues in contact with ASN 455 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M PHE* 3.3 27.2 - - + +
442M GLU 2.9 43.8 + - - -
443M THR* 4.5 0.8 + - - -
451M GLN 3.0 13.1 + - - +
452M PHE 4.1 0.7 - - - +
454M ILE* 1.3 73.7 - - - +
456M TYR* 1.4 56.1 + - - +
458M ASN* 3.3 3.7 + - - +
459M GLU* 3.0 34.2 + - - +
552M HIS* 3.9 11.7 - - + +
557M VAL* 4.2 14.6 - - - +
559M TYR* 3.0 29.8 + - - +
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Residues in contact with TYR 456 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452M PHE* 3.0 20.2 + + + +
453M CYS* 3.5 6.5 - - - +
455M ASN* 1.4 74.6 - - - +
457M ALA* 1.3 59.4 + - - +
459M GLU* 3.4 4.7 + - + +
460M LYS* 3.4 24.7 + - + +
496M ILE* 5.0 5.6 - - + -
499M ILE* 3.6 35.7 - - + -
500M GLU* 2.6 40.9 + - + +
506M LEU* 3.5 26.9 - - + -
552M HIS* 4.7 1.2 - - - -
637M GLY 5.2 0.4 - - - -
640M PHE* 3.9 25.6 - + - -
641M ARG* 3.2 31.2 - - - +
644M LEU* 3.5 20.5 - - + +
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Residues in contact with ALA 457 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M LEU* 3.8 29.2 - - + -
438M ILE* 5.5 2.9 - - + -
439M TYR* 4.3 7.9 - - + -
453M CYS 3.1 14.2 + - - +
454M ILE 3.5 9.0 - - - +
456M TYR* 1.3 75.1 - - - +
458M ASN* 1.3 62.7 + - - +
460M LYS* 3.3 5.9 + - - +
461M LEU* 3.1 27.6 + - + +
640M PHE* 4.2 5.2 - - + -
644M LEU* 3.7 18.3 - - + +
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Residues in contact with ASN 458 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162M SER* 5.6 1.2 - - - -
439M TYR* 3.8 13.8 - - - +
440M GLY* 2.9 47.1 + - - -
441M PHE* 3.6 27.5 + - + +
454M ILE* 2.8 29.1 + - - +
455M ASN 3.3 8.3 + - - +
457M ALA* 1.3 76.1 - - - +
459M GLU* 1.3 56.6 + - - +
461M LEU* 3.3 13.7 + - - +
462M GLN* 2.8 32.2 + - - +
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Residues in contact with GLU 459 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M PHE* 4.5 3.4 - - + -
455M ASN 3.0 17.6 + - - +
456M TYR* 3.7 10.5 - - + +
457M ALA 3.4 0.4 - - - -
458M ASN* 1.3 74.1 - - - +
460M LYS* 1.4 60.4 + - - +
462M GLN* 3.6 2.2 + - - -
463M GLN* 3.1 13.0 + - - +
492M ASN* 2.9 45.8 + - - +
495M CYS* 3.5 17.5 - - - -
496M ILE* 4.1 16.2 - - + -
499M ILE* 4.8 4.0 - - + -
552M HIS* 3.0 29.5 + - + +
553M PHE* 2.8 42.0 + - - +
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Residues in contact with LYS 460 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456M TYR* 3.4 11.1 + - + +
457M ALA 3.3 9.6 + - - +
459M GLU* 1.4 78.7 - - - +
461M LEU* 1.3 59.6 + - - +
463M GLN* 3.2 33.6 + - - +
464M GLN 3.4 5.2 + - - -
493M GLN* 5.4 1.2 + - - -
496M ILE* 3.9 21.2 - - + +
500M GLU* 2.6 44.7 + - - -
644M LEU* 3.7 27.4 - - + -
645M HIS* 2.9 28.6 + - + +
648M MET* 3.4 33.2 - - + +
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Residues in contact with LEU 461 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M ILE* 4.4 19.7 - - + -
162M SER* 6.2 1.1 - - - -
436M LEU* 4.5 3.6 - - + -
438M ILE* 4.0 39.3 - - + -
439M TYR* 5.4 0.7 - - + +
457M ALA* 3.1 21.4 + - + +
458M ASN* 3.7 16.4 - - - +
460M LYS* 1.3 72.2 - - - +
462M GLN* 1.3 64.8 + - - +
464M GLN* 3.2 7.2 + - - +
465M PHE* 3.1 21.4 + - - +
644M LEU* 6.1 0.4 - - + -
647M LEU* 5.2 4.3 - - + -
648M MET* 4.0 13.9 - - + -
651M LEU* 3.7 29.8 - - + -
658M TYR* 4.7 5.1 + - + -
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Residues in contact with GLN 462 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441M PHE* 5.3 7.1 - - + -
458M ASN 2.8 22.0 + - - +
459M GLU* 4.1 5.4 - - - +
461M LEU* 1.3 71.4 - - - +
463M GLN* 1.3 56.6 + - - +
465M PHE* 3.3 24.5 + - - +
466M ASN* 2.8 57.8 + - - +
492M ASN* 4.8 2.0 - - - +
553M PHE* 3.4 51.8 - - + -
660M ARG* 2.9 28.6 + - - -
686M GLY* 4.4 3.8 - - - -
690M THR* 3.6 9.1 + - - -
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Residues in contact with GLN 463 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459M GLU 3.1 17.0 + - - +
460M LYS* 3.2 28.2 + - - +
462M GLN* 1.3 74.1 - - - +
464M GLN* 1.4 63.4 + - - +
466M ASN* 3.4 4.9 + - - +
467M MET* 3.1 43.4 + - + +
489M PHE* 5.1 1.1 - - + -
491M ASP* 5.7 2.2 - - - +
492M ASN* 3.3 25.2 + - - +
493M GLN* 2.8 30.5 + - - +
496M ILE* 3.5 12.5 - - + +
648M MET* 4.5 8.3 - - - +
652M ASN* 6.0 0.8 - - - +
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Residues in contact with GLN 464 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160M ILE* 3.9 16.5 - - - +
460M LYS 3.4 2.4 + - - -
461M LEU* 3.2 11.3 + - - +
463M GLN* 1.4 81.1 - - - +
465M PHE* 1.3 57.2 + - - +
467M MET* 3.4 11.3 + - + +
468M HIS* 2.9 28.3 + - + +
648M MET* 3.9 21.3 - - + +
651M LEU* 2.8 39.1 + - - +
652M ASN* 2.9 32.5 + - - +
656M PRO* 4.2 11.3 - - + +
658M TYR* 3.5 15.4 + - - +
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Residues in contact with PHE 465 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE* 4.1 4.5 - - + -
106M VAL* 3.4 34.1 - - + -
461M LEU 3.1 13.2 + - - +
462M GLN* 3.3 34.5 - - - +
464M GLN* 1.3 75.4 - - - +
466M ASN* 1.4 58.8 + - - +
468M HIS* 3.2 3.4 + - - +
469M VAL* 2.9 59.8 + - + +
658M TYR* 3.6 50.3 + + + +
660M ARG* 4.4 8.1 - - - +
690M THR* 3.7 32.5 - - + -
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Residues in contact with ASN 466 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462M GLN* 2.8 49.6 + - - +
463M GLN* 3.4 6.3 + - - +
465M PHE* 1.4 75.1 - - - +
467M MET* 1.3 62.3 + - - +
469M VAL* 3.6 5.1 + - - +
470M PHE* 3.1 23.9 + - - +
489M PHE* 3.6 18.7 - - + -
490M TYR* 3.5 20.1 + - - +
492M ASN* 3.7 18.0 + - - +
553M PHE* 3.7 22.5 - - - -
693M ILE* 6.5 0.4 - - - -
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Residues in contact with MET 467 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463M GLN* 3.1 32.9 + - + +
464M GLN* 3.7 10.8 - - - +
466M ASN* 1.3 72.9 - - - +
468M HIS* 1.3 62.4 + - - +
470M PHE* 3.4 4.8 + - - +
471M LYS* 3.1 23.4 + - - +
489M PHE* 3.9 23.6 - - + -
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Residues in contact with HIS 468 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE* 4.0 10.7 - - + +
464M GLN* 2.9 19.1 + - + +
465M PHE* 3.5 7.9 - - - +
467M MET* 1.3 74.7 - - - +
469M VAL* 1.4 62.9 + - - +
471M LYS* 3.4 10.8 + - + +
472M LEU* 3.1 52.7 + - + +
655M THR* 3.3 27.9 - - + +
656M PRO* 3.2 46.8 + - + +
658M TYR* 4.1 3.1 - - + +
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Residues in contact with VAL 469 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE* 3.6 23.6 - - + -
465M PHE* 2.9 52.0 + - + +
466M ASN* 3.9 5.6 - - - +
468M HIS* 1.4 73.9 - - - +
470M PHE* 1.3 58.0 + - - +
472M LEU* 3.3 5.7 + - + +
473M GLU* 2.9 40.3 + - + +
690M THR* 5.7 3.1 - - + -
694M SER* 6.2 0.4 - - - +
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Residues in contact with PHE 470 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466M ASN 3.1 18.9 + - - +
467M MET* 3.5 5.8 - - - +
469M VAL* 1.3 76.3 - - - +
471M LYS* 1.4 62.3 + - - +
473M GLU* 3.5 6.3 + - - +
474M GLN* 3.1 59.3 + - - +
484M TRP 5.9 0.9 - - - -
487M ILE* 3.5 46.7 - - + -
488M ASP 4.3 2.2 - - - -
489M PHE* 3.6 41.7 - + + -
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Residues in contact with LYS 471 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467M MET 3.1 14.0 + - - +
468M HIS* 3.7 14.1 - - + +
470M PHE* 1.4 75.9 - - - +
472M LEU* 1.3 64.5 + - + +
474M GLN* 3.3 19.1 + - + +
475M GLU* 2.6 66.1 + - - +
478M MET* 5.6 2.0 - - - +
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Residues in contact with LEU 472 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105M ILE* 3.9 39.3 - - + -
468M HIS* 3.1 39.6 + - + +
469M VAL* 3.3 4.9 + - - +
471M LYS* 1.3 73.5 - - + +
473M GLU* 1.4 59.3 + - - +
475M GLU* 3.2 21.2 + - + +
476M GLU* 3.0 30.2 + - - +
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Residues in contact with GLU 473 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469M VAL* 2.9 29.9 + - + +
470M PHE* 3.8 7.0 - - - +
472M LEU* 1.4 73.4 - - - +
474M GLN* 1.3 57.0 + - - +
476M GLU* 3.5 8.2 + - - +
477M TYR* 2.9 44.7 + - - -
487M ILE* 3.8 22.1 - - + +
701M ARG* 2.6 48.6 + - - -
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Residues in contact with GLN 474 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470M PHE* 3.1 50.5 + - + +
471M LYS* 3.3 22.1 + - + +
473M GLU* 1.3 75.1 - - - +
475M GLU* 1.3 55.6 + - + +
477M TYR* 3.6 3.6 - - - +
478M MET* 2.9 44.8 + - + +
484M TRP* 4.6 25.6 + - + +
487M ILE* 4.2 15.9 - - + -
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Residues in contact with GLU 475 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471M LYS* 2.6 52.4 + - - +
472M LEU* 3.2 21.3 + - + +
474M GLN* 1.3 75.0 - - + +
476M GLU* 1.3 57.2 + - - +
478M MET* 3.4 18.4 + - + +
479M LYS* 3.0 27.5 + - - +
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Residues in contact with GLU 476 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472M LEU 3.0 16.6 + - - +
473M GLU* 3.6 9.0 - - - +
475M GLU* 1.3 70.6 - - - +
477M TYR* 1.4 67.0 + - + +
479M LYS* 3.3 20.5 + - - +
480M GLU* 3.3 13.9 + - - +
701M ARG* 2.7 41.1 + - - +
748M LYS* 2.6 38.3 + - - -
750M PHE* 3.3 10.0 - - + -
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Residues in contact with TYR 477 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473M GLU* 2.9 53.8 + - - +
474M GLN* 3.6 7.6 - - - +
476M GLU* 1.4 70.3 - - - +
478M MET* 1.4 60.3 + - - +
480M GLU* 3.4 4.7 + - - -
481M GLN 3.1 4.7 + - - -
482M ILE* 3.1 51.4 + - + +
483M PRO 3.6 26.0 - - - -
484M TRP* 4.2 7.2 - - + -
486M LEU* 3.8 24.7 - - + +
487M ILE* 3.6 34.6 - - + +
697M GLY* 5.0 1.7 - - - -
698M PHE* 3.8 20.9 + + - +
701M ARG* 4.1 3.2 + - - -
750M PHE* 4.0 22.9 - + - -
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Residues in contact with MET 478 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471M LYS* 5.6 2.5 - - - +
474M GLN* 2.9 31.7 + - + +
475M GLU* 3.7 24.0 - - + +
476M GLU 3.4 0.2 - - - -
477M TYR* 1.4 73.6 - - - +
479M LYS* 1.4 63.4 + - - +
481M GLN* 3.1 19.7 + - - +
482M ILE 5.1 1.6 - - - +
484M TRP* 4.9 23.8 - - + -
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Residues in contact with LYS 479 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475M GLU 3.0 14.0 + - - +
476M GLU* 3.3 18.1 + - - +
478M MET* 1.4 73.8 - - - +
480M GLU* 1.3 91.5 + - + +
481M GLN* 3.5 2.2 + - - +
746M LYS* 4.0 23.3 - - + +
747M THR* 3.2 16.0 + - - +
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Residues in contact with GLU 480 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476M GLU* 3.3 13.0 + - - +
477M TYR 3.9 6.7 - - - +
478M MET 3.2 0.6 - - - -
479M LYS* 1.3 104.5 + - + +
481M GLN* 1.4 69.0 + - - +
482M ILE* 4.0 10.5 - - + -
745M GLY* 3.3 15.0 - - - -
746M LYS* 2.9 28.3 + - - +
747M THR* 2.8 33.0 + - - -
748M LYS* 2.9 34.4 + - - +
750M PHE* 3.7 17.7 - - + -
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Residues in contact with GLN 481 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477M TYR 3.1 1.2 + - - -
478M MET* 3.1 17.9 + - - +
479M LYS 4.7 3.4 - - - +
480M GLU* 1.4 78.7 - - - +
482M ILE* 1.3 61.6 + - - +
483M PRO* 4.5 2.1 - - - +
744M PHE 5.3 2.8 - - - +
746M LYS* 3.3 36.0 - - + +
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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) + - + + + + + -
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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