Contacts of the helix formed by residues 432 - 463 (chain G) in PDB entry 5JLH
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 432 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D SER 6.0 2.2 - - - +
382G ARG* 5.1 3.6 - - - +
387G ASP* 3.4 34.5 - - - +
388G GLN 4.0 3.4 - - - +
431G GLN* 1.3 76.6 - - - +
433G LYS* 1.3 64.0 + - - +
434G GLU* 3.2 11.1 + - + +
435G GLN* 2.6 51.2 + - + +
436G ALA* 3.1 21.3 + - - +
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Residues in contact with LYS 433 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G LEU* 3.4 29.8 + - + +
381G LYS* 4.4 0.2 - - - -
382G ARG* 3.7 46.9 - - + +
387G ASP 4.1 3.0 + - - -
389G ALA* 3.9 20.1 - - + +
432G THR* 1.3 71.2 - - - +
434G GLU* 1.3 70.2 + - + +
436G ALA* 3.5 3.4 + - - +
437G ASP* 2.9 53.2 + - - +
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Residues in contact with GLU 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382G ARG* 6.3 1.1 - - - +
432G THR* 3.2 8.4 + - - +
433G LYS* 1.3 84.4 + - + +
435G GLN* 1.3 58.0 + - + +
437G ASP* 3.2 13.6 + - - +
438G PHE* 2.9 54.5 + - + -
612G MET* 5.2 14.0 - - - +
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Residues in contact with GLN 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D SER 6.4 0.2 - - - -
145D GLY* 6.3 1.4 - - - -
429G LYS* 5.1 10.9 + - - +
430G ALA 4.1 4.3 - - - +
431G GLN* 3.5 23.8 + - + +
432G THR* 2.6 46.5 + - + +
434G GLU* 1.3 74.7 - - + +
436G ALA* 1.3 56.2 + - - +
438G PHE* 3.2 14.9 + - + +
439G ALA* 2.9 25.8 + - - +
615G MET* 6.0 4.5 - - + -
617G PRO* 4.6 5.9 - - + +
666G MET* 5.3 11.5 - - - -
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Residues in contact with ALA 436 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380G LEU* 3.2 26.0 - - + -
389G ALA* 6.2 0.2 - - + -
415G LEU* 4.2 12.1 - - + +
416G LEU* 5.0 9.4 - - + -
431G GLN* 3.8 21.5 + - + +
432G THR 3.1 16.5 + - - +
433G LYS* 4.0 1.1 - - - +
435G GLN* 1.3 79.7 - - - +
437G ASP* 1.3 60.2 + - - +
439G ALA* 3.0 6.5 + - - +
440G LEU* 2.9 25.1 + - - +
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Residues in contact with ASP 437 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G ARG* 5.5 9.3 + - - +
380G LEU* 3.2 26.9 + - - +
433G LYS* 2.9 44.8 + - - +
434G GLU* 3.2 16.2 + - - +
436G ALA* 1.3 74.5 - - - +
438G PHE* 1.3 65.5 + - + +
440G LEU* 3.2 12.6 + - + +
441G GLU* 3.0 35.9 + - - +
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Residues in contact with PHE 438 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ARG* 5.9 0.4 - - - -
434G GLU* 2.9 53.2 + - + -
435G GLN* 3.6 11.7 - - + +
437G ASP* 1.3 77.5 - - + +
439G ALA* 1.3 53.3 + - - +
441G GLU* 3.2 19.9 + - - +
442G ALA* 2.7 35.3 + - - +
612G MET* 4.0 38.8 - - + -
615G MET* 3.7 46.7 - - + +
616G ASP* 5.1 0.9 - - - -
617G PRO* 3.6 20.6 - - + +
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Residues in contact with ALA 439 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415G LEU* 4.1 15.0 - - + -
431G GLN* 4.9 1.6 - - - +
435G GLN 2.9 13.0 + - - +
436G ALA* 3.0 11.9 + - - +
438G PHE* 1.3 76.2 - - - +
440G LEU* 1.3 57.0 + - - +
442G ALA* 3.2 1.9 + - - +
443G LEU* 2.9 37.5 + - + +
617G PRO* 3.7 19.0 + - + +
618G LEU* 5.0 0.2 - - - +
619G ASN* 4.1 24.5 - - + +
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Residues in contact with LEU 440 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329G PHE* 4.6 3.1 - - + -
375G PHE* 3.8 27.4 - - + +
378G ILE* 3.9 36.1 - - + +
380G LEU* 3.5 33.2 - - + +
411G PHE* 4.6 8.3 - - + -
415G LEU* 3.3 30.5 - - + -
436G ALA 2.9 14.7 + - - +
437G ASP* 3.4 12.6 - - - +
439G ALA* 1.3 75.3 - - - +
441G GLU* 1.3 61.0 + - + +
443G LEU* 3.4 3.7 + - + +
444G ALA* 2.9 28.1 + - - +
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Residues in contact with GLU 441 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292G ILE* 3.7 31.9 - - + +
293G ARG* 4.6 16.6 + - - -
328G ARG* 3.0 32.3 + - - +
329G PHE* 3.9 15.5 - - + -
437G ASP* 3.0 19.0 + - - +
438G PHE* 3.6 23.1 - - - +
440G LEU* 1.3 75.7 - - + +
442G ALA* 1.3 57.8 + - - +
444G ALA* 3.2 4.4 - - - +
445G LYS* 2.9 38.7 + - + +
612G MET* 5.1 4.2 - - - +
615G MET 5.6 2.7 - - - +
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Residues in contact with ALA 442 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438G PHE 2.7 16.7 + - - +
439G ALA 3.2 4.5 + - - +
441G GLU* 1.3 73.2 - - - +
443G LEU* 1.3 54.5 + - - +
445G LYS* 2.8 7.5 + - - +
446G ALA* 2.6 38.1 + - - +
615G MET 5.7 0.4 + - - -
616G ASP* 2.9 29.5 - - - +
617G PRO 3.0 29.2 - - - +
618G LEU* 4.2 7.0 - - + -
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Residues in contact with LEU 443 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375G PHE* 3.7 26.0 - - + -
411G PHE* 5.0 4.9 - - + -
415G LEU* 5.1 6.3 - - + -
439G ALA* 2.9 26.6 + - + +
440G LEU* 3.8 4.0 - - + +
442G ALA* 1.3 72.1 - - - +
444G ALA* 1.4 58.2 + - - +
446G ALA* 4.5 2.2 - - - -
447G THR* 2.5 36.4 + - - +
618G LEU* 3.4 25.5 - - + +
619G ASN* 5.6 3.1 - - + +
622G VAL* 3.4 37.7 - - + -
623G ALA* 4.9 5.4 - - - +
626G LEU* 4.3 21.8 - - + -
638G TRP* 4.4 7.2 - - + -
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Residues in contact with ALA 444 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291G ALA* 6.5 0.4 - - + -
292G ILE* 5.3 1.1 - - + -
329G PHE* 3.3 32.3 - - + -
372G VAL* 3.2 26.4 - - + +
375G PHE* 3.8 13.3 - - + -
440G LEU 2.9 11.6 + - - +
441G GLU 3.2 10.5 - - - +
443G LEU* 1.4 77.4 - - - +
445G LYS* 1.3 60.4 + - + +
447G THR* 3.2 2.6 - - - -
448G TYR* 2.9 24.4 + - - +
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Residues in contact with LYS 445 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G LYS* 3.7 42.8 - - + +
289G SER* 4.1 13.7 - - - +
291G ALA* 5.5 2.2 - - + -
292G ILE* 3.5 34.7 - - + +
372G VAL* 5.3 0.2 - - - -
441G GLU* 2.9 28.3 + - + +
442G ALA* 2.8 12.7 + - - +
444G ALA* 1.3 73.2 - - + +
446G ALA* 1.3 56.4 + - - +
448G TYR* 3.2 8.5 + - - +
449G GLU* 2.9 27.9 + - - +
612G MET 5.3 0.4 + - - -
613G LYS* 3.6 12.7 + - - +
615G MET 3.7 12.5 + - - +
616G ASP* 4.5 3.6 - - - +
670G VAL* 3.3 31.9 - - - +
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Residues in contact with ALA 446 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288G LYS* 4.3 7.7 - - - +
442G ALA 2.6 22.2 + - - +
443G LEU* 4.3 0.9 - - - +
445G LYS* 1.3 73.3 - - - +
447G THR* 1.3 56.2 + - - +
449G GLU* 3.2 8.6 + - - +
450G ARG* 2.9 38.8 + - + +
616G ASP* 5.2 1.3 - - - +
618G LEU* 4.5 11.2 - - + -
638G TRP* 4.0 17.5 - - + -
668G ARG* 4.1 20.0 - - - +
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Residues in contact with THR 447 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368G MET* 3.3 30.8 - - + +
371G ALA* 5.6 1.8 - - + -
372G VAL* 4.5 14.6 - - + -
375G PHE* 4.1 15.4 - - + -
443G LEU* 2.5 27.0 + - - +
444G ALA* 3.2 6.3 - - - +
446G ALA* 1.3 74.3 - - - +
448G TYR* 1.3 62.3 + - - +
450G ARG* 3.3 4.4 + - - +
451G LEU* 2.9 28.0 + - + +
626G LEU* 4.7 2.1 - - - +
638G TRP* 3.4 25.9 + - + +
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Residues in contact with TYR 448 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G PHE* 2.6 46.0 + + + +
286G LEU* 4.2 19.7 - - + -
288G LYS* 5.2 3.8 - - + -
291G ALA* 4.8 7.4 - - + -
301G PHE* 3.6 32.9 - + - -
303G ILE* 4.0 6.2 - - + +
304G PHE* 3.8 28.0 - + - -
369G VAL* 5.1 2.9 - - + -
372G VAL* 4.2 15.0 - - + -
444G ALA 2.9 12.9 + - - +
445G LYS* 3.5 10.3 - - - +
447G THR* 1.3 78.4 - - - +
449G GLU* 1.3 58.7 + - - +
451G LEU* 3.2 27.0 + - + +
452G PHE* 2.9 36.3 + + + +
----------------------------------------------------------
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Residues in contact with GLU 449 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G LEU* 4.2 26.7 - - + -
288G LYS* 3.9 28.2 + - + +
445G LYS 2.9 12.9 + - - +
446G ALA* 3.5 9.1 - - - +
448G TYR* 1.3 78.6 - - - +
450G ARG* 1.3 64.4 + - - +
452G PHE* 3.2 4.1 + - + +
453G ARG* 2.9 61.7 + - + +
668G ARG* 4.1 9.7 + - - -
673G LEU* 5.5 2.1 - - - +
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Residues in contact with ARG 450 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446G ALA* 2.9 27.5 + - - +
447G THR* 3.6 4.9 - - - +
449G GLU* 1.3 82.5 + - - +
451G LEU* 1.3 58.7 + - - +
453G ARG* 3.2 26.2 + - - +
454G TRP* 2.9 29.3 + - - +
618G LEU* 5.2 0.6 - - - +
637G ILE* 3.2 30.3 + - + +
638G TRP* 3.1 59.8 - - + +
640G ASP* 3.0 37.4 + - - +
664G ARG* 3.5 16.4 - - - +
668G ARG* 5.0 9.9 - - - +
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Residues in contact with LEU 451 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G PHE* 3.9 24.5 - - + -
365G MET* 4.9 13.0 - - + -
368G MET* 3.6 40.8 - - + +
369G VAL* 3.6 24.0 - - + +
372G VAL* 6.1 0.4 - - + -
447G THR* 2.9 12.8 + - + +
448G TYR* 3.3 28.3 - - + +
450G ARG* 1.3 76.7 - - - +
452G PHE* 1.3 57.2 - - - +
454G TRP* 3.2 16.3 + - + +
455G LEU* 2.9 24.8 + - + +
633G LEU* 5.8 0.4 - - + -
637G ILE* 4.2 10.2 - - - +
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Residues in contact with PHE 452 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G LEU* 4.4 15.0 - - + +
248G PHE* 4.1 32.1 - + + -
249G GLY* 4.3 12.3 - - - -
262G PHE* 3.7 37.0 - + + -
283G THR* 3.3 36.8 - - + -
286G LEU* 4.4 23.1 - - + -
448G TYR* 2.9 22.3 + + + +
449G GLU* 3.4 12.6 - - + +
451G LEU* 1.3 78.7 - - + +
453G ARG* 1.3 66.1 + - + +
455G LEU* 3.2 9.8 + - + +
456G VAL* 3.0 20.7 + - + +
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Residues in contact with ARG 453 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G THR* 5.3 4.5 - - - +
449G GLU* 2.9 45.7 + - + +
450G ARG* 3.2 25.2 + - - +
452G PHE* 1.3 81.5 - - + +
454G TRP* 1.3 60.8 + - - +
456G VAL* 2.7 31.6 - - + +
457G LEU* 3.0 20.8 + - + +
640G ASP* 5.7 4.6 + - - -
680G ARG* 5.2 13.5 - - - +
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Residues in contact with TRP 454 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G PHE* 5.8 1.8 - + - -
361G GLU* 5.1 15.5 - - + -
365G MET* 4.0 36.6 - - + -
450G ARG 2.9 13.6 + - - +
451G LEU* 3.2 16.1 + - + +
453G ARG* 1.3 75.3 - - - +
455G LEU* 1.3 81.2 + - + +
457G LEU* 3.2 10.1 + - + +
458G ARG* 2.8 62.9 + - + +
633G LEU* 3.6 27.5 - - + +
636G GLU* 2.9 43.5 + - - -
637G ILE* 4.0 15.9 - - + -
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Residues in contact with LEU 455 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ILE* 3.5 34.5 - - + -
245G LEU* 4.0 18.4 - - + -
248G PHE* 3.5 36.1 - - + -
352G LEU* 5.1 0.9 - - + -
357G PHE* 4.8 14.8 - - + -
365G MET* 4.3 15.7 - - + -
451G LEU* 2.9 13.1 + - + +
452G PHE* 3.4 11.2 - - + +
454G TRP* 1.3 90.2 - - + +
456G VAL* 1.3 57.8 + - - +
458G ARG* 3.7 0.4 - - - -
459G LEU* 2.8 41.6 + - + +
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Residues in contact with VAL 456 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245G LEU* 5.4 8.0 - - + +
281G ILE* 3.7 35.9 - - + +
282G GLU* 4.6 1.1 - - - -
283G THR* 4.0 35.7 - - + +
452G PHE* 3.0 10.4 + - + +
453G ARG* 2.7 32.3 + - + +
455G LEU* 1.3 77.5 - - - +
457G LEU* 1.3 65.5 + - + +
459G LEU* 3.3 7.5 + - + +
460G ASN* 2.9 33.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 457 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G ARG* 3.0 28.1 + - + +
454G TRP* 3.8 11.0 - - + +
456G VAL* 1.3 78.7 - - + +
458G ARG* 1.3 60.9 + - - +
460G ASN* 3.1 17.7 + - + +
461G ARG* 2.9 26.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 458 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G GLY 4.8 5.5 + - - -
357G PHE* 3.2 37.6 - - + -
361G GLU* 3.5 29.8 + - - -
454G TRP* 2.8 54.7 + - + +
455G LEU* 4.0 3.1 - - + +
457G LEU* 1.3 76.3 - - - +
459G LEU* 1.3 61.4 + - - +
461G ARG* 3.2 33.5 + - - +
462G ALA 3.1 16.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 459 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241G ALA* 4.3 25.6 - - + -
244G ILE* 5.1 5.8 - - + -
245G LEU* 4.6 24.5 - - + -
281G ILE* 5.2 9.0 - - + -
355G LEU* 4.0 31.0 - - + -
357G PHE* 3.9 8.7 - - + -
455G LEU* 2.8 28.7 + - + +
456G VAL* 3.5 7.4 - - + +
458G ARG* 1.3 72.6 - - - +
460G ASN* 1.4 62.2 + - - +
461G ARG 3.1 1.6 - - - -
462G ALA* 2.9 30.1 + - + +
463G LEU* 2.9 23.9 + - + +
----------------------------------------------------------
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Residues in contact with ASN 460 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G ASN* 3.7 16.9 - - + +
281G ILE* 2.9 51.3 + - - +
282G GLU* 5.4 0.6 - - - +
456G VAL* 2.9 23.6 + - - +
457G LEU* 3.1 18.7 + - + +
459G LEU* 1.4 75.7 - - - +
461G ARG* 1.3 52.8 + - - +
463G LEU* 2.7 42.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG 461 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G LEU 2.9 12.8 + - - +
458G ARG* 3.2 38.7 - - - +
460G ASN* 1.3 75.1 - - - +
462G ALA* 1.3 58.0 + - - +
463G LEU 3.0 11.6 + - - +
464G ASP* 3.5 16.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 462 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237G GLN* 3.1 19.2 + - - +
355G LEU* 3.5 27.6 - - + +
357G PHE* 3.7 24.2 - - + -
458G ARG* 3.1 5.7 + - - +
459G LEU* 2.9 21.1 + - + +
461G ARG* 1.3 74.7 - - - +
463G LEU* 1.3 56.7 + - - +
464G ASP* 3.8 10.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 463 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G GLU* 5.0 10.3 - - + +
237G GLN* 3.3 31.0 - - + +
238G LEU* 4.5 19.3 - - + -
279G ALA* 3.6 29.4 - - + +
280G ASN* 4.1 4.7 - - - -
281G ILE* 4.4 13.0 - - + -
459G LEU* 2.9 20.5 + - + +
460G ASN* 2.7 50.9 - - - +
461G ARG* 3.0 8.5 + - - +
462G ALA* 1.3 75.8 - - - +
464G ASP* 1.3 62.5 + - - +
465G ARG* 4.2 0.5 + - - +
----------------------------------------------------------
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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