Contacts of the helix formed by residues 462 - 492 (chain A) in PDB entry 4IKV
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 ASN 462 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A PHE* 2.9 38.3 + - - +
459A THR* 2.9 20.5 + - - +
461A GLU* 1.3 78.1 - - + +
463A GLU* 1.3 54.3 + - - +
464A THR 3.3 2.7 - - - -
465A ALA* 3.3 25.5 + - - +
466A TYR* 2.8 39.6 + - - +
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 4.0 16.4 + - - -
323A ARG* 2.7 51.9 + - - +
385A ILE 5.2 1.7 - - - +
386A LEU* 5.1 4.8 - - - +
389A GLY* 4.1 11.4 + - - -
458A TYR* 4.1 14.1 + - + -
459A THR 2.9 13.5 + - - +
460A PRO* 3.6 14.9 + - - +
461A GLU 3.5 2.2 - - - -
462A ASN* 1.3 77.0 - - - +
464A THR* 1.3 68.5 + - - +
466A TYR* 3.1 6.9 + - - +
467A PHE* 3.0 44.5 + - + -
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Residues in contact with THR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 4.1 32.0 + - + +
389A GLY 5.4 0.5 - - - -
390A HIS* 4.3 32.9 + - + +
461A GLU 5.4 0.6 + - - -
462A ASN 3.3 0.2 - - - -
463A GLU* 1.3 82.0 + - - +
465A ALA* 1.3 57.1 + - - +
468A GLY* 2.9 28.2 + - - -
608A OLA 4.0 21.4 - - + +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ASN* 3.3 29.1 + - - +
464A THR* 1.3 79.7 - - - +
466A TYR* 1.3 63.7 + - - +
469A THR* 2.8 34.1 + - - +
608A OLA 3.7 25.7 - - + +
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Residues in contact with TYR 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLN* 2.6 39.3 + - - -
315A ILE* 3.6 19.9 - - + +
382A PHE* 4.2 5.8 - + - -
451A ASN 5.4 0.7 + - - -
454A LEU* 3.5 29.9 + - + +
455A VAL* 6.0 0.2 - - - +
457A PHE* 3.8 30.1 - - + +
458A TYR* 3.7 26.9 - + + -
462A ASN* 2.8 25.0 + - - +
463A GLU* 3.1 8.0 + - - +
465A ALA* 1.3 73.7 - - - +
467A PHE* 1.3 73.0 + + - +
469A THR* 4.2 1.0 - - - -
470A ILE* 3.2 49.1 + - + +
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Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ILE* 3.9 20.9 - - + -
316A LEU* 4.0 19.3 - - + -
319A TYR* 4.1 14.8 - + - -
382A PHE* 3.6 47.0 - + - +
385A ILE* 3.6 26.0 - - + -
386A LEU* 3.8 18.8 - - + -
458A TYR* 3.8 22.7 - + - -
463A GLU* 3.0 43.7 + - + +
466A TYR* 1.3 80.8 - + - +
468A GLY* 1.3 58.5 + - - +
471A GLY* 2.8 29.3 + - - -
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Residues in contact with GLY 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 4.2 7.0 - - - +
386A LEU* 3.5 20.1 - - - +
464A THR 2.9 14.8 + - - -
467A PHE* 1.3 78.9 - - - +
469A THR* 1.3 53.6 + - - +
472A GLY* 2.7 31.5 + - - -
608A OLA 3.6 22.5 - - - +
611A OLA 4.4 0.9 - - - +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ALA* 2.8 26.4 + - - +
466A TYR* 4.2 1.8 - - - -
468A GLY* 1.3 73.9 - - - +
470A ILE* 1.3 64.2 + - + +
473A ALA* 2.9 29.0 + - + +
608A OLA 3.9 31.4 - - + +
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Residues in contact with ILE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 4.7 8.9 - - - +
307A ALA* 6.0 2.0 - - + -
308A ILE* 3.9 15.9 - - + -
311A GLN* 4.4 9.4 - - - +
382A PHE* 3.7 21.1 - - + -
454A LEU* 4.4 17.3 - - + -
466A TYR* 3.2 61.1 + - + +
469A THR* 1.3 78.8 - - + +
471A GLY* 1.3 66.9 + - - +
473A ALA* 3.3 6.5 + - - +
474A ALA* 3.1 21.3 + - - +
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Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 4.7 0.7 - - - -
379A GLY* 3.4 27.9 - - - -
382A PHE* 3.7 9.1 - - - -
383A ILE* 4.3 4.9 - - - -
467A PHE 2.8 19.4 + - - -
470A ILE* 1.3 77.6 - - - +
472A GLY* 1.3 55.7 + - - +
474A ALA 3.2 1.7 + - - -
475A LEU* 2.9 32.1 + - - +
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Residues in contact with GLY 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 4.2 2.4 - - - +
468A GLY 2.7 24.0 + - - -
469A THR 4.0 0.2 - - - -
471A GLY* 1.3 71.5 - - - +
473A ALA* 1.3 57.6 + - - +
475A LEU* 3.2 5.1 + - - +
476A VAL* 2.8 33.4 + - - +
608A OLA 3.9 12.1 - - - -
611A OLA 4.1 23.5 - - - +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 3.9 18.6 - - + -
469A THR* 2.9 21.1 + - + +
470A ILE* 3.7 7.4 - - - +
471A GLY 3.3 0.2 - - - -
472A GLY* 1.3 76.7 - - - +
474A ALA* 1.3 58.8 + - - +
476A VAL* 3.4 0.9 + - - +
477A LEU* 2.9 36.5 + - + +
608A OLA 3.8 22.8 - - + +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A MET* 4.1 9.6 - - + +
308A ILE* 3.7 20.9 - - + -
375A LEU* 3.4 33.7 - - + +
379A GLY* 3.6 18.2 - - - -
470A ILE 3.1 6.9 + - - +
471A GLY 3.6 7.6 - - - +
473A ALA* 1.3 78.5 - - - +
475A LEU* 1.3 56.6 + - - +
477A LEU* 4.7 0.4 - - - -
478A GLY* 2.8 26.3 + - - -
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Residues in contact with LEU 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.5 40.5 - - + +
379A GLY* 4.2 1.8 - - - -
380A LEU* 3.9 7.0 - - + +
383A ILE* 3.9 25.1 - - + -
471A GLY 2.9 20.2 + - - +
472A GLY* 3.5 5.6 - - - +
474A ALA* 1.3 75.5 - - - +
476A VAL* 1.3 61.2 + - - +
478A GLY 3.3 0.7 + - - -
479A LEU* 3.0 27.9 + - + +
610A OLA 4.0 24.0 - - + -
611A OLA 4.0 38.4 - - + -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A GLY 2.8 23.7 + - - +
473A ALA 3.8 3.8 - - - +
475A LEU* 1.3 72.7 - - - +
477A LEU* 1.3 64.6 + - + +
479A LEU* 3.3 10.5 + - + +
480A ILE* 3.1 40.5 + - + +
608A OLA 4.0 40.6 - - + -
611A OLA 4.4 20.4 - - + -
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO 5.9 0.9 - - - +
300A VAL* 3.9 27.8 - - + +
301A ALA* 5.4 3.1 - - + +
304A MET* 3.5 24.0 - - + -
375A LEU* 3.7 18.8 - - + +
473A ALA* 2.9 27.3 + - + +
474A ALA* 4.7 0.4 - - - -
476A VAL* 1.3 78.4 - - + +
478A GLY* 1.3 59.1 + - - +
480A ILE* 3.3 13.1 + - + +
481A LEU* 2.9 30.0 + - - +
608A OLA 5.2 13.5 - - + -
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Residues in contact with GLY 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ALA* 3.6 10.9 - - - +
375A LEU* 3.6 17.9 - - - +
376A LEU* 4.0 15.3 - - - -
474A ALA 2.8 18.4 + - - -
475A LEU 3.8 1.1 - - - -
477A LEU* 1.3 76.4 - - - +
479A LEU* 1.3 57.4 + - - +
481A LEU* 3.4 3.7 + - - -
482A LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.7 25.4 - - + -
475A LEU* 3.0 16.8 + - + +
476A VAL* 3.5 10.8 - - + +
478A GLY* 1.3 75.3 - - - +
480A ILE* 1.3 64.9 + - + +
482A LEU* 3.3 11.5 + - + +
483A ALA* 3.2 20.6 + - - +
611A OLA 3.8 28.7 - - + -
612A OLB 4.3 38.2 - - + +
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Residues in contact with ILE 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 3.1 33.9 + - + +
477A LEU* 3.3 13.4 + - + +
479A LEU* 1.3 79.8 - - + +
481A LEU* 1.3 64.3 + - - +
483A ALA* 3.1 16.5 + - + +
484A ILE* 3.1 29.5 + - + +
608A OLA 6.1 1.1 - - + -
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Residues in contact with LEU 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 4.2 13.2 - - + +
298A LEU* 4.0 13.2 - - + -
301A ALA* 3.6 30.7 - - + -
368A PRO* 3.9 10.1 - - + +
371A PHE* 3.7 24.7 - - + -
372A ALA* 3.7 12.3 - - + +
375A LEU* 5.5 0.2 - - + -
477A LEU 2.9 18.4 + - - +
478A GLY* 3.7 5.6 - - - +
480A ILE* 1.3 76.5 - - - +
482A LEU* 1.3 57.8 + - - +
484A ILE* 3.2 7.5 + - + -
485A ALA* 2.8 32.2 + - - +
488A ILE* 3.9 25.4 - - + -
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Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLN* 4.1 18.4 - - + +
372A ALA* 3.7 23.5 - - + +
373A LEU* 5.4 8.3 - - + +
376A LEU* 4.2 20.4 - - + -
478A GLY 3.0 10.2 + - - +
479A LEU* 3.3 16.8 - - + +
481A LEU* 1.3 75.1 - - - +
483A ALA* 1.3 62.8 + - - +
485A ALA* 3.3 9.2 + - - +
486A PRO* 3.7 0.5 - - - +
612A OLB 2.7 75.2 + - + +
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Residues in contact with ALA 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU 3.2 8.2 + - - +
480A ILE* 3.1 13.8 + - + +
482A LEU* 1.3 81.3 - - - +
484A ILE* 1.3 61.5 + - + +
486A PRO* 3.3 15.1 - - - +
612A OLB 4.3 15.2 - - + +
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Residues in contact with ILE 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 4.0 22.2 - - + -
480A ILE* 3.1 30.0 + - + +
481A LEU* 3.5 13.2 - - + +
483A ALA* 1.3 78.5 - - + +
485A ALA* 1.3 64.0 + - - +
486A PRO* 3.3 5.2 - - - -
487A ARG* 3.5 8.1 + - + +
488A ILE* 3.4 40.2 + - + +
605A OLA 4.8 15.2 - - + +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 4.9 2.9 + - - +
368A PRO* 3.7 26.3 - - + +
369A GLN* 3.9 24.5 - - + +
481A LEU 2.8 16.8 + - - +
482A LEU* 3.3 13.7 - - - +
484A ILE* 1.3 77.7 - - - +
486A PRO* 1.4 67.0 - - + +
488A ILE* 3.8 3.8 - - - +
489A GLY* 2.8 23.4 + - - -
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLN* 5.7 1.3 - - - +
482A LEU 3.7 8.1 - - - +
483A ALA 3.3 18.2 - - - +
484A ILE* 3.3 2.2 - - - -
485A ALA* 1.4 90.7 - - + +
487A ARG* 1.3 60.5 + - - +
489A GLY* 3.5 1.3 + - - -
490A ARG* 3.2 44.8 + - - +
612A OLB 3.9 21.8 - - - +
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 5.8 3.0 - - - -
484A ILE* 3.5 7.6 + - + +
485A ALA 3.4 0.6 - - - -
486A PRO* 1.3 76.0 - - - +
488A ILE* 1.3 67.2 + - - +
490A ARG* 3.3 30.4 + - - +
491A LEU* 3.2 54.8 + - - +
605A OLA 4.3 23.2 - - + +
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Residues in contact with ILE 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ALA* 3.9 20.2 - - + +
297A PRO* 3.7 28.0 - - + -
298A LEU* 4.2 14.1 - - + -
368A PRO* 3.5 18.6 - - + -
427A LEU* 4.4 5.2 - - + +
481A LEU* 3.9 13.9 - - + -
484A ILE* 3.4 31.6 - - + +
485A ALA* 3.3 7.3 + - - +
487A ARG* 1.3 76.0 - - - +
489A GLY* 1.3 62.5 + - - +
491A LEU* 3.2 16.8 + - - +
492A MET* 3.4 16.3 + - + +
605A OLA 4.0 17.3 - - + -
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Residues in contact with GLY 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 5.1 8.7 - - - -
368A PRO* 3.6 19.1 - - - +
485A ALA 2.8 20.9 + - - -
486A PRO* 3.8 1.6 - - - -
488A ILE* 1.3 73.6 - - - +
490A ARG* 1.3 60.2 + - - +
492A MET* 3.2 21.4 + - - +
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A PRO* 3.2 43.0 + - - +
487A ARG* 3.7 36.8 - - - +
488A ILE 3.3 0.6 - - - -
489A GLY* 1.3 76.7 - - - +
491A LEU* 1.3 63.3 + - + +
492A MET 3.4 5.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 4.4 20.4 - - - +
291A ARG* 3.2 33.8 + - + +
294A ALA* 3.8 27.6 - - + -
427A LEU* 4.4 1.3 - - + -
487A ARG* 3.2 51.7 + - - +
488A ILE 3.2 8.1 + - - +
490A ARG* 1.3 77.1 - - + +
492A MET* 1.3 66.3 + - - +
493A LYS* 4.3 0.7 - - - -
605A OLA 3.9 11.9 - - + -
----------------------------------------------------------
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Residues in contact with MET 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 3.5 32.3 - - + -
367A ILE* 4.0 32.5 - - + -
368A PRO* 3.9 24.9 - - + -
423A ALA* 4.0 9.2 - - + -
426A LYS* 4.3 14.8 - - + -
427A LEU* 3.6 27.1 - - + -
488A ILE* 3.5 11.9 - - + +
489A GLY* 3.5 12.5 - - - +
490A ARG 3.2 7.7 - - - +
491A LEU* 1.3 77.4 - - - +
493A LYS* 1.3 62.9 - - - +
----------------------------------------------------------
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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