Contacts of the helix formed by residues 482 - 505 (chain B) in PDB entry 1KOJ
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 482 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ILE* 5.6 8.3 - - + -
47B HIS 4.8 4.0 + - - +
170B LEU* 4.0 3.8 - - - -
173B TYR* 3.5 15.0 - - + +
480B LYS* 3.1 28.8 + - + +
481B LEU* 1.3 75.6 - - - +
483B PRO* 1.3 76.8 - - - +
484B PHE* 3.1 8.4 + - - +
485B ILE* 3.2 25.5 + - + +
486B LEU* 2.9 24.1 + - - +
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Residues in contact with PRO 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.8 27.1 - - + -
173B TYR* 3.5 39.3 - - + -
291B ASN* 3.5 39.0 - - + +
294B GLN* 3.9 8.1 - - + -
295B LEU* 3.2 19.1 - - - +
482B THR* 1.3 88.1 - - - +
484B PHE* 1.3 55.2 + - - +
486B LEU* 3.8 0.2 - - - +
487B GLY 3.1 21.0 + - - -
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Residues in contact with PHE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.4 30.5 - - + -
47B HIS* 3.7 42.8 - + + -
294B GLN* 3.5 33.9 + - + +
297B SER* 3.5 15.9 - - - -
298B GLY* 3.2 44.3 - - - -
301B TRP* 3.7 22.7 - + + -
482B THR* 3.1 7.5 + - - +
483B PRO* 1.3 77.9 - - - +
485B ILE* 1.3 73.7 + - + +
487B GLY 3.2 0.9 + - - -
488B ALA* 3.0 20.7 + - + +
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Residues in contact with ILE 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 4.2 9.0 - - + +
47B HIS 3.7 21.8 - - - +
48B GLY* 4.2 13.9 - - - -
49B HIS 5.0 1.6 - - - +
50B ILE* 4.4 18.2 - - + -
478B PHE* 3.9 23.1 - - + -
479B THR 5.8 0.2 - - - +
480B LYS 3.4 28.9 - - - +
481B LEU* 4.8 1.1 - - - -
482B THR* 3.2 14.8 + - + +
484B PHE* 1.3 81.5 - - + +
486B LEU* 1.3 67.4 + - - +
488B ALA* 3.1 5.2 + - + +
489B LEU* 2.9 37.3 + - + +
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Residues in contact with LEU 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B MET* 4.6 3.6 - - - -
166B VAL* 4.0 23.1 - - + -
169B ALA* 3.9 15.9 - - + -
170B LEU* 3.9 28.5 - - + -
295B LEU* 4.3 2.5 - - + -
344B LEU* 4.1 22.9 - - + -
347B PHE* 4.5 9.9 - - + -
481B LEU* 4.1 16.0 - - + +
482B THR 2.9 18.1 + - - +
483B PRO 3.8 3.1 - - - +
485B ILE* 1.3 77.1 - - - +
487B GLY* 1.3 62.9 - - - +
489B LEU* 3.0 8.2 + - + +
490B ILE* 2.9 47.2 + - + +
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Residues in contact with GLY 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B TRP* 3.6 10.6 - - - -
295B LEU* 3.6 34.0 - - - +
299B ALA* 3.5 9.2 - - - -
483B PRO 3.1 8.9 + - - -
484B PHE 3.2 1.3 + - - -
486B LEU* 1.3 79.8 - - - +
488B ALA* 1.3 56.3 + - - +
490B ILE* 3.5 0.6 + - - -
491B ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 5.4 0.7 - - + -
50B ILE* 4.4 11.9 - - + -
298B GLY* 3.2 23.6 - - - +
301B TRP* 4.9 6.1 - - + -
302B MET* 3.5 26.5 - - + +
484B PHE* 3.0 17.2 + - + +
485B ILE* 3.1 9.6 + - - +
487B GLY* 1.3 75.5 - - - +
489B LEU* 1.3 58.8 + - - +
491B ALA 3.4 0.5 + - - -
492B MET* 2.8 29.1 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.3 14.8 - - + -
344B LEU* 5.7 3.1 - - + -
347B PHE* 4.9 14.1 - - + -
406B LEU* 4.8 7.6 - - + -
476B ILE* 4.2 9.6 - - + -
478B PHE* 3.7 43.5 - - + -
481B LEU* 4.3 10.3 - - + -
485B ILE* 2.9 30.7 + - + +
486B LEU* 3.5 9.2 - - + +
488B ALA* 1.3 74.7 - - - +
490B ILE* 1.3 66.1 + - - +
492B MET* 3.2 27.1 + - + +
493B TYR* 3.2 28.6 + - + -
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Residues in contact with ILE 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B MET* 3.9 23.3 - - + -
166B VAL* 4.0 13.5 - - + -
275B LEU* 4.5 3.8 - - + -
276B TRP* 3.6 32.1 - - + -
295B LEU* 4.7 1.8 - - + -
347B PHE* 4.5 5.6 - - + -
350B TYR* 3.9 16.8 - - + +
351B PHE* 3.5 22.7 - - + -
486B LEU* 2.9 45.9 + - + +
487B GLY* 3.9 1.8 - - - +
489B LEU* 1.3 74.2 - - - +
491B ALA* 1.3 62.7 + - - +
493B TYR 3.3 1.6 + - - -
494B GLU* 3.0 32.6 + - + +
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Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 3.8 15.0 - - - +
276B TRP* 4.5 0.8 - - - -
299B ALA* 3.8 17.5 - - + +
302B MET* 3.7 18.8 - - + -
303B ASP* 4.1 1.8 - - - +
487B GLY 3.0 19.0 + - - +
488B ALA 3.6 4.5 - - - +
489B LEU 3.2 0.2 - - - -
490B ILE* 1.3 74.2 - - - +
492B MET* 1.3 65.8 + - - +
494B GLU* 3.2 13.2 + - - +
495B HIS* 3.1 28.6 + - - -
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Residues in contact with MET 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 5.6 0.7 - - - -
50B ILE* 5.2 9.2 - - - -
52B LEU* 5.4 4.9 - - - -
302B MET* 3.7 29.6 - - + -
315B ALA* 4.2 13.5 - - - -
316B PRO* 3.5 22.1 - - + +
319B LEU* 3.9 29.2 - - + -
476B ILE* 4.0 20.9 - - + -
488B ALA 2.8 16.8 + - - +
489B LEU* 3.4 33.2 - - + +
490B ILE 3.2 0.2 - - - -
491B ALA* 1.3 77.6 - - - +
493B TYR* 1.3 69.2 + - + +
495B HIS* 3.3 0.9 + - - -
496B LYS* 3.0 23.3 + - - +
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Residues in contact with TYR 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.1 18.6 - - + -
337B VAL* 5.1 8.9 - - + +
347B PHE* 3.6 38.6 - + - -
351B PHE* 3.3 35.7 - + + -
404B ASP* 2.7 36.5 + - + +
406B LEU* 3.7 12.6 - - + +
476B ILE* 3.4 19.0 - - + +
489B LEU* 3.2 11.9 + - + -
491B ALA 3.3 0.2 - - - -
492B MET* 1.3 81.4 - - + +
494B GLU* 1.3 65.7 + - - +
496B LYS* 3.1 24.0 + - + +
497B ILE* 3.0 27.9 + - + +
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Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B HIS* 3.7 7.8 + - - +
103B ARG* 2.7 36.1 + - - -
273B TYR* 3.5 42.4 + - + -
276B TRP* 3.0 27.1 + - - -
350B TYR* 4.2 7.6 + - - +
351B PHE* 4.2 6.2 - - + -
490B ILE* 3.0 28.2 + - + +
491B ALA* 3.2 7.3 + - - +
493B TYR* 1.3 76.8 - - - +
495B HIS* 1.3 61.8 + - - +
497B ILE* 3.3 10.2 + - - +
498B PHE* 3.0 23.9 + - - +
509B PHE* 6.2 0.2 - - - -
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Residues in contact with HIS 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 3.8 25.5 - - + +
84B PHE* 4.3 1.1 - + - -
99B HIS* 4.8 6.2 + - - -
100B VAL* 3.9 11.9 - - + -
103B ARG* 3.7 7.6 + - - -
302B MET* 4.4 5.6 - - + -
303B ASP* 2.7 35.4 + - - -
306B PHE* 3.4 43.3 - + + -
316B PRO* 3.6 19.7 - - + -
491B ALA 3.1 20.5 + - - +
494B GLU* 1.3 77.4 + - + +
496B LYS* 1.3 64.7 + - - +
498B PHE* 3.4 5.9 - - - +
499B VAL* 2.9 29.8 + - - +
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Residues in contact with LYS 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PRO* 3.5 17.4 - - + +
319B LEU* 3.6 32.4 + - + +
320B ALA* 3.4 21.1 - - - +
323B GLY* 5.2 2.0 - - - -
335B GLN* 3.8 33.1 + - - +
355B ASP* 4.8 10.9 + - - +
404B ASP* 4.8 7.7 + - - -
492B MET 3.0 14.4 + - - +
493B TYR* 3.1 27.7 + - + +
495B HIS* 1.3 76.2 - - - +
497B ILE* 1.3 65.9 + - + +
499B VAL 3.3 0.3 + - - -
500B GLN* 3.1 44.3 + - - +
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Residues in contact with ILE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B TYR* 3.7 11.9 - - + +
351B PHE* 4.1 18.4 - - + -
354B GLY* 3.7 6.3 - - - +
355B ASP* 3.6 46.7 - - + +
358B SER* 3.6 25.1 - - - -
359B ASN* 3.0 36.4 + - - +
493B TYR* 3.0 19.5 + - + +
494B GLU* 3.4 10.5 - - - +
496B LYS* 1.3 81.1 - - + +
498B PHE* 1.3 60.1 + - - +
500B GLN* 3.6 4.7 + - - +
501B GLY* 3.1 10.4 + - - -
508B SER* 4.1 1.5 + - - -
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Residues in contact with PHE 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.6 2.9 - - + -
79B ALA* 3.6 26.0 - - + -
80B ARG* 3.7 23.1 - - + -
83B MET* 4.0 21.8 - - + -
89B ILE* 4.0 8.7 - - + -
273B TYR* 5.8 0.4 - - - +
306B PHE* 3.8 26.2 - + - -
494B GLU 3.0 13.4 + - - +
495B HIS* 3.2 13.4 + - - +
497B ILE* 1.3 74.8 - - - +
499B VAL* 1.3 68.7 + - - +
501B GLY* 3.2 3.3 + - - -
502B VAL* 3.0 47.0 + - + +
508B SER* 4.7 4.6 + - - -
509B PHE* 3.4 39.3 - + + -
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.9 25.6 - - + -
306B PHE* 3.7 29.4 - - + -
316B PRO 4.3 0.9 - - - +
317B VAL* 4.0 23.3 - - + -
320B ALA* 3.5 22.0 - - + -
321B MET* 4.3 15.5 - - - -
495B HIS 2.9 21.1 + - - +
496B LYS 3.3 0.2 + - - -
498B PHE* 1.3 78.7 - - - +
500B GLN* 1.3 63.5 + - - +
502B VAL* 3.1 7.3 + - - +
503B VAL* 3.0 21.1 + - - +
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Residues in contact with GLN 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ALA* 3.1 32.4 + - + +
323B GLY* 3.6 22.4 - - - -
324B ILE* 3.8 11.5 - - + +
327B ILE* 4.4 8.5 - - - +
355B ASP* 4.5 11.4 - - - +
359B ASN* 4.1 5.6 - - - +
376B PRO* 4.9 3.9 - - - +
496B LYS* 3.1 38.7 + - - +
497B ILE* 3.9 6.0 - - - +
499B VAL* 1.3 77.4 - - - +
501B GLY* 1.3 63.3 + - - +
503B VAL* 3.2 4.2 + - - +
504B TRP* 2.9 55.9 + - + -
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Residues in contact with GLY 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ASN* 3.9 4.4 + - - -
497B ILE 3.1 11.3 + - - -
498B PHE 3.2 1.3 + - - -
500B GLN* 1.3 76.1 - - - +
502B VAL* 1.3 56.9 + - - +
504B TRP* 3.3 1.8 + - - -
505B ASP 2.9 22.3 + - - -
506B ILE* 3.0 30.2 + - - +
508B SER* 3.3 24.7 - - - -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 3.0 35.2 + - - +
76B VAL* 4.0 17.7 - - + -
79B ALA* 3.7 33.7 - - + -
365B LYS* 6.1 3.4 - - - +
498B PHE* 3.0 36.2 + - + +
499B VAL* 3.5 8.7 - - - +
501B GLY* 1.3 75.4 - - - +
503B VAL* 1.3 64.5 + - - +
505B ASP* 3.0 12.4 + - - +
506B ILE 5.2 1.3 - - - -
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 3.9 28.2 - - + +
70B LEU* 4.4 12.3 - - + +
71B ALA* 4.6 2.2 - - - -
74B ARG* 3.0 34.9 + - + +
76B VAL* 4.2 16.2 - - + -
321B MET* 4.0 26.0 - - + -
324B ILE* 4.1 21.8 - - + -
499B VAL 3.0 17.5 + - - +
500B GLN* 3.2 10.5 + - - +
502B VAL* 1.3 76.6 - - - +
504B TRP* 1.3 60.2 + - + +
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Residues in contact with TRP 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 5.8 0.2 - - - +
3B LEU* 3.7 15.6 + - + +
324B ILE* 3.4 22.6 - - + +
327B ILE* 3.8 27.1 - - + -
328B ASN* 2.8 20.0 + - - -
359B ASN* 3.8 14.8 - - + -
364B THR* 4.0 9.2 - - - +
372B HIS* 3.7 33.8 + + + -
373B GLN 3.3 8.5 + - - -
374B THR* 3.5 37.2 - - + -
375B GLY* 3.4 15.7 - - - -
376B PRO* 4.3 0.4 - - + -
500B GLN* 2.9 44.6 + - + +
501B GLY 3.9 3.1 - - - +
503B VAL* 1.3 74.9 - - - +
505B ASP* 1.3 70.2 + - - +
506B ILE* 3.4 24.3 + - + +
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Residues in contact with ASP 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ALA* 3.8 21.4 + - + +
74B ARG* 3.2 21.5 + - - +
364B THR* 3.2 20.5 + - + -
365B LYS* 2.9 43.4 + - - +
366B SER* 4.3 10.4 + - - -
501B GLY 2.9 4.9 + - - -
502B VAL* 3.0 11.5 + - - +
503B VAL 3.2 0.2 - - - -
504B TRP* 1.3 81.3 - - - +
506B ILE* 1.3 60.2 + - - +
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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