Contacts of the helix formed by residues 484 - 508 (chain B) in PDB entry 1Q6X
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 PRO 484 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ALA 4.6 0.7 - - - +
483B MET* 1.3 94.9 - - + +
485B ALA* 1.3 63.0 + - - +
486B SER* 3.0 19.9 + - - +
487B GLU* 3.2 28.5 + - + +
488B LYS* 3.4 12.6 + - - +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B MET 4.0 0.4 + - - -
484B PRO* 1.3 71.1 - - - +
486B SER* 1.3 58.2 + - - +
487B GLU 3.3 0.2 - - - -
488B LYS* 3.9 8.7 - - + +
489B LEU* 2.9 34.1 + - - +
613B LEU* 3.9 16.4 - - + +
616B SER* 3.5 33.0 - - - +
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B PRO* 3.0 11.8 - - - +
485B ALA* 1.3 80.3 - - - +
487B GLU* 1.3 61.9 + - - +
489B LEU* 3.9 6.9 - - - +
490B GLN* 3.4 19.9 + - - +
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B MET* 3.2 29.3 - - + +
484B PRO* 3.2 26.0 + - + +
486B SER* 1.3 78.2 - - - +
488B LYS* 1.3 67.8 + - - +
489B LEU 3.1 1.6 - - - -
490B GLN* 2.8 17.7 + - - +
491B LEU* 2.8 18.2 + - + +
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Residues in contact with LYS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PHE* 3.9 4.7 - - - -
475B ALA* 3.6 14.8 - - + +
476B MET* 3.8 23.9 + - + -
479B HIS* 2.6 47.4 + - - -
483B MET* 3.5 33.4 + - + +
484B PRO 3.4 6.1 + - - +
485B ALA* 4.0 6.3 - - - +
487B GLU* 1.3 77.8 - - - +
489B LEU* 1.3 62.7 + - - +
491B LEU* 3.2 7.1 + - - +
492B LEU* 3.0 24.3 + - - +
613B LEU* 3.7 25.6 - - + -
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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
----------------------------------------------------------
421B TYR* 4.5 3.8 + - - +
485B ALA 2.9 19.8 + - - +
486B SER* 3.9 7.4 - - - +
487B GLU 3.1 0.2 - - - -
488B LYS* 1.3 76.2 - - - +
490B GLN* 1.3 59.4 - - - +
492B LEU* 3.7 8.3 - - + +
493B GLN* 3.4 20.5 + - - +
613B LEU* 3.6 38.1 - - + +
614B CYS* 4.1 16.2 - - - -
616B SER 4.5 3.6 - - - +
617B ARG* 3.4 54.1 - - + +
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Residues in contact with GLN 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B SER 3.4 12.3 + - - +
487B GLU* 2.8 12.2 + - - +
489B LEU* 1.3 77.2 - - - +
491B LEU* 1.3 67.6 + - + +
492B LEU 3.1 1.6 - - - -
493B GLN* 3.1 26.6 + - - +
494B THR* 3.2 25.8 + - + +
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Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B GLU 4.6 1.6 - - - +
471B ALA* 3.9 26.2 - - + +
472B PHE* 4.1 15.6 - - + +
475B ALA* 3.5 32.8 - - + -
483B MET* 3.8 15.0 - - + -
487B GLU* 2.8 14.2 + - + +
488B LYS* 3.7 7.0 - - - +
490B GLN* 1.3 77.4 - - + +
492B LEU* 1.3 62.9 + - - +
494B THR* 2.8 25.4 + - + +
495B ALA* 3.0 12.8 + - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 3.1 39.5 - - + +
426B PHE* 5.1 2.5 - - + -
429B VAL* 5.6 1.6 - - + -
472B PHE* 3.5 33.8 - - + -
488B LYS 3.0 11.4 + - - +
489B LEU* 3.7 9.6 - - + +
491B LEU* 1.3 78.4 - - - +
493B GLN* 1.3 56.3 + - - +
495B ALA* 3.2 4.1 + - - +
496B MET* 2.8 36.8 + - + +
610B MET* 4.6 20.2 - - + +
613B LEU* 3.8 21.1 - - + -
614B CYS* 4.5 18.2 - - - -
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LYS* 5.7 5.8 + - - +
421B TYR* 3.0 43.7 + - - -
489B LEU* 3.4 12.5 + - - +
490B GLN* 3.1 26.9 + - - +
492B LEU* 1.3 78.9 - - - +
494B THR* 1.3 62.9 + - - +
496B MET* 3.2 4.8 + - - +
497B GLN* 2.9 24.3 + - + +
617B ARG* 4.2 11.0 + - - +
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Residues in contact with THR 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468B GLU* 4.0 18.1 + - - +
471B ALA* 6.2 0.2 - - - +
490B GLN* 3.2 23.7 + - + +
491B LEU* 2.8 32.3 + - + +
493B GLN* 1.3 78.9 - - + +
495B ALA* 1.3 55.8 + - - +
497B GLN* 3.3 9.0 + - - +
498B ALA* 3.0 27.5 + - - +
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Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B VAL* 4.5 16.2 - - + +
466B THR* 5.2 2.0 + - - -
468B GLU* 3.9 28.9 - - - +
469B ALA* 4.3 6.6 - - + +
472B PHE* 4.3 9.4 - - + -
491B LEU 3.0 14.2 + - - +
492B LEU* 3.4 11.4 - - - +
493B GLN 3.2 0.2 - - - -
494B THR* 1.3 76.0 + - - +
496B MET* 1.3 63.5 + - - +
498B ALA* 3.2 4.3 + - - +
499B GLN* 3.1 23.7 + - - +
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Residues in contact with MET 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B TYR* 3.8 36.6 - - + -
422B SER* 3.8 17.3 - - - +
425B GLY* 3.7 7.0 - - - +
426B PHE* 3.5 37.7 - - - +
429B VAL* 3.7 25.6 - - + -
492B LEU* 2.8 37.3 + - + +
493B GLN* 3.6 5.2 - - - +
495B ALA* 1.3 73.2 - - - +
497B GLN* 1.3 66.2 + - - +
499B GLN* 3.3 4.4 + - - +
500B THR* 3.1 31.0 + - - +
610B MET* 5.5 0.7 - - - -
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Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B GLN* 2.9 17.5 + - + +
494B THR* 3.5 9.6 - - - +
495B ALA 3.2 0.2 - - - -
496B MET* 1.3 77.3 - - - +
498B ALA* 1.3 61.1 + - - +
500B THR* 3.5 13.9 + - - +
501B GLU* 3.0 47.2 + - - +
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466B THR* 4.4 13.1 - - + +
468B GLU* 3.7 34.3 - - + +
494B THR 3.0 13.4 + - - +
495B ALA 3.5 8.7 - - - +
496B MET 3.2 0.2 - - - -
497B GLN* 1.3 75.5 - - - +
499B GLN* 1.3 65.0 + - - +
501B GLU* 3.2 7.3 + - - +
502B TYR* 2.9 24.8 + - - +
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Residues in contact with GLN 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ASP* 5.1 0.7 - - - +
425B GLY* 3.9 33.5 - - - +
428B GLN* 3.8 11.9 - - + +
429B VAL* 4.1 12.6 - - + -
447B GLU* 3.7 12.8 - - - +
462B ILE* 3.9 11.1 - - - +
463B ARG 4.6 0.4 + - - -
464B SER* 2.9 50.6 + - - +
466B THR* 4.5 7.0 - - - +
495B ALA 3.1 10.3 + - - +
496B MET* 3.3 9.6 + - - +
498B ALA* 1.3 74.5 - - - +
500B THR* 1.3 55.7 + - - +
502B TYR* 3.3 5.1 + - - +
503B THR* 2.7 42.0 + - - +
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Residues in contact with THR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B SER* 4.7 14.7 - - - -
425B GLY* 6.0 0.5 - - - -
496B MET* 3.1 18.9 + - - +
497B GLN* 3.8 15.8 + - - +
499B GLN* 1.3 78.6 - - - +
501B GLU* 1.3 58.3 + - - +
503B THR* 3.4 7.2 + - + -
504B VAL* 3.0 44.6 + - + +
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Residues in contact with GLU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B GLN* 3.0 41.1 + - - +
498B ALA* 3.5 8.1 - - - +
500B THR* 1.3 74.9 - - - +
502B TYR* 1.3 59.4 + - - +
504B VAL* 3.3 7.4 + - + +
505B MET* 2.9 29.1 + - - +
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Residues in contact with TYR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 4.4 3.2 - - + +
41B CYS* 4.0 21.6 - - - -
461B ASN 3.5 22.0 + - - -
462B ILE* 3.7 19.5 - - + -
463B ARG* 3.6 46.2 - - + +
466B THR* 5.0 8.5 - - + -
498B ALA 2.9 15.7 + - - +
499B GLN* 3.8 6.1 - - - +
501B GLU* 1.3 75.8 - - - +
503B THR* 1.3 58.6 + - - +
505B MET* 3.2 32.8 + - + +
506B ALA* 2.8 26.3 + - - +
511B ALA* 4.4 6.3 - - + -
512B ILE* 3.8 18.9 + - - +
513B ASP* 4.8 0.5 + - - -
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Residues in contact with THR 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B ASP* 5.0 6.8 + - - +
425B GLY* 6.0 0.7 - - - -
447B GLU* 4.8 0.5 + - - -
462B ILE* 3.6 29.0 - - + +
499B GLN* 2.7 32.6 + - - +
500B THR* 3.5 8.2 - - - +
502B TYR* 1.3 77.7 - - - +
504B VAL* 1.3 59.4 + - + +
506B ALA* 3.3 1.4 + - - +
507B ILE* 3.0 46.1 + - + +
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500B THR* 3.0 29.5 + - + +
501B GLU* 3.8 6.1 - - + +
503B THR* 1.3 75.1 - - + +
505B MET* 1.3 63.4 + - - +
507B ILE* 3.9 12.6 - - + -
508B THR* 2.9 46.2 + - + +
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Residues in contact with MET 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLN* 5.4 6.5 - - - -
37B THR* 4.3 20.9 - - + -
501B GLU* 2.9 18.4 + - + +
502B TYR* 3.2 60.3 + - + +
504B VAL* 1.3 78.2 - - - +
506B ALA* 1.3 59.3 + - - +
508B THR* 3.3 9.2 + - - -
510B MET* 2.8 59.0 + - + +
511B ALA* 3.8 6.5 - - - +
512B ILE* 5.3 0.2 - - + -
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Residues in contact with ALA 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B ALA* 4.0 10.8 - - + -
451B ILE* 3.5 13.9 - - - +
460B ASP* 4.5 6.7 - - + +
461B ASN 4.0 13.5 - - - +
462B ILE* 3.7 23.1 - - + -
502B TYR* 2.8 17.7 + - + +
503B THR 3.7 2.0 - - - +
504B VAL 3.3 0.2 - - - -
505B MET* 1.3 72.7 - - - +
507B ILE* 1.3 65.9 + - - +
508B THR 3.1 2.0 - - - -
509B GLY* 3.0 14.0 + - - -
511B ALA* 3.8 13.9 - - + -
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Residues in contact with ILE 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 4.3 15.3 - - + -
450B SER* 3.5 29.4 - - - +
451B ILE* 4.3 3.4 - - - +
453B ARG* 3.9 38.7 - - - +
454B PHE* 3.7 13.5 - - - -
503B THR* 3.0 29.9 + - + +
504B VAL* 3.6 18.4 - - + +
506B ALA* 1.3 74.0 - - - +
508B THR* 1.3 66.0 + - + +
509B GLY 3.3 0.9 - - - -
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Residues in contact with THR 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PRO* 4.0 7.6 - - - +
453B ARG* 5.4 6.5 - - - +
454B PHE* 3.6 20.9 - - - -
504B VAL* 2.9 34.5 + - + +
505B MET* 3.3 8.0 + - - -
506B ALA 3.1 1.2 - - - -
507B ILE* 1.3 88.2 - - + +
509B GLY* 1.3 60.2 + - - +
510B MET* 3.5 15.8 + - - +
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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
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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