Contacts of the helix formed by residues 484 - 506 (chain B) in PDB entry 6QVC
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 PHE 484 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 3.7 26.2 - - + +
279B PHE* 3.5 37.2 - + - -
288B PHE* 6.3 3.8 - + - -
482B GLY 3.3 3.4 + - - -
483B GLY* 1.3 78.1 - - - +
485B MET* 1.3 68.5 + - + +
486B PRO* 3.6 1.8 - - - +
487B VAL* 3.3 6.1 + - - +
488B PHE* 2.9 57.6 + + + +
533B THR* 3.3 26.2 + - + -
537B SER* 5.9 3.1 - - - -
542B THR* 3.6 22.7 - - + -
545B ILE* 3.6 22.9 - - + -
546B CYS* 6.4 0.2 - - - -
549B LEU* 5.6 4.0 - - + -
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Residues in contact with MET 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 6.4 1.3 - - + -
229B VAL 3.6 16.2 - - - +
230B GLY* 3.8 8.9 - - - -
231B LYS* 4.5 14.4 - - + +
279B PHE* 3.5 37.2 - - + -
420B PRO* 5.6 6.5 - - + -
421B ARG* 4.9 19.3 - - + +
424B ILE* 6.1 5.2 - - - -
484B PHE* 1.3 85.0 - - + +
486B PRO* 1.3 68.8 - - + +
488B PHE* 3.1 21.1 + - - +
489B VAL* 3.0 33.2 + - + +
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Residues in contact with PRO 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 4.1 23.1 - - + +
229B VAL* 3.8 19.5 - - - +
230B GLY* 4.0 3.4 - - - +
365B PHE* 6.2 0.7 - - + -
467B LYS* 6.2 2.0 - - - -
471B SER* 4.0 26.7 - - - +
475B THR* 6.4 2.0 - - - -
482B GLY 4.5 4.0 - - - +
483B GLY* 5.5 0.7 - - - -
484B PHE 3.8 5.2 - - - +
485B MET* 1.3 93.0 - - + +
487B VAL* 1.3 63.9 + - + +
489B VAL* 3.2 12.0 + - + +
490B LEU* 2.9 35.1 + - + +
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.0 31.9 - - + -
483B GLY* 3.5 25.1 - - - +
484B PHE 3.5 6.5 - - - +
485B MET 3.2 0.4 - - - -
486B PRO* 1.3 83.7 - - + +
488B PHE* 1.3 55.9 + - - +
490B LEU* 3.2 10.1 + - + +
491B GLY* 2.9 25.5 + - - -
532B LEU* 3.7 23.8 - - + +
533B THR* 3.7 25.2 + - - +
536B VAL* 4.1 14.1 - - + -
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Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PHE* 5.6 3.4 - + - -
424B ILE* 4.8 24.5 - - + -
428B PHE* 5.0 13.5 - + - -
484B PHE* 2.9 41.7 + + + +
485B MET* 3.3 26.7 - - - +
487B VAL* 1.3 75.9 - - - +
489B VAL* 1.3 62.2 + - + +
491B GLY* 3.4 0.7 + - - -
492B ALA* 3.0 23.2 + - + +
526B VAL* 5.9 0.4 - - + -
529B ALA* 3.2 46.3 - - + +
533B THR* 4.1 8.0 - - + -
542B THR* 6.0 0.2 - - + -
546B CYS* 4.2 24.9 - - + -
549B LEU* 4.9 19.7 - - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B PRO* 4.4 22.7 - - + +
423B ALA* 5.8 2.2 - - + -
424B ILE* 3.7 31.0 - - + -
427B LEU* 5.1 2.6 - - + +
463B PHE* 4.4 25.1 - - + -
467B LYS* 4.8 13.5 - - + -
485B MET* 3.0 22.3 + - + +
486B PRO* 3.4 13.7 - - + +
488B PHE* 1.3 78.4 - - + +
490B LEU* 1.3 59.0 + - + +
492B ALA* 3.2 3.5 + - - +
493B ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 4.7 5.4 - - + -
463B PHE* 6.0 0.7 - - + -
464B PHE* 3.3 51.6 - - + +
467B LYS* 3.7 15.7 - - + +
468B PHE* 3.6 39.7 - - + +
471B SER* 3.9 15.7 - - - +
486B PRO 2.9 19.4 + - - +
487B VAL* 3.2 14.6 + - + +
489B VAL* 1.3 76.8 - - + +
491B GLY* 1.3 57.9 + - - +
493B ALA* 3.3 4.1 + - + +
494B PHE* 3.0 24.1 + - - +
532B LEU* 5.0 9.2 - - + -
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Residues in contact with GLY 491 (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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358B CYS* 5.9 0.4 - - - -
487B VAL 2.9 14.6 + - - -
488B PHE 3.8 3.1 - - - -
490B LEU* 1.3 77.2 - - - +
492B ALA* 1.3 55.7 + - - +
494B PHE* 3.4 3.3 + - - +
495B GLY 3.0 23.4 + - - -
528B GLY* 3.5 17.5 - - - -
529B ALA* 3.5 16.7 + - - -
532B LEU* 4.2 17.6 - - - +
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Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B ILE* 4.6 11.4 - - + -
427B LEU* 3.3 20.6 - - + +
428B PHE* 4.8 14.1 - - + -
488B PHE* 3.0 15.6 + - + +
489B VAL* 3.6 10.8 - - - +
491B GLY* 1.3 75.9 - - - +
493B ALA* 1.3 57.5 + - - +
496B ARG* 3.0 25.8 + - - +
525B ALA* 3.6 16.0 - - + +
529B ALA* 3.5 11.1 - - + +
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Residues in contact with ALA 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 3.7 10.7 - - + +
460B ILE* 3.9 9.8 - - + +
463B PHE* 4.1 23.6 - - + -
464B PHE* 3.8 23.8 - - + -
489B VAL 2.9 13.4 + - - +
490B LEU* 3.4 11.4 - - + +
491B GLY 3.2 0.2 - - - -
492B ALA* 1.3 76.6 - - - +
494B PHE* 1.3 57.4 + - - +
496B ARG* 3.4 1.0 + - - +
497B LEU* 3.0 28.9 + - - +
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Residues in contact with PHE 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 4.0 18.6 - - + -
357B CYS* 4.4 21.3 - - + -
358B CYS* 3.5 32.8 - - - -
361B LEU* 4.7 11.7 - - + -
464B PHE* 4.0 27.8 - + + -
490B LEU 3.0 15.6 + - - +
491B GLY* 3.4 6.0 + - - +
493B ALA* 1.3 76.8 - - - +
495B GLY* 1.3 61.4 + - - +
497B LEU* 3.3 24.5 - - + +
498B VAL* 3.1 33.1 + - + +
528B GLY* 5.9 0.2 - - - -
532B LEU* 5.1 2.0 - - + -
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Residues in contact with GLY 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B ILE* 3.9 12.3 - - - -
491B GLY 3.0 14.5 + - - -
493B ALA 3.2 0.2 - - - -
494B PHE* 1.3 79.3 - - - +
496B ARG* 1.3 56.6 + - - +
498B VAL* 3.3 5.0 - - - +
499B GLY 2.9 23.4 + - - -
524B TYR* 3.4 26.3 - - - +
525B ALA* 3.7 11.7 - - - -
528B GLY* 4.7 0.4 - - - -
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Residues in contact with ARG 496 (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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427B LEU* 2.8 45.9 + - + +
429B ASP 2.9 21.6 + - - +
431B ASN 2.8 28.5 + - - -
433B TRP* 3.1 55.9 - - - +
460B ILE* 4.9 8.1 - - + -
492B ALA 3.0 16.6 + - - +
493B ALA 4.2 0.7 - - - +
495B GLY* 1.3 72.8 - - - +
497B LEU* 1.3 60.2 + - - +
499B GLY 4.3 0.9 - - - +
500B GLU* 2.9 45.7 + - + +
521B PRO* 3.7 19.7 - - + +
522B GLY 4.1 6.7 - - - +
525B ALA* 3.7 11.7 - - + +
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Residues in contact with LEU 497 (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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457B VAL* 3.8 34.3 - - + +
460B ILE* 3.8 26.6 - - + +
461B PHE* 4.5 25.4 - - + +
464B PHE* 5.6 5.8 - - + -
493B ALA 3.0 15.0 + - - +
494B PHE* 3.3 34.3 - - + +
496B ARG* 1.3 77.4 - - - +
498B VAL* 1.3 65.1 + - + +
500B GLU* 3.3 2.5 + - - +
501B ILE* 3.1 32.9 + - + +
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Residues in contact with VAL 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ALA* 5.8 8.3 - - + +
353B ALA* 6.3 2.7 - - + -
354B ILE* 3.7 28.5 - - + -
494B PHE* 3.1 21.0 + - + +
495B GLY 3.3 13.2 - - - +
497B LEU* 1.3 81.1 - - + +
499B GLY* 1.3 56.8 + - - +
501B ILE* 3.2 20.6 - - + +
502B MET* 2.9 38.8 + - + +
524B TYR* 4.7 8.5 - - + -
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Residues in contact with GLY 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B GLY 2.9 14.7 + - - -
498B VAL* 1.3 78.7 - - - +
500B GLU* 1.3 55.7 + - - +
502B MET* 3.3 3.6 + - - +
503B ALA* 2.9 27.0 + - - +
519B ILE* 4.5 3.5 - - - +
521B PRO* 3.6 15.0 - - - +
524B TYR* 3.7 30.1 - - - -
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Residues in contact with GLU 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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432B THR* 3.7 6.9 - - - +
433B TRP* 2.9 28.8 + - - +
434B VAL* 3.1 39.5 + - + +
456B VAL* 5.7 2.2 - - + -
457B VAL* 6.0 4.9 - - + -
460B ILE* 4.6 15.0 - - + -
496B ARG* 2.9 49.6 + - + +
497B LEU* 3.9 4.0 - - + +
499B GLY* 1.3 75.1 - - - +
501B ILE* 1.3 60.6 + - + +
503B ALA* 3.3 5.4 + - - +
504B MET* 2.9 26.3 + - - +
521B PRO* 3.3 11.0 - - + +
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Residues in contact with ILE 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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457B VAL* 3.8 29.6 - - + -
497B LEU* 3.1 18.6 + - + +
498B VAL* 3.2 33.0 - - + +
500B GLU* 1.3 78.4 - - + +
502B MET* 1.3 62.6 + - + +
504B MET* 3.4 21.6 + - + +
505B LEU* 2.9 26.5 + - - +
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Residues in contact with MET 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU* 4.5 15.5 - - + -
350B ALA* 4.5 22.0 - - + -
498B VAL* 2.9 32.0 + - + +
499B GLY* 3.7 6.3 - - - +
500B GLU 3.2 0.2 - - - -
501B ILE* 1.3 80.5 - - + +
503B ALA* 1.3 60.6 + - - +
505B LEU* 3.6 14.4 - - + +
506B PHE* 2.9 55.2 + - + +
519B ILE* 3.5 19.8 - - + +
524B TYR* 4.7 13.0 - - + +
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B THR* 3.7 34.3 - - + +
434B VAL* 6.0 0.2 - - - -
435B LYS* 6.2 0.2 - - - -
499B GLY 2.9 14.9 + - - +
500B GLU* 3.5 11.4 - - - +
502B MET* 1.3 76.8 - - - +
504B MET* 1.3 60.2 + - - +
506B PHE 3.2 19.2 - - - +
507B PRO* 3.5 7.8 - - - +
519B ILE* 3.6 19.9 - - + +
521B PRO* 5.4 3.4 - - + -
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Residues in contact with MET 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 4.8 25.5 - - + +
455B ASN* 5.1 13.0 - - - -
457B VAL* 5.9 5.2 - - + -
500B GLU 2.9 13.8 + - - +
501B ILE* 3.6 24.5 - - + +
503B ALA* 1.3 76.2 - - - +
505B LEU* 1.3 64.8 + - + +
507B PRO* 3.4 17.4 - - - +
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ILE 2.9 17.4 + - - +
502B MET* 3.2 20.8 + - + +
504B MET* 1.3 81.3 - - + +
506B PHE* 1.3 90.0 + - + +
507B PRO* 3.3 7.6 - - - +
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Residues in contact with PHE 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LYS* 6.1 6.5 - - + -
347B GLU* 6.3 1.8 - - + -
502B MET* 2.9 33.8 + - + +
503B ALA* 3.2 12.0 - - - +
505B LEU* 1.3 101.8 - - + +
507B PRO* 1.3 64.2 - - - +
508B ASP* 3.3 8.0 + - + +
509B GLY* 4.2 10.5 + - - +
518B LYS* 5.7 1.7 - - - +
519B ILE* 4.7 18.2 + - + +
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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) + - + + + + + -
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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