Contacts of the helix formed by residues 455 - 477 (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 ASN 455 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B VAL* 5.0 8.2 - - - +
437B ALA* 5.6 3.6 - - - +
453B ARG 4.1 1.8 + - - -
454B VAL* 1.3 78.3 - - - +
456B VAL* 1.3 76.3 + - - +
457B VAL* 3.2 23.4 + - + +
458B ILE* 3.0 41.5 + - + +
459B ILE* 3.5 2.4 + - - +
504B MET* 5.1 11.9 - - - -
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B TRP* 4.6 21.8 - - + +
434B VAL* 4.2 22.0 - - + -
437B ALA* 4.8 15.3 - - + -
449B TRP* 3.3 27.8 - - + +
450B ILE* 4.7 9.0 - - + -
451B HIS 5.2 1.3 - - - +
454B VAL 4.4 6.3 - - - +
455B ASN* 1.3 84.9 + - - +
457B VAL* 1.3 62.7 + - - +
458B ILE 3.2 0.2 - - - -
459B ILE* 3.2 15.6 - - + +
460B ILE* 3.0 39.6 + - + +
500B GLU* 5.3 2.2 - - + +
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Residues in contact with VAL 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 6.1 3.6 - - + -
455B ASN* 3.4 28.9 - - - +
456B VAL* 1.3 82.6 - - - +
458B ILE* 1.3 65.2 + - + +
460B ILE* 3.4 8.7 + - - +
461B PHE* 2.9 28.7 + - + +
497B LEU* 3.8 20.8 - - + +
500B GLU* 6.0 5.4 - - + -
501B ILE* 3.8 22.2 - - + -
504B MET* 5.9 5.6 - - + -
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Residues in contact with ILE 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B VAL* 3.9 20.2 - - + -
455B ASN* 3.0 29.6 + - + +
457B VAL* 1.3 87.1 - - + +
459B ILE* 1.3 57.7 + - - +
461B PHE* 3.3 8.1 + - + +
462B LEU* 2.9 51.0 + - + +
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Residues in contact with ILE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B GLN 5.5 0.4 - - - +
413B PHE* 4.0 30.0 - - + +
414B MET* 5.2 2.2 - - - +
415B ALA* 5.6 4.7 - - + +
448B VAL 4.8 2.2 - - - +
449B TRP* 3.4 56.4 - - + +
450B ILE 4.3 0.4 - - - +
451B HIS* 4.7 12.1 - - + +
454B VAL* 3.9 20.2 - - + +
455B ASN 3.7 13.0 - - - +
456B VAL* 3.2 16.4 - - + +
458B ILE* 1.3 76.6 - - - +
460B ILE* 1.3 60.6 + - - +
462B LEU* 4.0 2.7 - - + +
463B PHE* 2.9 30.5 + - - +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B LEU* 6.2 1.3 - - + -
433B TRP* 4.4 22.9 - - + -
449B TRP* 3.7 25.1 - - + -
456B VAL* 3.0 27.8 + - + +
457B VAL* 3.8 6.5 - - - +
458B ILE 3.3 0.2 - - - -
459B ILE* 1.3 78.3 - - - +
461B PHE* 1.3 56.2 + - - +
463B PHE* 3.4 8.2 + - + +
464B PHE* 2.9 29.2 + - + +
493B ALA* 3.9 15.7 - - + +
496B ARG* 4.9 9.4 - - + +
497B LEU* 3.8 32.5 - - + +
500B GLU* 4.6 18.8 - - + -
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Residues in contact with PHE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B VAL* 2.9 19.1 + - + +
458B ILE* 3.3 9.8 + - + +
460B ILE* 1.3 78.3 - - - +
462B LEU* 1.3 70.6 + - + +
464B PHE* 3.3 14.2 + + - +
465B VAL* 3.0 43.4 + - + +
497B LEU* 4.5 23.6 - - + -
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Residues in contact with LEU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B MET* 6.5 0.4 - - + -
413B PHE* 4.2 30.5 - - + +
414B MET* 4.1 4.3 - - - -
454B VAL* 6.4 0.4 - - + -
458B ILE* 2.9 35.9 + - + +
459B ILE* 4.0 3.6 - - + +
461B PHE* 1.3 85.2 - - + +
463B PHE* 1.3 60.2 + - - +
465B VAL* 3.4 13.7 - - + +
466B MET* 2.9 35.2 + - - +
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Residues in contact with PHE 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B MET* 3.6 42.9 - - + +
415B ALA 5.0 5.8 - - - -
418B LEU* 5.2 9.9 - - + -
423B ALA* 5.3 10.3 - - + -
427B LEU* 5.0 8.5 - - + -
449B TRP* 4.2 25.1 - + + -
459B ILE 2.9 19.4 + - - +
460B ILE* 3.5 7.6 - - + +
462B LEU* 1.3 75.9 - - - +
464B PHE* 1.3 58.8 + - - +
467B LYS* 2.9 65.8 + - + +
489B VAL* 4.4 19.1 - - + -
490B LEU* 6.0 0.4 - - + -
493B ALA* 4.1 23.6 - - + -
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 3.7 32.5 - - + -
460B ILE* 2.9 18.5 + - + +
461B PHE* 3.6 16.6 - + - +
463B PHE* 1.3 81.7 - - - +
465B VAL* 1.3 66.1 + - + +
468B PHE* 2.9 39.5 + + + +
490B LEU* 3.3 49.6 - - + +
493B ALA* 3.8 16.2 - - + -
494B PHE* 4.0 29.6 - + + -
497B LEU* 5.6 4.5 - - + -
532B LEU* 5.1 0.9 - - + -
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Residues in contact with VAL 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B PHE* 3.0 35.8 + - + +
462B LEU* 3.4 21.3 - - + +
464B PHE* 1.3 84.9 - - + +
466B MET* 1.3 62.7 + - + +
468B PHE* 3.3 13.9 - - + +
469B TRP* 3.0 35.4 + - + +
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Residues in contact with MET 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ILE* 5.6 0.4 - - + -
404B PHE* 3.5 45.5 - - + +
414B MET* 3.7 19.7 - - + -
462B LEU 2.9 19.6 + - - +
465B VAL* 1.3 78.9 - - + +
467B LYS* 1.3 63.7 + - - +
469B TRP* 3.2 36.7 + - + +
470B MET* 3.0 57.9 + - + +
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLY 5.2 1.8 + - - -
228B PRO* 3.6 40.2 - - - +
414B MET* 3.9 5.4 - - + -
418B LEU 5.7 2.8 + - - -
420B PRO* 4.9 11.6 - - - +
463B PHE* 2.9 55.7 + - + +
466B MET* 1.3 75.7 - - - +
468B PHE* 1.3 56.8 + - - +
470B MET* 3.7 19.8 - - + +
471B SER* 3.0 34.4 + - - -
486B PRO* 6.2 2.0 - - - -
489B VAL* 4.8 11.7 - - + -
490B LEU* 3.7 17.9 - - + -
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Residues in contact with PHE 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B LEU* 4.5 20.0 - - + -
364B VAL* 5.1 4.5 - - + -
365B PHE* 3.5 45.7 - + + -
368B LEU* 4.4 21.1 - - + -
464B PHE* 2.9 34.5 + + + +
465B VAL* 3.3 16.8 - - + +
466B MET 3.1 0.4 - - - -
467B LYS* 1.3 76.8 - - - +
469B TRP* 1.3 68.5 + - + +
471B SER* 3.3 14.9 + - - -
472B ILE* 3.7 10.5 - - + +
490B LEU* 3.6 24.7 - - + +
532B LEU* 6.2 2.7 - - + -
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Residues in contact with TRP 469 (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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400B VAL* 6.4 2.2 - - + -
401B ILE* 5.1 9.0 - - + -
404B PHE* 4.3 18.2 - + - -
465B VAL* 3.0 38.2 + - + +
466B MET* 3.2 40.6 - - + +
468B PHE* 1.3 83.5 - - + +
470B MET* 1.3 70.1 + - + +
472B ILE* 3.3 26.5 - - + +
473B VAL* 3.6 13.7 - - + +
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Residues in contact with MET 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 5.3 7.0 - - + -
401B ILE* 3.7 50.7 - - + +
404B PHE* 5.3 1.6 - - - +
405B THR* 4.7 7.0 - - + +
414B MET* 4.1 5.2 - - + -
466B MET* 3.0 67.2 + - + +
467B LYS* 3.2 27.3 + - + +
468B PHE 3.2 0.4 - - - -
469B TRP* 1.3 83.8 - - + +
471B SER* 1.3 60.2 + - - +
472B ILE 3.4 0.2 - - - -
473B VAL* 3.3 7.9 + - - +
474B ALA* 2.9 27.5 + - - +
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Residues in contact with SER 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 4.8 6.7 - - - +
365B PHE* 3.6 18.7 - - - -
467B LYS* 3.0 14.6 + - - -
468B PHE 3.3 11.8 + - - -
469B TRP 3.4 0.2 - - - -
470B MET* 1.3 74.1 - - - +
472B ILE* 1.3 63.6 + - - +
474B ALA* 3.1 9.5 + - - +
475B THR* 2.9 30.2 + - - +
486B PRO* 4.0 31.1 - - - +
487B VAL* 5.9 0.2 - - - +
490B LEU* 3.9 8.9 - - - +
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Residues in contact with ILE 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 3.5 45.1 - - + +
368B LEU* 5.0 14.8 - - + +
369B HIS* 4.6 21.8 + - + +
372B VAL* 5.4 9.6 - - + -
468B PHE* 3.7 11.2 - - + +
469B TRP* 3.3 29.4 - - + +
471B SER* 1.3 77.3 + - - +
473B VAL* 1.3 69.5 + - + +
475B THR* 3.3 9.0 - - + +
476B THR* 2.2 39.2 + - - +
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Residues in contact with VAL 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B VAL* 5.9 5.6 - - + -
393B TYR* 5.1 5.0 + - - +
397B VAL* 4.0 31.1 - - + +
401B ILE* 5.3 11.7 - - + -
469B TRP* 3.6 26.0 - - + +
470B MET* 3.3 9.1 + - - +
471B SER 3.2 0.6 - - - -
472B ILE* 1.3 86.8 - - + +
474B ALA* 1.3 61.8 + - - +
476B THR* 3.2 20.8 + - - +
477B MET* 3.4 12.6 + - + +
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Residues in contact with ALA 474 (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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227B ILE* 4.2 14.7 - - + +
228B PRO* 3.3 30.5 - - + +
229B VAL* 5.7 2.9 - - - +
401B ILE* 5.4 4.9 - - + +
470B MET 2.9 13.7 + - - +
471B SER* 3.1 12.5 + - - +
473B VAL* 1.3 78.0 - - - +
475B THR* 1.3 60.2 + - - +
477B MET* 3.3 31.4 - - - +
479B ILE* 4.0 6.4 - - - +
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Residues in contact with THR 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO 5.2 0.2 + - - -
365B PHE* 5.5 5.8 - - + -
369B HIS* 4.0 25.7 - - + +
373B MET* 5.8 0.2 - - - +
471B SER 2.9 16.0 + - - +
472B ILE* 3.3 20.9 - - + +
474B ALA* 1.3 73.9 - - - +
476B THR* 1.3 63.6 + - - +
477B MET 3.5 3.3 - - - +
481B CYS* 2.9 44.2 - - - +
482B GLY 5.0 5.4 + - - -
483B GLY* 5.8 1.9 - - - -
486B PRO* 6.4 2.0 - - - -
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Residues in contact with THR 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B HIS* 5.0 1.6 + - - -
372B VAL* 3.5 29.6 - - + +
373B MET* 4.5 14.9 - - - +
376B VAL* 3.9 26.2 - - + +
393B TYR* 3.3 23.2 - - + +
472B ILE 2.2 29.4 + - - -
473B VAL* 3.2 13.8 + - - -
475B THR* 1.3 78.3 - - - +
477B MET* 1.3 66.4 + - - +
478B PRO* 3.8 1.6 - - - +
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Residues in contact with MET 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 4.6 11.2 - - - -
227B ILE* 5.4 9.4 - - + -
393B TYR* 3.8 14.1 - - + -
394B PRO* 4.0 24.7 - - + +
397B VAL* 4.2 18.4 - - + -
398B THR* 4.2 20.6 - - - +
401B ILE* 6.1 2.5 - - + -
473B VAL* 3.4 21.2 + - + +
474B ALA* 3.3 25.1 - - + +
475B THR 3.9 2.3 - - - +
476B THR* 1.3 83.8 - - - +
478B PRO* 1.4 62.9 - - + +
479B ILE* 2.6 42.6 + - + +
481B CYS* 5.1 0.3 - - - -
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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