Contacts of the helix formed by residues 461 - 483 (chain B) in PDB entry 1YY4
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 LEU 461 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 5.6 0.7 - - - +
383B THR* 4.8 4.9 - - + -
386B ARG* 3.2 49.4 - - + +
387B PHE* 3.5 45.5 - - + +
390B LEU* 3.9 9.2 - - + -
457B ASN 3.4 16.8 - - - +
458B LEU* 3.2 10.8 - - - +
459B LEU 2.9 0.6 - - - -
460B MET* 1.3 76.7 - - - +
462B LEU* 1.3 63.8 + - - +
463B SER 3.1 2.5 - - - -
464B HIS* 2.9 39.1 + - + +
465B VAL* 3.1 14.7 + - - +
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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
----------------------------------------------------------
459A LEU 6.0 0.4 - - - +
460A MET* 4.8 9.6 - - + -
463A SER* 4.0 18.6 + - - +
337B GLU* 4.4 2.8 - - - +
387B PHE* 6.0 0.7 - - + -
400B VAL* 3.6 22.9 - - + -
403B MET* 5.2 10.3 - - + -
404B ILE* 3.6 37.0 - - + -
407B ASN* 4.8 9.9 - - - +
458B LEU 5.0 1.1 - - - +
459B LEU* 2.8 42.3 + - + +
461B LEU* 1.3 78.8 - - + +
463B SER* 1.3 56.0 + - - +
465B VAL* 3.3 10.5 + - + +
466B ARG* 2.8 28.5 + - - +
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU* 5.3 0.7 + - - -
407A ASN* 4.9 3.8 + - - -
462A LEU* 4.1 32.1 + - - +
463A SER* 4.1 5.9 + - - +
466A ARG* 3.7 28.9 + - - +
459B LEU 4.2 0.5 + - - -
460B MET* 3.6 13.2 + - - -
461B LEU 3.1 0.6 - - - -
462B LEU* 1.3 75.3 - - - +
464B HIS* 1.3 63.6 + - - +
466B ARG* 3.2 9.5 - - - +
467B HIS* 2.8 28.4 + - - +
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Residues in contact with HIS 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASN* 2.7 41.6 + - - -
409A SER* 3.0 23.7 + - - -
410A MET* 3.3 30.4 + - + +
466A ARG* 4.3 1.8 - - - -
379B MET* 5.7 0.5 - - - +
383B THR* 3.8 27.2 + - + +
386B ARG* 6.0 0.8 - - - +
460B MET 3.8 12.1 - - - -
461B LEU* 2.9 26.0 + - + +
463B SER* 1.3 74.5 - - - +
465B VAL* 1.3 68.2 + - - +
467B HIS* 3.3 2.3 + - - +
468B ALA* 3.0 24.1 + - - +
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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
----------------------------------------------------------
337B GLU* 3.7 35.0 - - + +
340B MET* 3.6 6.9 - - + +
341B MET* 4.5 5.4 - - - +
344B MET* 3.5 32.5 - - + -
383B THR* 4.3 9.2 - - + -
387B PHE* 4.4 8.5 - - + -
404B ILE* 4.4 11.4 - - + -
461B LEU 3.1 17.9 + - - +
462B LEU* 3.5 12.1 - - + +
464B HIS* 1.3 76.1 - - - +
466B ARG* 1.3 65.0 + - - +
468B ALA* 3.4 4.6 + - - +
469B SER* 3.0 21.5 + - - -
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Residues in contact with ARG 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A SER* 3.5 29.6 + - - +
464A HIS* 4.3 3.4 - - - -
466A ARG* 3.8 23.6 - - + -
467A HIS* 3.8 15.7 - - - -
333B SER 4.3 8.3 + - - -
337B GLU* 3.3 35.2 + - - +
407B ASN* 4.3 2.0 + - - -
408B SER* 4.3 9.5 - - - +
410B MET* 3.0 48.3 - - - +
462B LEU 2.8 15.0 + - - +
463B SER* 3.2 12.3 - - - +
465B VAL* 1.3 78.4 - - - +
467B HIS* 1.3 62.4 + - - +
469B SER* 3.3 2.8 + - - -
470B ASN* 3.1 43.8 + - - +
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Residues in contact with HIS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A SER* 6.2 4.3 - - - -
410A MET* 3.2 36.3 - - + +
466A ARG* 3.9 24.0 + - - +
470A ASN* 4.5 20.1 + - - -
379B MET* 4.5 13.7 - - + -
463B SER 2.8 19.0 + - - +
464B HIS 3.3 5.4 + - - +
466B ARG* 1.3 72.7 - - - +
468B ALA* 1.3 65.7 + - - +
470B ASN* 2.9 19.7 + - + +
471B LYS* 3.0 39.0 + - + +
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Residues in contact with ALA 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B MET* 3.4 19.1 - - + +
376B ILE* 5.2 4.3 - - + +
379B MET* 3.8 30.6 - - + +
380B LEU* 4.2 15.7 - - + -
383B THR* 5.8 0.9 - - - +
464B HIS 3.0 14.2 + - - +
465B VAL* 3.7 6.5 - - - +
467B HIS* 1.3 77.7 - - - +
469B SER* 1.3 53.2 + - - +
471B LYS* 3.6 0.7 - - - +
472B GLY* 2.7 33.8 + - - -
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Residues in contact with SER 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B SER 5.1 1.0 + - - -
336B MET* 3.2 12.8 + - - +
337B GLU* 3.3 31.0 - - - +
340B MET* 3.0 20.5 - - - +
465B VAL 3.0 2.0 + - - -
466B ARG 3.3 9.6 - - - -
467B HIS 3.1 0.2 - - - -
468B ALA* 1.3 77.0 - - - +
470B ASN* 1.3 56.2 + - - +
472B GLY* 3.5 0.2 - - - -
473B MET* 2.7 59.8 + - - +
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Residues in contact with ASN 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A HIS* 5.2 9.4 - - - -
470A ASN* 2.4 41.0 - - + +
471A LYS* 6.0 5.0 - - - +
466B ARG* 3.1 34.5 + - - +
467B HIS* 2.9 7.2 + - + +
469B SER* 1.3 85.2 + - - +
471B LYS* 1.3 63.9 + - + +
472B GLY 3.1 0.2 - - - -
473B MET* 4.3 12.2 - - - +
474B GLU* 3.0 30.1 + - - +
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Residues in contact with LYS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ASN* 6.2 0.9 - - - +
375B GLU* 3.2 28.2 + - - +
376B ILE* 3.5 10.4 - - + +
379B MET* 4.7 14.8 - - + -
467B HIS* 3.0 42.5 + - + +
468B ALA 4.3 1.8 - - - +
470B ASN* 1.3 78.4 - - + +
472B GLY* 1.3 60.1 + - - +
474B GLU* 3.8 25.8 + - + +
475B HIS* 3.2 24.6 + - - +
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Residues in contact with GLY 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 3.5 21.1 - - - +
336B MET* 4.3 9.3 - - - +
340B MET* 5.2 0.4 - - - -
376B ILE* 3.8 14.6 - - - -
468B ALA 2.7 18.9 + - - -
469B SER* 3.5 1.3 - - - -
470B ASN 3.1 0.2 - - - -
471B LYS* 1.3 79.4 - - - +
473B MET* 1.3 58.8 + - - +
476B LEU* 3.1 24.1 + - - +
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Residues in contact with MET 473 (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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332B GLU 5.2 1.8 - - - +
333B SER* 4.7 14.4 - - - +
335B TRP* 3.6 39.7 - - + +
336B MET* 3.7 20.4 - - + +
469B SER* 2.7 43.5 + - - +
470B ASN* 4.3 11.7 - - - +
472B GLY* 1.3 71.2 - - - -
474B GLU* 1.3 62.5 + - - +
476B LEU* 3.6 7.3 - - - +
477B LEU* 2.9 30.5 + - - +
494B MET 5.3 1.6 - - - +
495B LEU* 4.0 12.4 - - + +
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Residues in contact with GLU 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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470B ASN 3.0 20.6 + - - +
471B LYS* 3.8 27.1 + - + +
473B MET* 1.3 77.2 - - - +
475B HIS* 1.3 64.3 + - - +
477B LEU* 3.1 12.3 + - + +
478B ASN* 2.7 50.5 + - - +
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Residues in contact with HIS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 2.2 45.7 + + + -
295B MET* 4.2 0.4 - - - -
370B VAL* 3.7 19.7 - - + +
371B GLU 3.3 25.9 + - - -
372B GLY 3.5 18.2 + - - -
373B ILE* 3.9 4.1 - - + +
376B ILE* 3.5 11.4 - - + -
471B LYS 3.2 19.3 + - - +
472B GLY 3.6 2.0 - - - +
474B GLU* 1.3 81.2 - - - +
476B LEU* 1.3 62.1 + - - +
478B ASN* 3.1 12.0 + - - +
479B MET* 3.0 44.7 + - + +
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Residues in contact with LEU 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B 4NA 3.4 31.8 + - + +
295B MET* 5.7 0.2 - - - -
299B THR* 4.1 9.9 - - + -
335B TRP* 4.0 17.7 - - + -
336B MET* 4.7 4.9 - - + -
472B GLY 3.1 14.7 + - - +
473B MET* 3.6 7.0 - - - +
474B GLU 3.3 0.2 - - - -
475B HIS* 1.3 79.1 - - - +
477B LEU* 1.3 63.5 + - - +
479B MET* 3.2 7.7 + - + +
480B LYS* 3.1 21.0 + - - +
485B VAL* 5.5 0.7 - - + -
487B VAL* 4.0 21.1 - - + -
491B LEU* 4.2 15.5 - - + -
495B LEU* 3.5 32.5 - - + -
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Residues in contact with LEU 477 (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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473B MET 2.9 14.5 + - - +
474B GLU* 3.3 13.7 - - + +
476B LEU* 1.3 76.4 - - - +
478B ASN* 1.3 64.9 + - - +
480B LYS* 3.3 15.2 + - + +
481B CYS* 3.1 33.4 + - - -
495B LEU* 4.6 28.0 - - + +
496B ASN* 4.9 13.0 - - - +
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Residues in contact with ASN 478 (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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474B GLU* 2.7 38.0 + - - +
475B HIS* 3.4 13.0 + - - +
477B LEU* 1.3 77.1 - - - +
479B MET* 1.3 74.5 + - + +
481B CYS* 3.1 10.7 + - - +
482B LYS* 2.8 32.4 + - + +
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Residues in contact with MET 479 (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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202B 4NA 4.1 2.0 - - - +
291B GLU* 5.3 3.4 - - - -
295B MET* 3.9 18.2 - - - +
370B VAL* 4.8 5.6 - - - -
371B GLU* 4.2 13.2 - - + +
475B HIS* 3.0 49.8 + - + +
476B LEU* 3.4 11.0 - - + +
478B ASN* 1.3 83.6 - - + +
480B LYS* 1.3 52.5 + - - +
482B LYS* 2.9 22.1 + - - +
483B ASN 2.7 29.5 + - - -
484B VAL* 3.1 40.4 + - + -
485B VAL* 4.6 13.2 - - + -
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Residues in contact with LYS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B LEU 3.1 8.9 + - - +
477B LEU* 3.5 17.9 - - + +
478B ASN 3.2 0.2 - - - -
479B MET* 1.3 75.4 - - - +
481B CYS* 1.3 57.7 + - - +
482B LYS 2.9 4.7 - - - -
483B ASN* 2.7 36.1 + - - +
485B VAL 4.5 11.4 - - - +
487B VAL* 3.3 38.8 + - + +
488B TYR* 4.3 12.5 + - - -
492B LEU* 3.5 34.1 - - + +
495B LEU* 4.5 12.8 - - + -
496B ASN* 5.4 0.9 - - - +
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Residues in contact with CYS 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B LEU* 3.1 27.4 + - - +
478B ASN* 3.1 13.0 + - - +
480B LYS* 1.3 82.8 - - - +
482B LYS* 1.3 60.4 + - + +
483B ASN* 3.4 6.2 + - - +
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Residues in contact with LYS 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B GLU* 5.2 12.1 - - - +
478B ASN* 2.8 19.5 + - + +
479B MET* 3.0 25.5 - - + +
480B LYS 2.9 0.2 - - - -
481B CYS* 1.3 79.2 - - + +
483B ASN* 1.3 69.3 + - - +
484B VAL* 3.0 25.9 + - + +
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Residues in contact with ASN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B MET 2.7 4.4 + - - -
480B LYS* 2.7 24.9 + - - +
481B CYS* 4.2 6.4 + - - +
482B LYS* 1.3 81.1 - - - +
484B VAL* 1.3 57.6 + - - +
485B VAL* 2.9 19.5 + - - +
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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