Contacts of the helix formed by residues 456 - 479 (chain B) in PDB entry 5I4V
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 456 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B ASP* 3.7 4.9 + - - +
454B LEU* 4.5 3.4 - - - -
455B SER* 1.3 85.6 + - - +
457B PRO* 1.3 65.6 - - - +
458B SER* 3.2 21.6 + - - -
459B GLU* 3.3 50.0 + - - +
460B VAL* 3.6 10.0 + - - +
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Residues in contact with PRO 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B PRO* 3.6 25.8 - - + +
454B LEU* 4.0 28.5 - - + +
455B SER 4.0 5.2 - - - +
456B ASN* 1.3 86.7 - - - +
458B SER* 1.3 59.8 + - - +
460B VAL* 3.2 1.8 + - + -
461B GLU* 2.8 30.0 + - - +
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Residues in contact with SER 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ASN* 3.2 14.5 + - - -
457B PRO* 1.3 78.6 - - - +
459B GLU* 1.3 64.0 + - - +
461B GLU* 3.0 13.3 + - - +
462B VAL* 2.9 32.5 + - - +
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Residues in contact with GLU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER* 5.1 2.8 - - - +
363B LEU* 3.9 25.4 - - + +
364B PRO* 4.4 16.3 - - - +
367B ASP* 5.5 0.7 - - - +
456B ASN* 3.3 36.5 + - - +
457B PRO 3.3 0.2 - - - -
458B SER* 1.3 78.4 - - - +
460B VAL* 1.3 64.0 + - + +
462B VAL* 3.3 9.0 + - - +
463B LEU* 3.3 28.5 + - + +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LEU* 4.4 22.0 - - + -
367B ASP* 5.3 3.6 - - - +
371B LEU* 4.2 7.2 - - + -
447B PHE* 3.6 34.3 - - + +
448B ASN 3.8 4.9 - - - +
449B PRO* 3.7 16.6 - - + -
454B LEU* 4.2 21.5 - - + -
456B ASN 3.8 11.9 - - - +
457B PRO 3.2 6.2 + - - +
458B SER 3.2 0.2 - - - -
459B GLU* 1.3 77.2 - - + +
461B GLU* 1.3 65.0 + - - +
463B LEU* 3.2 10.1 + - - +
464B ARG* 3.1 21.1 + - - +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ARG* 4.4 18.7 + - - -
420A ARG* 6.1 0.5 - - - +
424A LYS* 5.6 3.3 + - - -
449B PRO* 3.8 24.3 - - + +
457B PRO 2.8 14.6 + - - +
458B SER* 3.4 15.0 + - - +
460B VAL* 1.3 76.0 - - - +
462B VAL* 1.3 63.6 + - + +
464B ARG* 3.3 8.9 + - + +
465B GLU* 3.0 43.8 + - + +
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B SER* 2.9 23.4 + - - +
459B GLU* 3.5 11.4 - - - +
461B GLU* 1.3 77.8 - - + +
463B LEU* 1.3 63.1 + - + +
465B GLU* 3.3 16.2 + - - +
466B LYS* 3.1 45.3 + - + +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.7 9.6 - - + +
359B HIS* 3.8 31.0 - - + -
363B LEU* 3.7 31.4 - - + -
447B PHE* 3.7 37.7 - - + -
459B GLU* 3.3 16.6 + - + +
460B VAL* 3.2 9.0 + - - +
462B VAL* 1.3 75.7 - - + +
464B ARG* 1.3 66.4 + - - +
466B LYS* 3.3 23.9 + - + +
467B VAL* 3.2 23.6 + - - +
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Residues in contact with ARG 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A MET* 3.6 25.1 - - - +
426A VAL* 5.7 1.0 - - - +
444B ILE* 2.6 36.4 + - + +
445B ILE* 4.7 3.4 - - - +
447B PHE* 2.2 58.9 + - + +
448B ASN* 3.2 17.2 + - - +
449B PRO* 3.9 17.0 - - - +
450B ASP* 5.9 0.6 + - - -
460B VAL 3.1 7.6 + - - +
461B GLU* 3.5 11.9 - - - +
463B LEU* 1.3 75.3 - - - +
465B GLU* 1.3 58.3 + - - +
467B VAL* 2.8 27.1 + - - +
468B TYR* 3.0 46.0 + - + +
497B ARG* 5.1 8.5 - - - +
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 3.7 23.1 - - + +
420A ARG* 3.0 44.5 + - - +
461B GLU* 3.0 38.1 + - + +
462B VAL* 3.6 19.0 - - - +
463B LEU 3.2 0.4 - - - -
464B ARG* 1.3 77.6 - - + +
466B LYS* 1.3 60.9 + - - +
468B TYR* 3.2 28.4 + - + +
469B ALA* 3.1 18.2 + - - +
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Residues in contact with LYS 466 (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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298B GLU* 3.1 57.2 + - + +
299B MET* 3.7 16.4 - - + -
359B HIS* 5.1 7.1 + - - -
462B VAL* 3.1 36.9 + - + +
463B LEU* 3.6 26.1 - - + +
464B ARG 3.2 0.4 - - - -
465B GLU* 1.3 72.3 - - + +
467B VAL* 1.3 61.4 + - - +
469B ALA* 3.3 7.1 + - - +
470B SER* 2.9 32.8 + - - +
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Residues in contact with VAL 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B MET* 3.8 23.1 - - + -
304B ILE* 4.9 2.7 - - + -
440B CYS* 3.4 43.1 - - + +
443B ALA* 4.0 19.1 - - + -
444B ILE* 3.5 14.8 - - + -
447B PHE* 4.2 9.4 - - + -
463B LEU 3.3 15.3 - - - +
464B ARG* 2.8 9.6 + - - +
466B LYS* 1.3 75.1 - - - +
468B TYR* 1.3 66.0 + - - +
470B SER* 4.5 0.9 - - - -
471B LEU* 2.8 28.5 + - - +
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Residues in contact with TYR 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 4.1 12.3 - - + -
419A PRO* 3.8 32.5 - - + -
420A ARG* 4.4 14.4 - - + -
423A MET* 2.9 38.8 - - + +
444B ILE* 3.9 24.2 - - + -
464B ARG* 3.0 43.7 + - + -
465B GLU* 3.2 36.1 + - + +
467B VAL* 1.3 75.1 - - - +
469B ALA* 1.3 58.4 + - - +
471B LEU* 4.7 0.9 - - - -
472B GLU* 2.9 31.9 + - - +
486B PHE* 3.6 11.4 - - + -
490B LEU* 4.8 4.9 - - + -
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Residues in contact with ALA 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 4.4 12.8 - - + -
297B GLU* 5.3 6.5 - - - +
465B GLU 3.1 9.1 + - - +
466B LYS* 3.7 9.9 - - - +
467B VAL 3.2 0.2 - - - -
468B TYR* 1.3 80.7 - - - +
470B SER* 1.3 60.3 + - - +
472B GLU* 3.4 4.8 + - - +
473B THR* 2.9 31.8 + - - +
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Residues in contact with SER 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.3 18.1 - - - +
299B MET* 2.6 37.2 + - - +
301B VAL* 3.8 16.5 - - - +
304B ILE* 5.7 0.9 - - - -
440B CYS* 5.6 1.6 - - - -
466B LYS* 2.9 17.0 + - - +
467B VAL* 3.9 3.8 - - - -
469B ALA* 1.3 76.2 - - - +
471B LEU* 1.3 57.9 + - - +
473B THR* 3.4 6.5 + - - -
474B TYR* 2.9 29.3 + - - +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLU* 4.4 12.6 - - + -
440B CYS* 3.8 37.6 - - + -
441B LEU* 4.2 15.9 - - + +
444B ILE* 4.1 19.3 - - + -
467B VAL 2.8 17.5 + - - +
468B TYR 3.7 2.9 - - - +
470B SER* 1.3 74.2 - - - +
472B GLU* 1.3 66.1 + - - +
474B TYR* 3.1 11.6 + - + +
475B CYS* 2.9 39.3 + - - -
486B PHE* 3.8 21.8 - - + -
489B LEU* 4.0 13.7 - - + -
490B LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 472 (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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404A LEU* 5.4 1.4 - - - +
408A ARG* 3.2 40.0 + - - -
415A GLN* 4.4 5.5 - - - +
419A PRO* 5.3 0.9 - - - +
468B TYR 2.9 18.5 + - - +
469B ALA* 3.9 4.7 - - - +
471B LEU* 1.3 76.5 - - - +
473B THR* 1.3 64.8 + - - +
475B CYS* 3.0 5.2 + - - +
476B LYS* 2.9 50.6 + - + +
486B PHE* 3.3 48.4 - - + +
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Residues in contact with THR 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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297B GLU* 4.2 17.2 + - + +
469B ALA* 2.9 23.8 + - - +
470B SER* 3.5 7.0 - - - -
472B GLU* 1.3 78.0 - - - +
474B TYR* 1.3 65.3 + - - +
476B LYS* 3.2 7.2 + - - +
477B GLN* 3.0 48.8 + - + +
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Residues in contact with TYR 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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301B VAL* 3.8 27.6 - - + -
434B ASP* 2.8 32.0 + - - -
436B THR* 3.8 28.7 + - + -
437B GLU* 3.9 18.8 - - + -
470B SER 2.9 14.5 + - - +
471B LEU* 3.1 12.8 + - + +
473B THR* 1.3 76.8 - - - +
475B CYS* 1.3 64.0 + - - +
477B GLN* 3.2 9.4 + - + +
478B LYS* 2.8 59.8 + - + +
479B TYR* 4.1 9.9 - + - -
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Residues in contact with CYS 475 (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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437B GLU* 4.2 10.1 - - - -
471B LEU* 2.9 25.0 + - - -
472B GLU 3.4 8.1 - - - +
474B TYR* 1.3 82.1 - - - +
476B LYS* 1.3 57.9 + - + +
479B TYR* 3.0 38.1 + - - +
482B GLN 5.0 2.6 - - - +
485B ARG* 4.2 8.3 - - + -
486B PHE* 4.1 26.2 - - + +
489B LEU* 3.6 31.6 - - - -
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Residues in contact with LYS 476 (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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408A ARG* 4.2 10.6 - - - +
415A GLN* 4.7 7.1 + - - -
472B GLU* 2.9 50.0 + - + +
473B THR* 3.8 5.6 - - - +
475B CYS* 1.3 76.6 - - + +
477B GLN* 1.3 63.3 + - + +
479B TYR 4.9 0.2 - - - -
480B PRO* 3.3 28.8 - - - +
483B GLN 6.2 0.4 - - - -
486B PHE* 6.5 0.4 - - + -
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Residues in contact with GLN 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 THR* 3.0 41.6 + - + +
474B TYR* 3.7 9.4 - - + +
476B LYS* 1.3 78.1 - - + +
478B LYS* 1.3 61.5 + - + +
480B PRO* 3.4 13.2 - - - +
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASP* 5.1 1.8 + - - +
474B TYR* 2.8 52.9 + - + +
477B GLN* 1.3 75.2 - - + +
479B TYR* 1.3 92.9 + - + +
480B PRO* 3.4 4.5 - - - +
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Residues in contact with TYR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B ARG* 4.5 3.4 + - + -
434B ASP* 2.7 32.2 + - - +
437B GLU* 3.4 16.4 - - - -
474B TYR* 4.1 4.7 - + - -
475B CYS* 3.0 26.4 + - - +
476B LYS* 4.9 0.7 - - - -
478B LYS* 1.3 110.2 - - + +
480B PRO* 1.3 59.6 - - - +
481B GLU* 3.2 3.4 - - - -
482B GLN* 2.8 45.8 + - + +
485B ARG* 3.8 39.9 + - + -
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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