Contacts of the helix formed by residues 486 - 501 (chain D) in PDB entry 1QQW
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 HIS 486 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444D ARG* 4.6 8.9 - - + +
447D TYR* 3.8 17.0 - + + -
448D VAL* 3.8 26.7 - - + +
482D PHE 3.1 1.1 + - - +
483D THR* 3.1 9.1 + - - +
485D VAL* 1.3 86.8 + - + +
487D PRO* 1.3 85.7 - - + +
488D ASP* 3.1 50.0 + - + -
489D TYR* 2.9 29.4 + - + +
490D GLY 3.2 5.5 + - - -
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Residues in contact with PRO 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D THR* 3.5 19.4 - - + +
485D VAL 4.9 0.2 - - - +
486D HIS* 1.3 99.7 - - + +
488D ASP* 1.3 67.8 + - - +
490D GLY* 3.6 0.9 + - - -
491D SER* 3.0 26.6 + - - -
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Residues in contact with ASP 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D TYR* 3.6 11.1 + - + +
486D HIS* 3.1 24.1 + - + -
487D PRO* 1.3 81.7 - - - +
489D TYR* 1.3 67.0 + - - +
491D SER* 3.4 7.4 + - - -
492D HIS* 3.1 28.6 + - - +
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Residues in contact with TYR 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D LEU* 5.2 0.2 - - + -
197D SER* 2.5 32.5 + - - -
443D VAL* 4.7 0.9 - - + -
447D TYR* 3.3 40.9 + + + -
459D LEU* 3.6 19.0 - - + +
460D CYS* 3.8 15.2 - - - -
463D ILE* 3.6 9.0 - - + +
482D PHE* 3.4 35.7 - + - +
485D VAL* 3.5 36.8 - - + -
486D HIS* 2.9 21.3 + - + +
488D ASP* 1.3 80.1 - - - +
490D GLY* 1.3 66.0 + - - +
493D ILE* 3.4 22.0 + - + +
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Residues in contact with GLY 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D VAL* 4.1 10.1 - - - +
482D PHE* 4.0 10.6 + - - -
483D THR* 3.9 25.6 - - - -
486D HIS 3.2 7.3 + - - -
487D PRO 4.1 0.2 - - - -
489D TYR* 1.3 76.7 - - - +
491D SER* 1.3 56.0 + - - +
493D ILE* 2.7 28.5 + - - +
494D GLN* 2.8 11.3 + - - +
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Residues in contact with SER 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D THR* 4.7 2.0 + - - -
487D PRO 3.0 20.1 + - - -
488D ASP* 3.4 11.8 + - - -
490D GLY* 1.3 72.0 - - - +
492D HIS* 1.3 57.4 + - - +
494D GLN* 3.1 10.2 + - - +
495D ALA* 2.8 36.0 + - - +
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Residues in contact with HIS 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D TYR* 4.7 5.1 + - - -
456D ARG* 4.6 1.6 + - - +
457D LYS* 3.7 37.5 + - + +
460D CYS* 3.6 29.3 - - + +
461D GLU* 4.5 5.9 + - - -
488D ASP 3.1 17.8 + - - +
490D GLY 3.1 0.2 + - - -
491D SER* 1.3 80.6 + - - +
493D ILE* 1.3 63.4 + - - +
495D ALA* 3.5 8.5 - - + +
496D LEU* 3.3 30.8 + - + +
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Residues in contact with ILE 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D CYS* 4.2 21.1 - - - +
463D ILE* 4.3 11.4 - - + -
464D ALA* 4.8 3.1 - - + +
467D LEU* 4.2 11.0 - - + -
479D VAL* 4.2 11.4 - - + -
482D PHE* 3.7 43.1 - - + -
489D TYR* 3.4 27.1 + - + +
490D GLY* 2.7 13.7 + - - +
492D HIS* 1.3 71.9 - - - +
494D GLN* 1.3 68.2 + - - +
496D LEU* 2.9 11.6 + - - +
497D LEU* 2.9 45.3 + - + +
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Residues in contact with GLN 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D GLN* 5.0 4.7 + - - +
476D LYS* 5.6 6.8 - - - +
479D VAL* 3.7 32.1 - - + +
490D GLY 2.8 10.6 + - - +
491D SER* 3.4 13.9 - - - +
493D ILE* 1.3 79.0 - - - +
495D ALA* 1.3 62.6 + - - +
497D LEU* 3.3 11.3 + - - +
498D ASP* 2.8 56.4 + - - +
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Residues in contact with ALA 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D SER 2.8 20.4 + - - +
492D HIS* 3.5 11.7 - - + +
494D GLN* 1.3 75.1 - - - +
496D LEU* 1.3 65.5 + - + +
498D ASP* 3.2 17.3 + - - +
499D LYS* 3.4 9.5 + - - +
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Residues in contact with LEU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D CYS* 3.6 11.4 - - + +
461D GLU* 3.6 50.5 - - + +
464D ALA* 3.6 12.6 - - + -
492D HIS* 3.3 27.3 + - + +
493D ILE* 2.9 10.0 + - - +
495D ALA* 1.3 75.3 - - + +
497D LEU* 1.3 63.4 + - - +
499D LYS* 3.2 19.6 + - + +
500D TYR* 3.1 31.1 - - + +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ALA* 3.9 20.6 - - + +
467D LEU* 3.9 14.4 - - + -
468D LYS* 3.8 32.5 - - + +
475D GLN* 3.9 23.1 - - + +
479D VAL* 3.9 19.1 - - + -
493D ILE* 2.9 35.9 + - + +
494D GLN* 3.5 16.2 - - - +
496D LEU* 1.3 74.0 - - - +
498D ASP* 1.3 67.4 + - - +
500D TYR* 2.9 6.9 + - - +
501D ASN* 2.8 28.5 + - - +
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Residues in contact with ASP 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D GLN* 2.8 43.2 + - - +
495D ALA* 3.2 11.2 + - - +
497D LEU* 1.3 76.2 - - - +
499D LYS* 1.3 52.6 + - - +
501D ASN* 4.3 9.1 + - - -
502D ALA* 2.7 37.1 + - - +
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Residues in contact with LYS 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D ALA 3.4 4.3 + - - +
496D LEU* 3.2 17.2 + - + +
497D LEU 3.0 0.8 - - - -
498D ASP* 1.3 78.7 - - - +
500D TYR* 1.3 78.8 + - + +
502D ALA* 3.3 15.4 - - - +
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Residues in contact with TYR 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D GLU* 4.6 7.6 + - - +
464D ALA* 3.9 22.7 - - + -
465D GLY* 4.2 14.1 + - - -
468D LYS* 3.6 48.2 - - + -
496D LEU* 3.1 42.7 - - + +
497D LEU* 2.9 5.6 + - - +
499D LYS* 1.3 84.7 - - + +
501D ASN* 1.3 67.5 + - - +
502D ALA 3.1 6.1 + - - -
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Residues in contact with ASN 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D LYS* 4.0 9.4 - - - +
472D ILE* 3.6 23.5 - - - +
475D GLN* 2.7 44.2 - - - +
497D LEU* 2.8 25.1 + - - +
498D ASP* 3.9 8.9 + - - +
500D TYR* 1.3 74.9 - - - +
502D ALA* 1.3 63.7 + - - +
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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
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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