Contacts of the helix formed by residues 490 - 508 (chain A) in PDB entry 2QFZ
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 ASP 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A ARG* 4.7 5.8 - - - +
434A CYS* 4.8 3.1 - - - -
488A HIS 4.3 7.1 - - - +
489A TRP* 1.3 73.0 - - - +
491A ASP* 1.3 63.1 + - - +
492A GLU* 3.1 27.5 + - - +
493A ASP* 3.0 23.2 + - - +
494A ILE* 3.3 15.6 + - - +
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Residues in contact with ASP 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ARG* 5.1 17.1 - - + +
490A ASP* 1.3 76.8 - - - +
492A GLU* 1.3 62.8 + - - +
494A ILE* 3.3 8.4 + - - +
495A SER* 2.8 32.3 + - - +
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A ASP* 3.1 15.3 + - - +
491A ASP* 1.3 80.8 - - - +
493A ASP* 1.3 60.9 + - - +
495A SER* 3.6 5.8 + - - -
496A LEU* 3.2 30.7 + - + +
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Residues in contact with ASP 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A ARG* 5.1 6.9 + - - -
488A HIS* 4.4 4.9 + - - +
489A TRP* 3.5 46.4 + - + -
490A ASP* 3.0 36.3 + - - +
492A GLU* 1.3 76.5 - - - +
494A ILE* 1.3 59.5 + - - +
496A LEU* 3.4 2.8 + - - -
497A LEU* 3.0 15.1 + - - +
1008A UNX 2.8 23.8 - - - -
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Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL* 5.1 4.5 - - + -
434A CYS* 3.8 38.1 - - + +
437A ARG* 3.7 27.8 - - + -
438A LEU* 3.8 36.6 - - + +
489A TRP* 4.0 22.0 - - + -
490A ASP 3.3 11.3 + - - +
491A ASP* 3.3 6.3 + - - +
493A ASP* 1.3 75.2 - - - +
495A SER* 1.3 59.0 + - - +
497A LEU* 3.2 9.0 + - + +
498A LEU* 2.9 36.9 + - + +
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Residues in contact with SER 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TRP* 5.6 1.7 - - - -
437A ARG* 4.1 23.7 + - - +
491A ASP* 2.8 26.1 + - - +
492A GLU* 3.9 6.8 - - - -
494A ILE* 1.3 74.9 - - - +
496A LEU* 1.3 58.2 + - - +
498A LEU* 3.5 4.1 + - - +
499A ALA* 3.0 29.3 + - - +
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A GLU* 3.2 19.5 + - + +
493A ASP* 3.6 5.2 - - - +
495A SER* 1.3 76.3 - - - +
497A LEU* 1.3 66.7 + - - +
499A ALA* 3.1 8.6 + - - +
500A GLU* 3.0 29.4 + - + +
1008A UNX 3.7 9.0 - - - -
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A LEU* 5.6 1.1 - - + -
430A VAL* 5.9 1.6 - - + -
438A LEU* 4.4 7.0 - - + -
456A VAL* 3.9 24.9 - - + +
459A ALA* 3.5 16.4 - - + +
460A PHE* 3.4 53.4 - - + +
463A ARG* 4.9 4.9 - - + -
489A TRP* 4.1 17.5 - - + -
493A ASP 3.0 15.3 + - - +
494A ILE* 3.2 19.5 + - + +
496A LEU* 1.3 74.1 - - - +
498A LEU* 1.3 59.2 + - - +
500A GLU* 3.4 6.0 + - + +
501A ALA* 2.9 28.4 + - - +
1008A UNX 3.5 5.7 - - - -
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TRP* 3.7 16.8 - - + +
437A ARG* 3.5 24.2 - - - +
438A LEU* 4.0 18.6 - - + -
441A THR* 3.2 34.5 - - + +
442A TYR* 4.8 2.9 - - + -
452A PHE* 3.9 26.6 - - + -
456A VAL* 3.9 15.5 - - + -
494A ILE* 2.9 29.7 + - + +
495A SER* 3.9 4.3 - - - +
497A LEU* 1.3 76.7 - - - +
499A ALA* 1.3 57.3 + - - +
501A ALA* 3.4 3.9 + - - +
502A TYR* 2.9 30.0 + - - +
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TRP* 4.4 7.5 - - + -
495A SER 3.0 18.1 + - - +
496A LEU* 3.1 7.8 + - - +
498A LEU* 1.3 76.1 - - - +
500A GLU* 1.3 63.7 + - - +
502A TYR* 3.4 8.3 + - - +
503A ARG* 3.1 25.5 + - - +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459A ALA* 3.9 13.5 - - + +
462A VAL* 6.5 0.4 - - + -
496A LEU* 3.0 16.8 + - + +
497A LEU* 3.6 9.9 - - + +
499A ALA* 1.3 78.7 - - - +
501A ALA* 1.3 64.8 + - - +
503A ARG* 3.1 40.8 + - - +
504A LEU* 2.9 30.0 + - + +
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Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A PHE* 3.8 10.1 - - + -
455A TYR* 3.6 33.7 - - - +
456A VAL* 3.7 27.8 - - + +
459A ALA* 3.8 3.2 - - + +
497A LEU 2.9 20.4 + - - +
498A LEU 3.6 5.8 - - - +
500A GLU* 1.3 71.2 - - - +
502A TYR* 1.3 57.4 + - - +
504A LEU* 3.3 2.3 + - - +
505A LYS* 3.0 25.6 + - - +
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Residues in contact with TYR 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TRP* 3.6 30.5 - + + -
445A GLU* 3.8 17.9 - - - -
452A PHE* 3.9 15.2 - + - -
498A LEU 2.9 18.4 + - - +
499A ALA* 3.5 6.1 - - - +
501A ALA* 1.3 76.5 - - - +
503A ARG* 1.3 63.2 + - - +
505A LYS* 3.2 26.9 - - + +
506A PHE* 3.4 43.7 - + - -
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Residues in contact with ARG 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A VAL* 5.9 3.4 - - - +
499A ALA 3.1 12.2 + - - +
500A GLU* 3.1 35.8 + - - +
502A TYR* 1.3 78.1 - - - +
504A LEU* 1.3 87.9 + - - +
506A PHE* 2.9 24.1 + - - +
507A ALA* 3.1 21.1 + - + +
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Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LEU* 4.8 2.3 - - + +
399A ILE* 3.5 48.8 - - + +
455A TYR* 3.9 14.4 - - + +
458A ALA* 3.9 7.2 - - + -
459A ALA* 3.5 38.1 - - + +
462A VAL* 4.9 3.4 - - + -
500A GLU* 2.9 17.2 + - + +
501A ALA* 3.3 4.5 + - - +
503A ARG* 1.3 108.2 - - - +
505A LYS* 1.3 63.2 + - - +
507A ALA* 3.7 4.4 - - + +
508A PHE* 3.2 27.7 + - - +
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Residues in contact with LYS 505 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A GLU* 4.2 15.5 + - - +
446A PRO* 5.6 5.9 + - - +
451A HIS* 4.2 20.4 + - + -
452A PHE* 4.0 26.0 - - + -
455A TYR* 3.6 31.9 + - + -
501A ALA 3.0 12.7 + - - +
502A TYR* 3.2 22.7 - - + +
504A LEU* 1.3 78.0 - - - +
506A PHE* 1.3 83.0 + - + +
508A PHE* 3.9 12.1 - - - -
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Residues in contact with PHE 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A TYR* 3.4 53.2 - + - -
503A ARG* 2.9 9.2 + - - +
505A LYS* 1.3 100.4 - - + +
507A ALA* 1.3 64.8 + - - +
508A PHE 3.6 6.3 - - - +
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Residues in contact with ALA 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A ILE* 4.8 11.9 - - + -
503A ARG* 3.1 22.6 + - + +
504A LEU* 3.3 13.0 + - - +
506A PHE* 1.3 74.6 - - - +
508A PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A LEU* 3.7 26.7 - - + -
398A ARG* 5.6 13.2 - - + +
399A ILE* 5.0 4.6 - - + +
455A TYR* 4.3 12.8 - - + +
504A LEU 3.2 11.9 + - - +
505A LYS 3.9 13.5 - - - -
506A PHE 3.7 6.0 - - - +
507A ALA* 1.3 85.2 - - - +
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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
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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