Contacts of the helix formed by residues 430 - 447 (chain A) in PDB entry 1QF6
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 SER 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A GLY* 1.3 74.2 - - - -
431A ASP* 1.3 59.0 + - - +
432A GLU* 3.0 23.3 + - - +
433A MET* 2.8 54.5 + - - +
434A TRP* 3.0 12.4 + - - -
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Residues in contact with ASP 431 (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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423A ARG* 3.0 26.1 + - - +
427A ARG* 3.4 27.6 + - - -
429A GLY 4.2 4.7 - - - +
430A SER* 1.3 73.7 - - - +
432A GLU* 1.3 70.7 + - - +
434A TRP* 3.9 1.6 - - - -
435A ASP* 2.9 22.7 + - - +
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Residues in contact with GLU 432 (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 SER* 3.0 25.6 - - - +
431A ASP* 1.3 87.0 + - - +
433A MET* 1.3 64.9 + - + +
435A ASP* 3.2 11.3 + - - +
436A ARG* 3.0 24.9 + - - +
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Residues in contact with MET 433 (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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429A GLY* 4.0 10.3 - - - -
430A SER* 2.8 46.1 + - - +
432A GLU* 1.3 74.6 - - + +
434A TRP* 1.3 65.5 + - + +
436A ARG* 3.1 10.9 - - - +
437A ALA* 3.0 24.0 + - - +
487A PHE* 3.6 51.7 - - + +
488A SER* 4.7 3.6 - - - +
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Residues in contact with TRP 434 (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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423A ARG* 3.0 62.4 - - + +
424A PRO* 3.7 7.9 - - + -
427A ARG* 3.5 24.4 - - + +
428A ILE 2.9 19.8 + - - -
429A GLY* 3.6 10.2 + - - -
430A SER 3.0 26.4 + - - -
431A ASP* 4.6 1.3 - - - -
432A GLU 3.3 0.2 - - - -
433A MET* 1.3 79.4 - - + +
435A ASP* 1.3 50.9 + - - +
437A ALA* 3.3 2.8 + - - +
438A GLU* 2.7 46.3 + - + +
459A GLY 5.5 0.2 - - - -
460A ALA 3.3 11.7 - - - -
461A PHE 3.5 16.2 - - - -
462A TYR 3.9 2.0 - - - -
463A GLY* 3.1 31.0 - - - -
464A PRO* 3.2 33.0 - - + -
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Residues in contact with ASP 435 (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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423A ARG* 2.9 25.4 + - - +
431A ASP 2.9 17.8 + - - +
432A GLU* 3.2 10.5 + - - +
434A TRP* 1.3 71.9 - - - +
436A ARG* 1.3 69.5 + - - +
438A GLU* 4.6 2.9 - - - -
439A ALA* 3.0 25.5 + - - +
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Residues in contact with ARG 436 (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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390A GLU* 3.9 21.3 + - - +
393A ILE* 3.5 24.4 - - - +
432A GLU 3.0 14.6 + - - +
433A MET* 3.1 13.7 - - - +
435A ASP* 1.3 80.0 - - - +
437A ALA* 1.3 57.3 + - - +
439A ALA* 3.7 2.8 - - - +
440A ASP* 2.9 67.0 + - - +
487A PHE* 4.2 12.9 - - + -
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Residues in contact with ALA 437 (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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433A MET 3.0 8.6 + - - +
434A TRP* 3.7 3.8 - - + +
436A ARG* 1.3 76.5 - - - +
438A GLU* 1.3 68.0 + - - +
440A ASP* 3.1 16.5 + - - +
441A LEU* 3.2 16.1 + - - +
464A PRO* 3.6 27.8 - - + -
485A LEU* 4.3 8.7 - - + +
487A PHE* 3.5 27.5 - - + -
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Residues in contact with GLU 438 (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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420A LEU* 4.8 6.8 - - + +
422A THR* 3.1 19.3 - - + +
423A ARG* 2.8 65.4 + - - +
434A TRP* 2.7 31.5 + - + +
435A ASP* 4.2 3.3 - - - +
437A ALA* 1.3 72.0 - - - +
439A ALA* 1.3 64.3 + - - +
441A LEU* 3.3 4.0 + - - +
442A ALA* 3.0 22.6 + - - +
454A TYR* 5.3 7.2 + - + -
464A PRO* 4.2 20.9 - - + -
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Residues in contact with ALA 439 (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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435A ASP 3.0 18.9 + - - +
436A ARG* 3.7 2.9 - - - +
438A GLU* 1.3 74.7 - - - +
440A ASP* 1.3 68.0 + - - +
442A ALA* 3.6 6.5 - - - +
443A VAL* 2.9 35.5 + - + +
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Residues in contact with ASP 440 (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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393A ILE* 4.3 13.2 - - + +
394A ARG* 6.1 1.6 - - - -
397A VAL* 5.3 1.7 - - - +
436A ARG* 2.9 65.6 + - - +
437A ALA* 3.1 9.1 + - - +
439A ALA* 1.3 76.8 - - - +
441A LEU* 1.3 65.0 + - - +
443A VAL* 3.5 6.0 + - - +
444A ALA* 3.0 23.2 + - - +
485A LEU* 4.3 13.0 - - + -
487A PHE* 4.2 5.2 - - - -
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Residues in contact with LEU 441 (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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397A VAL* 4.3 13.0 - - + -
420A LEU* 4.0 15.7 - - + -
437A ALA 3.2 8.1 + - - +
438A GLU 3.7 4.7 - - - +
440A ASP* 1.3 73.6 - - - +
442A ALA* 1.3 67.3 + - - +
444A ALA* 2.9 16.6 + - - +
445A LEU* 2.9 14.0 + - - +
464A PRO* 3.4 50.5 - - + +
465A LYS* 4.0 9.2 - - - +
466A ILE* 3.9 25.0 - - + +
483A VAL* 4.5 10.5 - - + +
485A LEU* 3.5 27.1 - - + -
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Residues in contact with ALA 442 (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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420A LEU* 3.9 13.1 - - + +
438A GLU 3.0 15.1 + - - +
439A ALA* 3.6 8.5 - - - +
441A LEU* 1.3 77.4 - - - +
443A VAL* 1.3 59.2 + - + +
445A LEU* 2.8 24.1 + - - +
446A GLU* 3.0 13.2 + - - +
452A PHE* 4.3 10.2 - - + -
454A TYR* 3.5 24.5 - - - +
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Residues in contact with VAL 443 (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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394A ARG* 5.7 6.3 - - + +
439A ALA* 2.9 30.5 + - + +
440A ASP* 3.7 6.1 - - - +
442A ALA* 1.3 73.5 - - + +
444A ALA* 1.3 58.3 + - - +
446A GLU* 3.2 19.4 + - + +
447A GLU* 2.8 43.6 + - + +
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Residues in contact with ALA 444 (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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394A ARG* 5.1 4.0 - - + +
397A VAL* 3.5 28.0 - - + -
398A ASN* 3.4 23.1 - - - +
401A ILE* 5.0 3.8 - - + -
440A ASP 3.0 12.4 + - - +
441A LEU 2.9 9.4 + - - +
443A VAL* 1.3 78.4 - - - +
445A LEU* 1.3 62.0 + - - +
447A GLU* 3.5 4.2 + - - -
448A ASN* 2.4 34.6 + - - +
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Residues in contact with LEU 445 (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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401A ILE* 3.8 26.9 - - + -
418A VAL* 4.4 4.0 - - + -
420A LEU* 3.5 33.7 - - + -
441A LEU 2.9 5.5 + - - +
442A ALA 2.8 12.5 + - - +
444A ALA* 1.3 77.4 - - - +
446A GLU* 1.3 59.3 + - - +
448A ASN* 3.1 12.8 + - - +
449A ASN 3.1 0.2 + - - -
450A ILE* 3.1 46.7 + - + +
452A PHE* 3.5 33.2 - - + -
466A ILE* 3.9 27.6 - - + -
468A PHE* 5.1 1.1 - - + -
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Residues in contact with GLU 446 (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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442A ALA 3.0 10.4 + - - +
443A VAL* 3.4 22.5 - - + +
445A LEU* 1.3 72.4 - - - +
447A GLU* 1.3 63.2 + - + +
448A ASN 2.8 4.9 - - - -
449A ASN* 2.7 32.7 + - - +
450A ILE 4.9 2.5 - - - +
452A PHE* 4.8 5.1 - - + -
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Residues in contact with GLU 447 (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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394A ARG* 3.6 46.2 + - - +
398A ASN* 3.9 22.6 + - - +
443A VAL* 2.8 33.4 + - + +
444A ALA* 3.7 6.5 - - - +
446A GLU* 1.3 78.0 - - + +
448A ASN* 1.3 60.3 + - - +
449A ASN* 3.5 6.0 + - - -
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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