Contacts of the helix formed by residues 431 - 441 (chain B) in PDB entry 1QK0
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 PHE 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369B ASN* 4.1 12.3 - - - -
398B GLY 2.8 20.8 + - - +
400B CYS* 3.9 24.5 - - + +
421B LEU* 3.5 38.1 - - + -
422B GLN* 4.3 2.5 - - - -
423B PRO* 3.2 25.8 - - + -
424B ALA* 3.5 17.5 - - + -
425B PRO* 3.8 14.1 - - + -
430B TRP* 1.3 75.1 - - - +
432B GLN* 1.3 67.8 + - - +
433B ALA* 3.6 22.0 - - + -
434B TYR* 2.9 26.6 + - + +
435B PHE* 3.0 10.7 + - - +
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Residues in contact with GLN 432 (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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111B LEU 3.4 2.2 - - - +
112B ALA* 3.1 33.4 + - - +
115B SER* 4.1 4.0 - - - -
116B LEU* 3.9 14.5 - - - +
430B TRP* 3.0 34.6 + - + +
431B PHE* 1.3 73.2 - - - +
433B ALA* 1.3 64.1 + - - +
435B PHE* 3.0 6.3 + - - +
436B VAL* 2.9 51.4 + - + +
508B MAN 3.2 43.7 - - - +
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Residues in contact with ALA 433 (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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421B LEU* 3.8 12.9 - - + +
422B GLN 5.8 1.8 - - - +
423B PRO* 6.5 0.4 - - + -
431B PHE* 3.3 20.0 - - + -
432B GLN* 1.3 79.0 - - - +
434B TYR* 1.3 62.1 + - - +
436B VAL* 3.5 9.1 + - - +
437B GLN* 3.2 20.8 + - - +
508B MAN 5.3 1.9 + - - +
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Residues in contact with TYR 434 (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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306B TYR* 3.2 18.9 - - - -
353B ARG* 3.7 20.4 - - - -
369B ASN* 3.4 26.2 - - + -
370B VAL 2.6 30.8 + - - -
373B THR* 2.7 14.2 + - - -
398B GLY* 4.6 8.1 - - - +
399B GLU 6.1 0.9 - - - -
421B LEU* 3.7 23.7 - - + +
431B PHE* 2.9 30.4 + + + +
433B ALA* 1.3 75.8 - - - +
435B PHE* 1.3 66.4 + - - +
437B GLN* 3.1 8.8 + - - +
438B LEU* 2.9 52.4 + - + +
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Residues in contact with PHE 435 (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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104B TYR* 3.8 16.6 - - - -
108B VAL* 4.0 18.4 - - + -
112B ALA* 3.7 25.1 - - + -
116B LEU* 4.3 6.3 - - + -
124B ALA* 3.8 32.8 - - + -
127B VAL* 4.0 11.0 - - + -
375B PHE* 3.8 17.0 - + - -
397B GLY 3.7 12.8 - - - -
398B GLY* 4.2 7.8 - - - -
430B TRP* 3.6 24.2 - + + -
431B PHE 3.0 9.6 + - - +
432B GLN* 3.0 15.2 + - - +
434B TYR* 1.3 77.3 - - - +
436B VAL* 1.3 60.8 + - - +
438B LEU* 3.2 6.7 + - - +
439B LEU* 2.9 35.9 + - + +
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Residues in contact with VAL 436 (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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116B LEU* 4.1 15.7 - - + -
120B MET* 3.9 17.7 - - + +
432B GLN* 2.9 44.7 + - + +
433B ALA* 3.8 8.1 - - - +
435B PHE* 1.3 79.6 - - + +
437B GLN* 1.3 54.8 + - - +
439B LEU* 3.8 5.9 - - - +
440B THR* 2.7 42.1 + - - +
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Residues in contact with GLN 437 (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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370B VAL 3.3 12.3 + - - -
371B ILE* 3.6 10.2 - - - +
372B GLY 3.5 16.2 + - - +
373B THR* 2.8 42.5 + - - +
421B LEU* 4.1 17.0 - - + +
433B ALA 3.2 13.7 + - - +
434B TYR* 3.1 22.0 + - - +
436B VAL* 1.3 77.6 - - - +
438B LEU* 1.3 62.5 + - - +
440B THR* 3.4 4.2 + - - -
441B ASN* 3.0 39.4 + - - +
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Residues in contact with LEU 438 (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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352B GLY 4.7 0.2 - - - +
353B ARG* 3.8 14.8 - - + -
373B THR* 3.4 26.2 - - - +
374B GLY* 3.4 22.2 - - - +
375B PHE* 3.2 33.6 + - + +
397B GLY* 3.3 40.6 - - - -
398B GLY 3.7 0.4 - - - +
434B TYR* 2.9 38.1 + - + +
435B PHE* 3.5 7.2 - - - +
437B GLN* 1.3 78.1 - - - +
439B LEU* 1.3 61.0 + - - +
442B ALA 3.0 17.2 + - - -
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Residues in contact with LEU 439 (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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116B LEU* 4.7 2.9 - - + -
120B MET* 3.6 46.9 - - + +
123B ALA* 3.8 9.9 - - + +
124B ALA* 3.8 15.3 - - + +
127B VAL* 3.7 20.2 - - + -
375B PHE* 3.6 9.4 - - + -
435B PHE* 2.9 25.3 + - + +
436B VAL* 3.8 4.0 - - - +
438B LEU* 1.3 74.7 - - - +
440B THR* 1.3 66.9 + - - +
442B ALA* 3.1 18.1 + - - +
445B SER* 5.5 0.3 + - - -
446B PHE* 3.7 32.4 + - + -
447B LEU* 4.6 7.8 - - + +
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Residues in contact with THR 440 (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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120B MET* 3.4 17.7 - - - +
436B VAL* 2.7 27.0 + - - +
437B GLN* 3.8 5.8 - - - -
438B LEU 3.4 0.2 - - - -
439B LEU* 1.3 77.9 - - - +
441B ASN* 1.3 66.9 + - - +
442B ALA 3.4 3.1 + - - +
447B LEU* 4.7 13.3 - - + +
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Residues in contact with ASN 441 (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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356B LYS* 3.7 36.3 + - + +
372B GLY* 4.3 3.4 - - - -
373B THR 2.9 34.6 + - - +
374B GLY* 3.7 9.8 - - - -
375B PHE 4.2 0.5 - - - +
437B GLN* 3.0 25.2 + - - +
438B LEU 3.6 2.0 - - - -
440B THR* 1.3 85.1 - - - +
442B ALA* 1.3 66.3 + - - +
443B ASN* 3.4 8.5 + - - +
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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
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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