Contacts of the helix formed by residues 431 - 441 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A ASN* 3.9 21.3 - - - -
398A GLY 2.7 19.8 + - - +
400A CYS* 4.0 16.8 - - + +
421A LEU* 3.6 33.9 - - + -
422A GLN* 4.5 1.1 - - - -
423A PRO* 3.3 26.9 - - + -
424A ALA* 3.5 14.4 - - + -
425A PRO* 3.8 14.8 - - + -
430A TRP* 1.3 74.2 - - - +
432A GLN* 1.3 66.7 + - - +
433A ALA* 3.9 19.5 - - + -
434A TYR* 3.0 35.7 + + + +
435A PHE* 3.0 10.7 + - - +
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Residues in contact with GLN 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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111A LEU 3.8 0.7 - - - +
112A ALA* 3.2 37.0 + - - +
115A SER* 3.8 10.3 - - - -
116A LEU* 3.8 9.5 - - - +
430A TRP* 3.1 31.8 + - + +
431A PHE* 1.3 72.2 - - - +
433A ALA* 1.3 64.4 + - - +
435A PHE* 3.0 6.2 + - - +
436A VAL* 2.9 42.9 + - + +
508A MAN 3.6 36.5 + - - +
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Residues in contact with ALA 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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421A LEU* 3.8 13.7 - - + +
431A PHE* 3.4 19.0 - - + -
432A GLN* 1.3 80.2 - - - +
434A TYR* 1.3 56.5 + - - +
436A VAL* 3.8 7.8 - - - +
437A GLN* 3.1 25.3 + - - +
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Residues in contact with TYR 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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306A TYR* 3.2 19.1 - - - -
353A ARG* 3.8 19.7 - - - -
369A ASN* 3.3 34.1 - - + -
370A VAL 2.5 31.8 + - - -
373A THR* 2.7 18.6 + - - -
398A GLY* 4.6 7.9 - - - -
399A GLU 6.0 0.7 - - - -
400A CYS* 6.5 0.2 - - - -
421A LEU* 3.8 19.6 - - + +
431A PHE* 3.0 30.1 + + + +
433A ALA* 1.3 75.7 - - - +
435A PHE* 1.3 61.3 + - - +
437A GLN* 3.2 9.0 + - - +
438A LEU* 2.9 50.7 + - + +
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Residues in contact with PHE 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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104A TYR* 3.8 10.1 - - - -
108A VAL* 3.9 21.1 - - + -
112A ALA* 3.8 23.8 - - + -
116A LEU* 4.4 3.1 - - + -
124A ALA* 3.8 26.5 - - + -
127A VAL* 3.9 11.7 - - + -
375A PHE* 3.8 21.3 - + - -
397A GLY 3.9 9.0 - - - -
398A GLY* 4.0 8.0 - - - -
430A TRP* 3.5 33.9 - + + -
431A PHE 3.0 9.8 + - - +
432A GLN* 3.4 11.7 - - - +
434A TYR* 1.3 77.2 - - - +
436A VAL* 1.3 65.5 + - + +
438A LEU* 3.2 6.0 + - - +
439A LEU* 2.9 38.4 + - + +
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Residues in contact with VAL 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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116A LEU* 4.1 13.9 - - + -
120A MET* 3.9 13.9 - - + -
432A GLN* 2.9 43.5 + - + +
433A ALA* 3.8 8.3 - - - +
435A PHE* 1.3 79.6 - - + +
437A GLN* 1.3 57.5 + - - +
439A LEU* 3.8 5.8 - - - +
440A THR* 2.8 48.5 + - - +
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Residues in contact with GLN 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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370A VAL 3.2 15.0 + - - -
371A ILE* 3.6 9.4 - - - +
372A GLY 3.5 17.6 + - - +
373A THR* 2.8 38.8 + - - +
421A LEU* 3.9 17.4 - - + +
433A ALA 3.1 16.2 + - - +
434A TYR* 3.5 21.9 - - - +
436A VAL* 1.3 77.4 - - - +
438A LEU* 1.3 61.0 + - - +
440A THR* 3.4 4.2 + - - -
441A ASN* 3.0 40.2 + - - +
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Residues in contact with LEU 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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352A GLY 4.5 0.4 - - - +
353A ARG* 3.9 19.3 - - + -
373A THR* 3.6 23.1 - - - +
374A GLY* 3.5 24.6 - - - +
375A PHE* 3.1 28.8 + - + +
397A GLY* 3.4 34.3 - - - -
398A GLY 3.7 3.8 - - - +
434A TYR* 2.9 38.3 + - + +
435A PHE* 3.5 6.1 - - - +
437A GLN* 1.3 76.8 - - - +
439A LEU* 1.3 57.9 + - - +
441A ASN 3.4 0.5 + - - -
442A ALA* 2.9 25.6 + - - +
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Residues in contact with LEU 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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116A LEU* 4.5 2.2 - - + -
120A MET* 3.7 47.8 - - + +
123A ALA* 4.0 8.5 - - + -
124A ALA* 3.8 16.8 - - + +
127A VAL* 3.7 17.5 - - + -
375A PHE* 3.4 10.2 - - + -
435A PHE* 2.9 26.7 + - + +
436A VAL 3.8 4.3 - - - +
438A LEU* 1.3 76.0 - - - +
440A THR* 1.3 62.4 + - - +
442A ALA* 3.4 15.2 - - - +
445A SER* 5.5 0.9 + - - -
446A PHE* 3.5 35.6 + - + -
447A LEU* 4.7 8.6 - - + +
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Residues in contact with THR 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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120A MET* 4.0 9.5 - - - +
436A VAL* 2.8 34.6 + - - +
437A GLN* 3.7 7.0 - - - -
439A LEU* 1.3 79.3 - - - +
441A ASN* 1.3 70.3 + - - +
442A ALA 3.3 1.8 + - - +
447A LEU* 4.9 12.5 - - + +
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Residues in contact with ASN 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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355A GLY 4.3 2.9 - - - +
356A LYS* 3.9 34.7 - - + +
372A GLY* 4.7 3.6 - - - -
373A THR 3.3 28.2 + - - +
374A GLY* 3.5 9.8 - - - -
437A GLN* 3.0 34.1 + - - +
438A LEU 3.6 2.0 - - - -
440A THR* 1.3 86.5 - - - +
442A ALA* 1.3 64.8 + - - +
443A ASN* 3.6 3.5 + - - +
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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