Contacts of the helix formed by residues 364 - 375 (chain A) in PDB entry 2QUK
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 THR 364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A THR 4.3 5.6 - - - +
363A ASP* 1.3 75.8 - - - +
365A ALA* 1.3 56.3 + - - +
366A LYS* 3.6 8.6 + - - +
367A GLN* 2.9 40.6 + - - +
368A ILE* 2.7 37.3 + - - +
446A GLN* 4.7 7.4 - - - +
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Residues in contact with ALA 365 (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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364A THR* 1.3 73.5 - - - +
366A LYS* 1.3 64.0 + - - +
368A ILE* 3.5 9.0 + - - +
369A LYS* 3.1 12.6 + - - +
439A GLN* 3.0 42.8 + - + +
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Residues in contact with LYS 366 (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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364A THR* 3.2 8.8 + - - +
365A ALA* 1.3 80.1 - - - +
367A GLN* 1.3 61.1 + - + +
369A LYS* 3.1 8.7 + - - +
370A THR* 2.9 32.8 + - - +
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Residues in contact with GLN 367 (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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362A THR 4.2 1.6 - - - +
363A ASP* 3.5 23.3 + - + -
364A THR* 2.9 47.9 + - - +
366A LYS* 1.3 75.2 - - + +
368A ILE* 1.3 65.8 + - - +
370A THR* 3.2 7.1 + - - -
371A LYS* 3.0 35.6 + - + +
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Residues in contact with ILE 368 (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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359A ILE* 4.0 23.8 - - + -
363A ASP* 4.0 9.6 - - + +
364A THR 2.7 28.3 + - - +
365A ALA* 3.8 6.1 - - - +
367A GLN* 1.3 72.6 - - - +
369A LYS* 1.3 64.7 + - - +
371A LYS* 3.5 3.2 + - - +
372A VAL* 3.0 36.7 + - + +
435A ILE* 4.5 3.4 - - + -
438A LEU* 3.9 24.0 - - + +
439A GLN* 4.0 28.0 - - + +
442A ILE* 3.7 36.8 - - + -
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Residues in contact with LYS 369 (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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365A ALA 3.1 11.2 + - - +
366A LYS* 3.3 12.3 - - - +
368A ILE* 1.3 80.7 - - - +
370A THR* 1.3 61.5 + - - +
373A ASN* 3.1 41.7 + - - +
432A LYS* 6.6 0.2 - - - -
435A ILE* 3.5 30.6 - - + +
439A GLN* 3.9 8.1 - - - +
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Residues in contact with THR 370 (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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366A LYS* 2.9 18.7 + - - +
367A GLN* 3.2 9.3 + - - -
369A LYS* 1.3 74.9 - - - +
371A LYS* 1.3 62.7 + - - +
373A ASN* 3.2 3.2 + - - +
374A LYS* 2.8 56.6 + - + +
375A HIS* 5.6 2.9 - - - +
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Residues in contact with LYS 371 (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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343A LEU* 3.9 7.4 - - + +
356A ASN* 3.8 37.3 - - - +
358A SER 2.8 26.1 + - - +
359A ILE* 3.6 20.4 - - + -
360A PHE* 3.1 20.2 - - - -
363A ASP* 2.6 36.0 + - - +
367A GLN* 3.0 22.6 + - + +
368A ILE 3.9 0.4 - - - +
370A THR* 1.3 76.0 - - - +
372A VAL* 1.3 57.6 + - - +
375A HIS* 2.8 38.8 + - + +
376A ALA 3.2 6.4 + - - -
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Residues in contact with VAL 372 (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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343A LEU* 5.0 2.5 - - + -
359A ILE* 4.2 15.9 - - + -
368A ILE* 3.0 27.4 + - + +
371A LYS* 1.3 76.1 - - - +
373A ASN* 1.3 57.9 + - - +
376A ALA* 3.0 25.5 + - + +
399A SER* 4.8 0.2 - - - -
402A TYR* 6.3 0.2 - - + -
431A LYS* 2.8 38.5 + - + +
434A LEU* 3.8 24.7 - - + -
435A ILE* 3.8 24.5 - - + -
438A LEU* 4.4 11.7 - - + -
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Residues in contact with ASN 373 (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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369A LYS* 3.1 44.4 + - - +
370A THR* 3.9 2.4 - - - +
372A VAL* 1.3 77.8 - - - +
374A LYS* 1.3 70.7 + - + +
428A GLY* 5.0 4.2 - - - +
431A LYS* 3.0 39.9 + - - +
432A LYS* 5.1 0.5 + - - -
435A ILE* 3.4 14.6 - - - +
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Residues in contact with LYS 374 (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 THR* 2.8 45.5 + - + +
373A ASN* 1.3 86.6 - - + +
375A HIS* 1.3 81.6 + - + +
376A ALA 5.3 0.2 - - - -
431A LYS* 5.1 0.4 - - - -
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Residues in contact with HIS 375 (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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343A LEU* 3.5 17.2 - - + +
344A GLN* 3.6 39.0 + - - +
356A ASN* 3.0 44.2 + - + -
370A THR* 5.6 2.6 - - - +
371A LYS* 2.8 34.6 + - + +
374A LYS* 1.3 94.7 + - + +
376A ALA* 1.3 67.8 + - - +
377A PHE* 2.7 7.8 + - - -
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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