Contacts of the helix formed by residues 430 - 438 (chain A) in PDB entry 1KNU
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 GLN 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A LYS* 5.7 2.8 - - - +
428A SER 3.8 0.2 + - - -
429A SER* 1.3 75.6 - - - +
431A LEU* 1.3 60.0 + - - +
432A PHE* 3.1 4.9 - - - +
433A ALA* 3.2 17.9 + - - +
434A LYS* 2.9 35.9 + - - +
411B ASP* 3.5 32.1 - - - +
414B LEU* 3.2 34.7 - - + +
415B GLN* 3.8 21.8 + - + +
418B GLU* 3.7 21.6 + - - -
432B PHE* 3.9 7.6 - - - -
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Residues in contact with LEU 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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377A LEU* 4.1 41.5 - - + +
379A LEU* 4.1 15.3 - - + -
421A LEU* 4.2 15.9 - - + +
425A HIS* 3.4 46.0 - - + +
428A SER* 3.4 29.1 + - - +
429A SER 3.1 3.3 - - - -
430A GLN* 1.3 75.3 - - - +
432A PHE* 1.3 61.1 + - - +
434A LYS* 3.2 7.9 + - + +
435A LEU* 2.8 33.2 + - + +
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Residues in contact with PHE 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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414A LEU* 3.9 29.4 - - + -
417A LEU* 4.1 18.6 - - + -
418A GLU* 4.0 40.4 - - + +
421A LEU* 3.5 28.9 - - + +
422A LYS* 5.9 4.9 - - + +
430A GLN* 4.9 2.2 - - - -
431A LEU* 1.3 81.9 - - - +
433A ALA* 1.3 63.3 + - - +
435A LEU* 3.3 1.9 + - + +
436A LEU* 3.2 51.7 + - + +
418B GLU* 5.4 0.4 - - - -
432B PHE* 4.6 17.5 - + + -
433B ALA* 3.8 27.4 - - + -
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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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430A GLN* 3.2 31.8 + - - +
432A PHE* 1.3 80.8 - - - +
434A LYS* 1.3 63.7 + - - +
436A LEU* 3.6 3.3 + - - +
437A GLN* 3.4 27.0 + - - +
414B LEU* 3.8 21.3 - - + -
432B PHE* 4.6 1.5 - - + -
436B LEU* 3.7 28.8 - - + +
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Residues in contact with LYS 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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377A LEU* 4.1 21.8 - - + -
429A SER 4.6 5.5 + - - -
430A GLN* 2.9 27.1 + - - +
431A LEU* 3.8 8.9 - - + +
433A ALA* 1.3 78.3 - - - +
435A LEU* 1.3 61.4 + - - +
437A GLN* 3.3 22.4 + - + +
438A LYS* 3.5 28.5 + - - +
407B GLU* 3.8 29.2 - - - +
410B GLN* 5.4 9.0 - - - +
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Residues in contact with LEU 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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374A PHE* 3.4 37.7 - - + -
377A LEU* 3.9 13.2 - - + +
379A LEU* 3.8 22.0 - - + -
383A ASP* 5.7 0.7 - - + +
387A PHE* 3.7 43.6 - - + -
417A LEU* 4.3 10.3 - - + -
421A LEU* 4.2 19.5 - - + -
431A LEU* 2.8 18.1 + - + +
432A PHE* 3.3 5.1 + - + +
434A LYS* 1.3 75.1 - - - +
436A LEU* 1.3 65.8 + - + +
438A LYS* 3.0 20.1 + - + +
439A MET 4.2 0.5 + - - -
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Residues in contact with LEU 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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387A PHE* 5.2 6.1 - - + -
390A VAL* 4.9 9.0 - - + -
414A LEU* 3.9 22.9 - - + -
417A LEU* 5.0 7.2 - - + -
432A PHE* 3.2 42.7 + - + +
433A ALA 4.0 3.6 - - - +
435A LEU* 1.3 77.9 - - - +
437A GLN* 1.3 59.4 + - - +
439A MET* 2.9 35.5 - - + +
433B ALA* 4.0 13.5 - - + +
436B LEU* 3.8 40.6 - - + -
437B GLN* 5.2 10.6 - - + +
440B THR* 4.0 5.7 - - - +
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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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433A ALA* 3.4 18.7 + - - +
434A LYS* 3.3 20.5 + - + +
435A LEU 3.1 0.8 - - - -
436A LEU* 1.3 79.2 - - - +
438A LYS* 1.3 62.1 + - - +
439A MET 3.1 2.2 + - - -
440A THR* 3.3 21.9 + - - -
441A ASP* 4.0 3.0 - - - +
390B VAL* 5.9 0.8 - - - +
394B SER* 4.9 2.0 + - - -
396B ASP* 6.3 0.8 - - - -
410B GLN* 4.3 20.6 + - - +
414B LEU* 5.4 2.6 - - - +
436B LEU* 4.8 11.7 - - + +
439B MET* 3.2 43.4 - - + +
440B THR* 4.4 7.4 - - + -
443B ARG* 4.9 12.1 - - - +
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Residues in contact with LYS 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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370A PHE* 3.7 11.4 - - + -
373A LYS* 4.6 16.3 + - + +
374A PHE* 3.4 38.8 - - + +
377A LEU* 3.6 37.2 - - - +
387A PHE* 5.2 2.9 - - + -
434A LYS* 3.5 29.6 + - - +
435A LEU 3.0 15.9 + - - +
437A GLN* 1.3 75.3 - - - +
439A MET* 1.3 63.6 + - - +
440A THR 3.1 0.7 - - - -
441A ASP* 3.0 36.7 + - - +
442A LEU* 3.3 9.5 + - + +
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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