Contacts of the helix formed by residues 385 - 394 (chain A) in PDB entry 1KHU
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 ASN 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A TYR* 3.6 20.9 + - - -
341A GLY* 2.7 42.4 + - - +
342A GLU* 3.6 1.6 + - - -
383A PHE* 3.9 16.1 - - - -
384A ASN* 1.3 68.6 - - - +
386A GLN* 1.3 58.0 + - - +
388A PHE* 2.9 2.4 + - - +
389A ALA* 2.6 38.4 + - - +
442A GLY* 5.5 0.2 - - - -
443A PRO* 4.1 13.5 - - - +
446A TRP* 2.9 40.3 - - + -
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Residues in contact with GLN 386 (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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341A GLY 4.8 0.8 + - - -
384A ASN* 3.5 19.5 + - - +
385A ASN* 1.3 77.0 - - - +
387A GLU* 1.3 68.9 + - - +
389A ALA* 3.8 7.1 - - - +
390A GLN* 2.7 49.8 + - - +
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Residues in contact with GLU 387 (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 ASN* 4.0 14.6 + - - +
362A TYR* 5.6 2.6 - - - +
363A HIS* 2.8 57.6 + - - +
381A LYS* 5.9 0.5 - - - +
384A ASN* 2.7 45.6 + - - +
386A GLN* 1.3 83.9 - - - +
388A PHE* 1.3 63.3 + - - +
390A GLN* 3.1 8.6 + - - +
391A LEU* 3.0 28.5 + - + +
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Residues in contact with PHE 388 (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 ASN* 4.0 4.9 + - - +
383A PHE* 3.4 26.2 - + + -
384A ASN 3.1 3.0 + - - +
385A ASN 2.9 6.3 + - - +
387A GLU* 1.3 75.2 - - - +
389A ALA* 1.3 63.1 + - - +
391A LEU* 3.1 9.0 + - + +
392A LEU* 2.8 46.5 + - + +
406A LEU* 3.9 20.2 - - + -
409A MET* 3.4 46.4 - - + -
410A CYS* 3.4 18.4 - - - -
443A PRO* 3.8 33.9 - - + -
446A TRP* 4.3 10.1 - + - -
447A LEU* 4.7 5.8 - - + -
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Residues in contact with ALA 389 (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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385A ASN 2.6 21.3 + - - +
386A GLN* 3.8 9.0 - - - +
388A PHE* 1.3 76.2 - - - +
390A GLN* 1.3 57.7 + - - +
392A LEU* 3.1 13.1 + - + +
393A ALA* 2.8 28.2 + - - +
446A TRP* 5.0 12.1 - - + -
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Residues in contact with GLN 390 (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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386A GLN* 2.7 40.6 + - - +
387A GLU* 3.2 11.1 - - - +
389A ALA* 1.3 78.7 - - - +
391A LEU* 1.3 59.7 + - + +
393A ALA* 3.1 9.4 + - + +
394A GLN* 2.8 54.5 + - + +
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Residues in contact with LEU 391 (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 TYR* 3.8 51.6 - - + +
387A GLU* 3.0 19.0 + - + +
388A PHE* 3.5 14.8 - - + +
390A GLN* 1.3 80.5 - - + +
392A LEU* 1.3 61.7 + - - +
394A GLN* 3.5 24.1 + - + +
395A SER* 3.0 18.5 + - - -
406A LEU* 4.2 17.4 - - + +
409A MET* 5.3 9.4 - - + -
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Residues in contact with LEU 392 (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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388A PHE* 2.8 24.9 + - + +
389A ALA* 3.2 15.0 - - + +
391A LEU* 1.3 77.7 - - - +
393A ALA* 1.3 63.3 + - - +
395A SER* 3.3 11.8 + - - -
396A VAL* 3.3 13.5 + - - +
403A VAL* 4.6 5.6 - - + +
406A LEU* 3.5 25.7 - - + +
446A TRP* 4.0 19.5 - - + +
447A LEU* 3.5 46.2 - - + +
450A VAL* 4.2 19.1 - - + +
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Residues in contact with ALA 393 (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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389A ALA 2.8 13.0 + - - +
390A GLN* 3.3 12.6 - - + +
392A LEU* 1.3 72.6 - - - +
394A GLN* 1.3 55.2 + - + +
395A SER 2.8 17.0 + - - -
396A VAL* 3.1 27.4 + - - +
397A ASN* 5.4 0.2 - - - +
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Residues in contact with GLN 394 (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 TYR* 5.6 1.9 + - - -
390A GLN* 2.8 53.6 + - + +
391A LEU* 3.9 20.2 - - + +
392A LEU 3.4 0.4 - - - -
393A ALA* 1.3 70.9 - - + +
395A SER* 1.3 58.4 + - - +
396A VAL* 3.8 0.4 - - - -
397A ASN* 5.5 2.8 - - - +
398A HIS* 4.0 12.6 + - - +
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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