Contacts of the helix formed by residues 385 - 396 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338D TYR* 3.9 16.0 + - - -
341D GLY* 3.3 40.3 + - - +
343D VAL* 5.7 0.6 - - - +
383D PHE* 3.4 28.7 - - + -
384D ASN* 1.3 69.7 - - - +
386D GLN* 1.3 57.4 + - - +
388D PHE* 3.7 7.9 - - + -
389D ALA* 3.5 18.9 + - - +
443D PRO* 4.2 6.1 - - + +
446D TRP* 3.5 38.4 - - + -
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Residues in contact with GLN 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D GLY 4.8 2.0 + - - +
384D ASN* 2.8 18.5 + - - +
385D ASN* 1.3 75.2 - - - +
387D GLU* 1.3 68.9 + - - +
388D PHE 3.1 1.3 - - - -
389D ALA* 3.4 6.3 + - - +
390D GLN* 3.2 37.5 + - - +
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D ASN* 4.4 9.4 + - - +
362D TYR* 5.1 6.6 - - + -
363D HIS* 2.9 52.6 + - - +
384D ASN* 2.7 46.7 - - - +
386D GLN* 1.3 83.9 - - - +
388D PHE* 1.3 57.4 + - - +
390D GLN* 3.6 10.1 - - - +
391D LEU* 3.1 37.6 + - + +
409D MET* 5.9 0.2 - - - -
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Residues in contact with PHE 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D ASN* 4.1 5.6 + - - +
383D PHE* 3.9 15.3 - + + -
384D ASN 3.3 2.2 + - - -
385D ASN* 3.7 17.0 - - - -
386D GLN 3.1 0.2 - - - -
387D GLU* 1.3 77.3 - - - +
389D ALA* 1.3 61.2 + - - +
390D GLN 3.0 1.3 - - - -
391D LEU* 3.0 6.7 + - + +
392D LEU* 2.8 41.1 + - + +
406D LEU* 4.0 24.7 - - + -
409D MET* 3.5 46.9 - - + -
410D CYS* 3.7 18.8 - - - -
443D PRO* 3.7 35.0 - - + -
446D TRP* 4.1 13.9 - + - -
447D LEU* 4.8 7.6 - - + -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D ASN 3.5 17.8 + - - +
386D GLN* 3.4 8.0 + - - +
388D PHE* 1.3 82.1 - - - +
390D GLN* 1.3 61.4 + - - +
392D LEU* 3.7 11.6 - - + +
393D ALA* 3.1 22.5 + - - +
446D TRP* 5.2 7.6 - - + -
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Residues in contact with GLN 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D GLN* 3.2 27.4 + - - +
387D GLU* 3.6 14.3 - - - +
388D PHE 3.0 0.2 - - - -
389D ALA* 1.3 75.6 - - - +
391D LEU* 1.3 68.2 + - + +
393D ALA* 2.9 8.7 + - + +
394D GLN* 2.8 48.8 + - + +
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Residues in contact with LEU 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D TYR* 4.1 44.4 - - + +
387D GLU* 3.1 23.5 + - + +
388D PHE* 3.0 12.6 + - + +
390D GLN* 1.3 80.4 - - + +
392D LEU* 1.3 57.8 + - - +
394D GLN* 3.3 19.8 + - + +
395D SER* 2.5 37.4 + - - +
406D LEU* 4.3 23.1 - - + -
409D MET* 4.9 11.7 - - + -
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D PHE* 2.8 30.4 + - + +
389D ALA* 3.7 11.2 - - - +
391D LEU* 1.3 73.7 - - - +
393D ALA* 1.3 58.4 + - - +
395D SER* 3.2 4.7 + - - -
396D VAL* 3.0 23.9 + - - -
403D VAL* 4.5 2.0 - - + -
406D LEU* 3.7 17.0 - - + +
446D TRP* 4.1 28.3 - - + +
447D LEU* 3.7 31.4 - - + +
450D VAL* 3.9 38.2 - - + +
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Residues in contact with ALA 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D ALA 3.1 14.5 + - - +
390D GLN* 2.9 12.6 + - + +
392D LEU* 1.3 73.1 - - - +
394D GLN* 1.3 53.6 + - + +
395D SER 3.0 4.9 - - - -
396D VAL* 2.7 39.7 - - - +
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Residues in contact with GLN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D TYR* 5.5 4.0 + - - -
390D GLN* 2.8 54.0 + - + +
391D LEU* 3.8 19.6 - - + +
393D ALA* 1.3 73.8 - - + +
395D SER* 1.3 61.2 + - - +
396D VAL* 4.3 4.4 - - - +
398D HIS* 4.2 13.9 + - - +
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D LEU* 2.5 21.4 + - - +
392D LEU 3.4 9.2 - - - -
393D ALA 3.0 0.4 - - - -
394D GLN* 1.3 79.8 - - - +
396D VAL* 1.3 66.4 + - - +
397D ASN 2.6 5.7 + - - -
398D HIS* 2.8 22.6 + - - +
399D GLY 4.4 3.1 - - - +
402D THR* 4.8 6.8 + - - -
403D VAL* 4.3 20.7 - - - +
406D LEU* 3.4 25.3 - - - +
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Residues in contact with VAL 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392D LEU 3.0 10.0 + - - +
393D ALA* 2.7 27.8 + - - +
394D GLN* 4.3 4.9 - - - +
395D SER* 1.3 74.9 - - - +
397D ASN* 1.3 86.6 + - + +
398D HIS 4.1 0.2 + - - -
399D GLY 4.3 0.7 - - - +
403D VAL* 5.5 0.5 - - - +
450D VAL* 5.0 11.3 - - + +
453D GLN* 3.1 28.6 + - - +
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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