Contacts of the helix formed by residues 406 - 415 (chain D) in PDB entry 2QJK
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 VAL 406 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402D ALA* 2.9 20.2 + - + +
404D PHE 3.4 0.6 - - - -
405D LEU* 1.3 90.2 - - + +
407D ILE* 1.3 65.6 + - + +
409D PRO* 2.7 22.7 - - - +
410D ILE* 3.0 38.0 + - + +
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Residues in contact with ILE 407 (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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366D TYR* 3.2 59.2 - - + -
399D TYR* 3.9 23.8 - - + +
402D ALA* 3.0 18.4 + - + +
403D TYR* 3.8 20.6 - - + +
406D VAL* 1.3 78.4 - - + +
408D LEU* 1.3 64.5 + - - +
410D ILE* 3.1 5.7 + - - +
411D LEU* 2.8 36.9 + - + +
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Residues in contact with LEU 408 (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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121D TYR* 5.1 0.9 - - - +
346D VAL* 4.3 22.0 - - + -
349D LEU* 3.7 10.7 - - + +
350D ASP* 3.7 22.7 - - + +
351D THR* 3.5 7.1 + - - -
360D ARG* 4.4 3.4 + - - +
363D PHE* 3.5 37.5 - - + -
403D TYR* 3.2 48.7 + - + +
404D PHE* 4.3 9.4 - - + +
407D ILE* 1.3 78.4 - - + +
409D PRO* 1.4 73.4 - - + +
411D LEU* 3.5 7.5 + - + +
412D GLY* 3.3 14.4 + - - -
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Residues in contact with PRO 409 (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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349D LEU* 3.3 26.0 - - + +
351D THR* 2.7 27.0 + - + +
404D PHE 3.4 14.1 - - - +
405D LEU 3.6 17.5 - - - +
406D VAL 2.7 23.1 - - - +
408D LEU* 1.4 88.0 - - + +
410D ILE* 1.3 64.4 + - + +
412D GLY* 3.5 0.7 + - - -
413D ALA* 4.2 2.8 + - - +
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Residues in contact with ILE 410 (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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406D VAL* 3.0 35.6 + - + +
407D ILE* 3.6 7.0 - - - +
409D PRO* 1.3 73.5 - - + +
411D LEU* 1.3 57.4 + - + +
412D GLY 2.5 16.8 + - - -
413D ALA* 2.7 20.8 + - - +
414D ILE* 3.2 38.5 + - + -
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Residues in contact with LEU 411 (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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352D SER* 5.0 0.5 - - - -
360D ARG* 4.2 13.3 + - - +
362D MET* 3.7 31.2 - - + -
363D PHE* 4.0 25.1 - - + +
366D TYR* 3.6 30.5 - - + -
403D TYR* 6.0 0.2 - - + -
407D ILE* 2.8 43.7 + - + +
408D LEU* 4.0 9.6 - - + +
410D ILE* 1.3 76.2 - - + +
412D GLY* 1.3 59.1 + - - +
413D ALA 3.2 0.2 - - - -
414D ILE* 4.4 3.8 - - + -
415D GLU* 2.9 40.8 + - + +
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Residues in contact with GLY 412 (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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351D THR* 3.3 23.5 - - - +
352D SER* 3.5 29.0 - - - -
353D PRO* 4.6 6.4 - - - +
360D ARG* 4.8 0.2 - - - +
408D LEU 3.3 6.3 + - - -
410D ILE 2.5 7.9 + - - -
411D LEU* 1.3 77.4 - - - +
413D ALA* 1.3 57.7 + - - +
415D GLU* 4.9 2.4 + - - +
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Residues in contact with ALA 413 (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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351D THR* 5.4 0.2 - - - -
409D PRO 4.2 2.8 + - - +
410D ILE* 2.7 13.8 + - - +
412D GLY* 1.3 74.3 - - - +
414D ILE* 1.3 65.0 + - + +
415D GLU 3.6 4.0 - - - +
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Residues in contact with ILE 414 (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 MET* 4.2 21.8 - - + -
410D ILE* 3.2 35.5 + - + +
411D LEU* 4.4 3.8 - - + -
413D ALA* 1.3 82.8 - - + +
415D GLU* 1.3 66.1 + - - +
416D LYS* 3.7 5.2 + - - +
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Residues in contact with GLU 415 (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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352D SER* 6.0 1.6 - - - +
360D ARG* 3.1 46.4 + - + +
361D PRO* 3.3 2.2 - - + -
362D MET* 2.5 47.8 + - + +
363D PHE* 2.9 14.8 + - - +
411D LEU* 2.9 29.1 + - + +
412D GLY 5.2 2.2 - - - +
413D ALA 4.3 4.3 - - - +
414D ILE* 1.3 81.2 - - - +
416D LYS* 1.3 74.7 + - - +
417D PRO* 3.0 16.9 - - + +
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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