Contacts of the helix formed by residues 406 - 415 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402J ALA* 2.9 20.4 + - + +
404J PHE 3.4 0.6 - - - -
405J LEU* 1.3 90.1 - - + +
407J ILE* 1.3 67.5 + - + +
409J PRO* 2.7 21.9 - - - +
410J ILE* 3.0 37.0 + - + +
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Residues in contact with ILE 407 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366J TYR* 3.3 58.6 - - + -
399J TYR* 3.9 23.1 - - + +
402J ALA* 3.0 17.3 + - + +
403J TYR* 3.8 22.4 - - + +
406J VAL* 1.3 78.4 - - + +
408J LEU* 1.3 58.3 + - - +
410J ILE* 3.3 4.5 + - - +
411J LEU* 2.8 44.2 + - + +
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Residues in contact with LEU 408 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J TYR* 5.0 1.1 - - - +
346J VAL* 4.3 22.2 - - + -
349J LEU* 3.4 12.6 - - + +
350J ASP* 3.4 31.2 - - + +
351J THR* 3.4 7.6 + - - -
360J ARG* 4.3 4.2 + - - +
363J PHE* 3.6 27.6 - - + -
403J TYR* 3.1 50.7 + - + +
404J PHE* 4.3 8.5 - - + +
407J ILE* 1.3 75.4 - - - +
409J PRO* 1.3 74.7 - - + +
411J LEU* 3.6 6.5 + - + +
412J GLY* 3.3 15.6 + - - -
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Residues in contact with PRO 409 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349J LEU* 3.1 25.8 - - + +
351J THR* 2.6 28.1 + - + +
404J PHE 3.4 14.4 - - - +
405J LEU* 3.6 17.7 - - - +
406J VAL* 2.7 22.7 - - - +
408J LEU* 1.3 87.6 - - + +
410J ILE* 1.3 63.2 + - + +
412J GLY* 3.9 0.3 - - - -
413J ALA* 4.2 3.1 + - - +
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Residues in contact with ILE 410 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406J VAL* 3.0 37.0 + - + +
407J ILE* 3.7 4.5 - - - +
409J PRO* 1.3 73.5 - - + +
411J LEU* 1.3 62.6 + - + +
412J GLY 2.5 17.7 + - - -
413J ALA* 2.7 20.3 + - - +
414J ILE* 3.2 33.5 + - + +
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Residues in contact with LEU 411 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352J SER* 4.9 0.7 - - - -
360J ARG* 4.2 8.2 + - - +
362J MET* 3.9 35.4 - - + -
363J PHE* 4.0 25.6 - - + +
366J TYR* 3.5 35.9 - - + -
403J TYR* 6.2 0.7 - - + -
407J ILE* 2.8 37.0 + - + +
408J LEU* 4.0 7.4 - - + +
410J ILE* 1.3 81.2 - - + +
412J GLY* 1.3 58.2 + - - +
413J ALA 3.2 0.4 - - - -
414J ILE* 4.4 2.5 - - + +
415J GLU* 2.9 47.9 + - + +
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Residues in contact with GLY 412 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351J THR* 3.1 25.4 - - - +
352J SER* 3.4 29.3 - - - -
353J PRO* 4.6 6.8 - - - +
408J LEU 3.3 7.4 + - - -
410J ILE 2.5 7.7 + - - -
411J LEU* 1.3 75.4 - - - +
413J ALA* 1.3 56.7 + - - +
415J GLU* 4.9 2.4 + - - +
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Residues in contact with ALA 413 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351J THR* 5.2 0.2 - - - -
409J PRO 4.2 3.2 + - - +
410J ILE* 2.7 13.7 + - - +
412J GLY* 1.3 74.4 - - - +
414J ILE* 1.3 65.4 + - + +
415J GLU 3.6 4.1 + - - +
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Residues in contact with ILE 414 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362J MET* 4.2 26.5 - - + +
410J ILE* 3.2 31.0 + - + +
411J LEU* 4.6 2.7 - - + -
413J ALA* 1.3 83.2 - - + +
415J GLU* 1.3 66.4 + - - +
416J LYS* 3.6 4.3 + - - +
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Residues in contact with GLU 415 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352J SER* 4.8 2.6 + - - +
360J ARG* 2.9 52.7 + - + -
362J MET* 3.0 32.3 + - + +
363J PHE* 2.7 30.9 + - - +
411J LEU* 2.9 28.9 + - - +
412J GLY 5.2 2.0 - - - +
413J ALA 3.6 4.9 - - - +
414J ILE* 1.3 77.5 - - - +
416J LYS* 1.3 76.3 + - - +
417J PRO* 3.2 14.6 - - + +
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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