Contacts of the helix formed by residues 406 - 415 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402P ALA* 2.9 19.2 + - - +
404P PHE 3.5 0.8 - - - -
405P LEU* 1.3 90.4 - - + +
407P ILE* 1.3 58.6 + - + +
409P PRO* 2.7 20.7 - - - +
410P ILE* 2.8 47.1 + - + +
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Residues in contact with ILE 407 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366P TYR* 3.3 59.9 - - + -
399P TYR* 3.9 23.1 - - + +
402P ALA* 3.0 17.0 + - + +
403P TYR* 3.8 20.9 - - + +
406P VAL* 1.3 76.3 - - + +
408P LEU* 1.3 56.7 + - - +
410P ILE* 3.1 6.2 + - - +
411P LEU* 2.7 47.8 + - + +
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Residues in contact with LEU 408 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P LEU* 6.2 0.2 - - + -
121P TYR* 4.8 1.6 - - - +
346P VAL* 4.1 24.7 - - + -
349P LEU* 3.7 10.3 - - + +
350P ASP* 3.6 23.0 - - + +
351P THR* 3.7 6.6 + - - -
360P ARG* 4.4 3.4 + - - +
363P PHE* 3.5 36.3 - - + -
403P TYR* 3.0 50.3 + - + +
404P PHE* 4.3 8.3 - - + +
407P ILE* 1.3 79.0 - - - +
409P PRO* 1.4 73.5 - - + +
411P LEU* 3.6 6.7 + - + +
412P GLY* 3.3 14.0 + - - -
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Residues in contact with PRO 409 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349P LEU* 3.2 24.7 - - + +
351P THR* 2.7 26.3 + - + +
404P PHE 3.2 26.5 - - - +
405P LEU 3.4 15.5 - - - +
406P VAL* 2.7 22.7 - - - +
408P LEU* 1.4 85.1 - - + +
410P ILE* 1.3 62.3 + - + +
412P GLY* 3.9 0.2 - - - -
413P ALA* 4.2 2.9 + - - +
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Residues in contact with ILE 410 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406P VAL* 2.8 39.9 + - + +
407P ILE* 3.5 8.7 - - - +
409P PRO* 1.3 69.8 - - + +
411P LEU* 1.3 61.6 + - + +
412P GLY 2.5 17.4 + - - -
413P ALA* 2.7 18.7 + - - +
414P ILE* 3.2 37.2 + - + -
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Residues in contact with LEU 411 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352P SER* 5.0 1.0 - - - -
360P ARG* 4.1 13.4 + - - +
362P MET* 3.7 35.7 - - + -
363P PHE* 4.0 24.9 - - + +
366P TYR* 3.4 37.0 - - + -
403P TYR* 6.0 0.7 - - + -
407P ILE* 2.7 32.1 + - + +
408P LEU* 4.0 8.5 - - + +
410P ILE* 1.3 78.7 - - + +
412P GLY* 1.3 62.0 + - - +
413P ALA 3.2 0.2 - - - -
414P ILE* 3.8 6.3 - - + -
415P GLU* 2.9 35.9 + - + +
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Residues in contact with GLY 412 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351P THR* 3.1 24.6 - - - +
352P SER* 3.5 28.9 - - - -
353P PRO* 4.7 6.2 - - - +
408P LEU 3.3 6.8 + - - -
410P ILE 2.5 8.1 + - - -
411P LEU* 1.3 77.7 - - - +
413P ALA* 1.3 56.8 + - - +
415P GLU* 4.9 2.6 + - - +
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Residues in contact with ALA 413 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351P THR* 4.3 0.6 + - - -
409P PRO 4.2 3.4 + - - +
410P ILE* 2.7 13.5 + - - +
412P GLY* 1.3 73.8 - - - +
414P ILE* 1.3 63.4 + - + +
415P GLU 3.9 4.0 + - - +
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Residues in contact with ILE 414 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362P MET* 4.1 22.4 - - + -
410P ILE* 3.2 34.1 + - + +
411P LEU* 4.3 4.7 - - + -
413P ALA* 1.3 83.3 - - + +
415P GLU* 1.3 69.7 + - - +
416P LYS* 3.6 5.9 + - - +
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Residues in contact with GLU 415 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352P SER* 4.8 2.6 + - - +
360P ARG* 2.8 50.9 + - - +
361P PRO* 4.7 1.3 - - + -
362P MET* 2.8 42.9 + - + +
363P PHE* 2.8 13.9 + - - +
411P LEU* 2.9 29.7 + - + +
412P GLY 5.1 2.1 - - - +
413P ALA 4.3 4.2 - - - +
414P ILE* 1.3 81.8 - - - +
416P LYS* 1.3 74.9 + - - +
417P PRO* 3.1 14.4 - - + +
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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