Contacts of the helix formed by residues 406 - 415 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402M ALA* 2.9 18.9 + - + +
404M PHE 3.4 0.4 - - - -
405M LEU* 1.3 89.6 - - + +
407M ILE* 1.3 66.2 + - + +
409M PRO* 2.7 22.6 - - - +
410M ILE* 3.1 35.1 + - + +
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Residues in contact with ILE 407 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366M TYR* 3.2 59.7 - - + -
399M TYR* 3.8 23.8 - - + +
402M ALA* 3.0 18.1 + - + +
403M TYR* 3.8 22.2 - - + +
406M VAL* 1.3 78.8 - - + +
408M LEU* 1.3 63.9 + - - +
410M ILE* 3.2 4.2 + - - +
411M LEU* 2.9 35.0 + - + +
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Residues in contact with LEU 408 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M TYR* 4.8 1.8 - - - +
346M VAL* 3.8 28.5 - - + -
349M LEU* 3.7 9.5 - - + +
350M ASP* 3.7 27.2 - - + +
351M THR* 3.5 7.4 + - - -
360M ARG* 4.8 2.0 + - - +
363M PHE* 3.5 24.2 - - + -
403M TYR* 3.2 54.5 + - + +
404M PHE* 4.4 9.4 - - + +
407M ILE* 1.3 74.7 - - - +
409M PRO* 1.3 74.5 - - + +
411M LEU* 3.6 9.1 + - + +
412M GLY* 3.3 15.2 + - - -
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Residues in contact with PRO 409 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349M LEU* 3.3 24.2 - - + +
351M THR* 2.6 26.6 + - + +
404M PHE 3.5 13.2 - - - +
405M LEU 3.6 18.4 - - - +
406M VAL* 2.7 23.6 - - - +
408M LEU* 1.3 89.8 - - + +
410M ILE* 1.3 64.7 + - + +
412M GLY* 3.4 0.7 + - - -
413M ALA* 4.2 2.8 + - - +
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Residues in contact with ILE 410 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406M VAL* 3.1 30.9 + - + +
407M ILE* 3.8 7.2 - - - +
409M PRO* 1.3 78.0 - - + +
411M LEU* 1.3 57.9 + - + +
412M GLY 2.5 17.1 + - - -
413M ALA* 2.7 18.2 + - + +
414M ILE* 3.2 41.0 + - + -
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Residues in contact with LEU 411 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352M SER* 5.0 0.9 - - - -
360M ARG* 4.1 14.3 + - - +
362M MET* 3.4 47.8 - - + -
363M PHE* 4.1 20.4 - - + +
366M TYR* 3.5 17.3 - - + -
403M TYR* 5.9 0.2 - - + -
407M ILE* 2.9 47.8 + - + +
408M LEU* 3.8 10.3 - - + +
410M ILE* 1.3 74.2 - - + +
412M GLY* 1.3 62.8 + - - +
413M ALA 3.2 0.2 - - - -
414M ILE* 3.9 3.4 - - + -
415M GLU* 2.9 40.0 + - + +
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Residues in contact with GLY 412 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351M THR* 3.3 22.6 - - - +
352M SER* 3.6 29.0 - - - -
353M PRO* 4.6 7.1 - - - +
408M LEU 3.3 6.1 + - - -
409M PRO 3.4 0.2 + - - -
410M ILE 2.5 7.9 + - - -
411M LEU* 1.3 77.2 - - - +
413M ALA* 1.3 55.9 + - - +
415M GLU 4.9 2.6 + - - +
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Residues in contact with ALA 413 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351M THR* 4.6 0.2 + - - -
409M PRO 4.2 2.8 + - - +
410M ILE* 2.7 14.3 + - - +
412M GLY* 1.3 73.3 - - - +
414M ILE* 1.3 63.9 + - + +
415M GLU 4.3 3.9 - - - +
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Residues in contact with ILE 414 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362M MET* 3.8 30.9 - - + +
410M ILE* 3.2 36.1 + - + +
411M LEU* 4.3 5.4 - - + -
413M ALA* 1.3 83.2 - - + +
415M GLU* 1.3 68.1 + - - +
416M LYS* 3.7 5.0 + - - +
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Residues in contact with GLU 415 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352M SER* 4.6 2.3 + - - -
354M VAL* 6.1 0.2 - - - +
360M ARG* 2.9 74.6 + - - +
361M PRO* 3.0 4.5 - - + +
362M MET* 3.1 22.2 + - + -
363M PHE* 3.5 5.5 + - - +
411M LEU* 2.9 32.4 + - + +
412M GLY 5.1 2.1 - - - +
413M ALA 3.7 4.7 - - - +
414M ILE* 1.3 82.8 - - - +
416M LYS* 1.3 75.3 + - - +
417M PRO* 3.3 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