Contacts of the helix formed by residues 328 - 338 (chain B) in PDB entry 2QNJ
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 ASP 328 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325B ASP* 3.7 16.3 + - - +
327B SER* 1.3 73.6 - - - +
329B GLN* 1.3 59.2 + - - +
330B LYS* 3.2 16.9 + - - +
331B ARG* 2.8 43.0 + - - +
332B ILE* 3.1 25.7 + - - +
361B TYR* 3.2 18.6 + - - +
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Residues in contact with GLN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B SER 2.7 12.0 + - - +
328B ASP* 1.3 70.3 + - - +
330B LYS* 1.3 59.3 + - - +
331B ARG 3.2 2.0 - - - -
332B ILE* 3.6 20.1 - - + +
333B ASP* 2.8 61.3 + - - +
342B GLN* 3.7 21.4 + - - +
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Residues in contact with LYS 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328B ASP* 3.2 12.5 + - - +
329B GLN* 1.3 76.0 - - - +
331B ARG* 1.3 62.9 + - - +
333B ASP* 3.5 7.0 + - - +
334B ILE* 3.3 32.2 + - + +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B LEU* 5.6 2.6 - - - +
325B ASP* 4.2 7.3 + - - +
328B ASP* 2.8 39.1 + - - +
330B LYS* 1.3 78.8 - - - +
332B ILE* 1.3 64.1 + - - +
334B ILE* 3.3 12.7 + - - +
335B MET* 3.2 25.8 + - - +
361B TYR* 2.7 81.4 + - + -
362B LEU* 4.5 2.6 - - - +
364B LEU* 3.6 42.4 - - + +
365B GLY 4.4 15.0 + - - +
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Residues in contact with ILE 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B ILE 4.3 10.3 - - - +
327B SER* 4.2 19.1 - - - +
328B ASP 3.1 19.3 + - - +
329B GLN* 3.2 25.3 + - - +
331B ARG* 1.3 75.4 - - - +
333B ASP* 1.3 59.2 + - - +
335B MET* 3.2 6.9 + - - +
336B VAL* 2.9 30.1 + - + +
342B GLN* 3.9 22.9 - - + +
345B ILE* 3.7 37.9 - - + +
346B GLN* 6.6 0.2 - - - -
349B LEU* 5.0 0.4 - - + -
361B TYR* 4.5 8.7 - - + -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B GLN* 2.8 40.3 + - - +
330B LYS* 3.8 6.8 - - - +
331B ARG 3.3 0.2 - - - -
332B ILE* 1.3 76.3 - - - +
334B ILE* 1.3 66.0 + - + +
336B VAL* 3.2 12.4 + - - +
337B GLY* 3.0 18.2 + - - -
342B GLN* 5.3 3.3 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B LYS* 3.3 25.0 + - + +
331B ARG* 3.3 12.8 + - + +
333B ASP* 1.3 78.2 - - + +
335B MET* 1.3 57.8 + - - +
337B GLY* 3.0 5.8 + - - -
338B MET* 3.0 49.1 + - + +
364B LEU* 4.1 21.5 - - + +
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Residues in contact with MET 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ARG 3.2 13.8 + - - +
332B ILE* 3.2 7.9 + - - +
334B ILE* 1.3 75.3 - - - +
336B VAL* 1.3 66.4 + - - +
337B GLY 3.1 1.3 - - - -
338B MET* 2.9 20.6 + - - +
339B GLY 3.3 0.3 + - - -
340B TYR* 3.0 27.6 + - + +
345B ILE* 3.7 28.3 - - + -
349B LEU* 5.2 0.2 - - + -
357B ILE* 3.5 45.1 - - + +
360B THR* 3.8 20.9 - - + -
361B TYR* 3.8 36.6 - - + -
364B LEU* 4.4 4.3 - - + -
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ILE* 2.9 29.4 + - + +
333B ASP* 3.4 14.6 - - - +
335B MET* 1.3 76.9 - - - +
337B GLY* 1.3 56.0 + - - +
339B GLY* 2.8 22.5 + - - -
340B TYR 3.2 18.9 + - - +
341B SER* 5.9 0.4 - - - -
342B GLN* 4.0 29.4 - - + +
345B ILE* 4.2 2.7 - - + +
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Residues in contact with GLY 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ASP 3.0 12.8 + - - -
334B ILE* 3.0 8.0 + - - -
336B VAL* 1.3 74.1 - - - +
338B MET* 1.3 56.8 + - - +
339B GLY* 2.9 9.4 + - - -
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Residues in contact with MET 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B LEU* 3.4 47.9 - - + +
78B THR* 4.4 5.2 - - - +
334B ILE* 3.0 34.3 + - + +
335B MET* 2.9 16.8 + - - +
337B GLY* 1.3 76.9 - - - +
339B GLY* 1.3 59.5 + - - +
340B TYR* 3.5 16.1 + - + -
360B THR* 3.7 31.4 - - + -
364B LEU* 4.5 6.1 - - + -
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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