Contacts of the helix formed by residues 328 - 338 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325A ASP* 3.8 6.4 + - - +
326A ILE 3.8 0.2 - - - -
327A SER* 1.3 73.9 - - - +
329A GLN* 1.3 57.9 + - - +
330A LYS* 3.3 20.4 + - - +
331A ARG* 2.8 42.8 + - - +
332A ILE* 2.9 30.3 + - - +
361A TYR* 3.2 19.0 + - + +
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Residues in contact with GLN 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A SER* 3.1 14.5 + - - +
328A ASP* 1.3 69.7 + - - +
330A LYS* 1.3 57.6 + - - +
332A ILE* 3.5 30.3 - - - +
333A ASP* 2.7 64.7 + - - +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ASP* 3.2 12.8 + - - +
329A GLN* 1.3 80.0 - - - +
331A ARG* 1.3 62.4 + - + +
333A ASP* 3.5 6.9 + - - +
334A ILE* 3.1 30.9 + - + +
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Residues in contact with ARG 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 6.2 0.6 - - - +
325A ASP* 4.1 10.1 + - - +
328A ASP* 2.8 34.7 + - - +
330A LYS* 1.3 77.8 - - + +
332A ILE* 1.3 58.9 + - - +
334A ILE* 3.2 14.7 + - + +
335A MET* 2.8 31.8 + - - +
361A TYR* 3.1 75.3 + - + -
362A LEU* 4.4 4.9 - - - +
364A LEU* 3.7 31.5 - - + +
365A GLY* 3.6 16.3 - - - -
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Residues in contact with ILE 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE 4.0 20.4 - - - +
327A SER* 4.1 4.0 - - - -
328A ASP 2.9 26.2 + - - +
329A GLN* 3.0 35.6 + - - +
331A ARG* 1.3 72.3 - - - +
333A ASP* 1.3 53.7 + - - +
335A MET* 3.0 10.1 + - - +
336A VAL* 2.7 42.1 + - + +
342A GLN* 5.1 8.3 - - + +
345A ILE* 4.0 28.0 - - + -
346A GLN* 4.1 14.4 - - - +
361A TYR* 4.3 12.6 - - + -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLN* 2.7 46.8 + - - +
330A LYS* 3.8 6.3 - - - +
332A ILE* 1.3 69.8 - - - +
334A ILE* 1.3 65.0 + - + +
336A VAL* 3.2 10.7 + - - +
337A GLY* 3.0 19.8 + - - -
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Residues in contact with ILE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 3.1 22.3 + - + +
331A ARG* 3.3 13.9 - - + +
333A ASP* 1.3 78.4 - - + +
335A MET* 1.3 62.4 + - - +
337A GLY* 3.1 12.6 + - - -
338A MET* 3.2 35.1 + - + +
364A LEU* 3.9 18.8 - - + -
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Residues in contact with MET 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A ARG 2.8 15.1 + - - +
332A ILE* 3.0 8.9 + - - +
334A ILE* 1.3 76.4 - - - +
336A VAL* 1.3 56.8 + - - +
338A MET* 2.8 30.0 + - - +
339A GLY 3.3 4.7 + - - -
340A TYR* 3.4 22.5 + - + -
345A ILE* 3.9 18.6 - - + -
357A ILE* 3.3 45.8 - - + +
360A THR* 3.6 20.4 - - + -
361A TYR* 3.8 36.8 - - - -
364A LEU* 3.8 14.8 - - + -
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 2.7 34.2 + - + +
333A ASP* 3.7 11.0 - - - +
335A MET* 1.3 71.8 - - - +
337A GLY* 1.3 58.4 + - - +
339A GLY* 2.9 20.4 + - - -
340A TYR 3.4 21.5 - - - +
342A GLN* 4.2 34.3 - - + +
345A ILE* 4.5 2.0 - - + -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ASP 3.0 14.0 + - - -
334A ILE* 3.1 8.7 + - - -
336A VAL* 1.3 77.6 - - - +
338A MET* 1.3 56.9 + - - +
339A GLY 3.3 0.4 + - - -
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A LEU* 3.6 45.5 - - + +
78A THR* 4.7 0.2 - - - +
334A ILE* 3.4 35.4 - - + +
335A MET* 2.8 15.3 + - - +
337A GLY* 1.3 73.3 - - - +
339A GLY* 1.3 58.2 + - - +
340A TYR* 3.6 18.0 - - + -
360A THR* 3.9 23.1 - - + -
364A LEU* 4.0 21.3 - - + -
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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