Contacts of the helix formed by residues 355 - 365 (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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A GLU* 3.7 7.4 - - - -
121A VAL 4.9 2.7 - - - -
348A SER* 2.8 25.0 + - - -
353A LYS* 3.8 26.1 + - + +
354A TYR* 1.3 80.2 - - - +
356A GLU* 1.3 70.2 + - + +
357A ILE* 3.3 9.1 + - - +
358A THR* 2.8 25.1 + - - -
359A ALA* 2.9 28.4 + - - +
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Residues in contact with GLU 356 (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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54A GLY* 5.2 7.4 - - - -
55A ASN* 3.4 27.0 + - - +
75A HIS* 5.2 0.2 - - - -
120A GLU* 3.6 18.7 + - - +
122A ILE* 5.9 1.7 - - - +
340A TYR* 3.6 14.2 + - + +
355A ASP* 1.3 82.1 - - + +
357A ILE* 1.3 58.9 + - + +
359A ALA* 4.0 0.5 - - - +
360A THR* 3.0 33.6 + - - -
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Residues in contact with ILE 357 (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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335A MET* 3.3 24.0 - - + +
340A TYR* 3.5 27.4 - - + -
344A GLU* 3.7 27.6 - - + +
345A ILE* 3.8 31.0 - - + +
348A SER* 3.0 31.6 - - - +
349A LEU* 4.9 3.1 - - + -
355A ASP* 3.3 7.7 + - - +
356A GLU* 1.3 76.3 - - + +
358A THR* 1.3 68.8 + - - +
360A THR 3.2 1.0 + - - -
361A TYR* 2.9 21.0 + - - +
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Residues in contact with THR 358 (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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119A PHE 4.4 1.6 - - - +
348A SER* 3.7 18.0 + - - -
349A LEU* 4.0 15.7 - - + -
352A MET* 3.5 38.8 - - + -
353A LYS 3.8 0.2 + - - -
354A TYR* 3.6 21.3 + - - +
355A ASP* 2.8 20.2 + - - -
357A ILE* 1.3 76.6 - - - +
359A ALA* 1.3 65.1 + - - +
361A TYR* 3.1 1.9 + - - +
362A LEU* 3.0 32.3 + - + +
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Residues in contact with ALA 359 (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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56A TYR* 3.4 11.4 - - - +
75A HIS* 5.0 2.0 - - + -
119A PHE* 3.5 28.2 + - + +
120A GLU* 3.1 29.2 - - + +
355A ASP 2.9 11.9 + - - +
356A GLU 4.0 1.8 - - - +
358A THR* 1.3 76.3 - - - +
360A THR* 1.3 67.5 + - - +
361A TYR 3.1 0.3 + - - -
362A LEU* 3.2 1.6 + - - +
363A LEU* 3.0 28.6 + - + +
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Residues in contact with THR 360 (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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75A HIS* 3.2 29.0 + - - +
77A LEU* 3.7 4.2 - - + +
78A THR* 4.4 1.5 + - - +
335A MET* 3.6 30.7 - - + -
338A MET* 3.9 22.7 - - + -
340A TYR* 3.7 10.6 + - + -
356A GLU 3.0 21.4 + - - -
357A ILE 3.7 3.6 - - - -
359A ALA* 1.3 77.6 - - - +
361A TYR* 1.3 61.1 + - - +
363A LEU* 3.8 1.7 - - - +
364A LEU* 3.0 28.6 + - + +
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Residues in contact with TYR 361 (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* 5.1 7.2 - - + -
325A ASP 2.5 30.6 + - - -
326A ILE* 4.1 11.2 - - + -
327A SER 3.4 0.7 + - - -
328A ASP* 3.2 26.8 + - + +
331A ARG* 3.1 67.2 + - + -
332A ILE* 4.3 10.5 - - + -
335A MET* 3.8 19.3 - - - -
349A LEU* 3.8 34.8 - - + -
357A ILE 2.9 20.0 + - - +
358A THR 3.1 4.0 + - - +
360A THR* 1.3 72.4 - - - +
362A LEU* 1.3 72.2 + - + +
364A LEU* 3.2 14.3 + - - +
365A GLY 3.4 0.9 + - - -
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Residues in contact with LEU 362 (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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117A LYS* 6.5 2.9 - - + -
118A LEU 4.5 12.3 - - - +
119A PHE* 4.3 26.9 - - + +
324A LEU* 4.0 33.9 - - + -
331A ARG* 4.4 5.2 - - - +
349A LEU* 6.2 0.2 - - + -
352A MET* 4.2 11.4 - - + -
354A TYR* 5.1 0.2 - - + -
358A THR* 3.0 37.8 + - + +
359A ALA 4.0 2.0 - - - +
361A TYR* 1.3 85.0 - - + +
363A LEU* 1.3 56.6 + - - +
365A GLY* 2.8 25.3 + - - -
366A ARG* 3.9 10.4 + - - +
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Residues in contact with LEU 363 (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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56A TYR* 4.1 12.1 - - - +
75A HIS* 3.6 39.7 - - + +
78A THR* 3.9 13.5 - - + +
80A ARG* 2.9 36.2 + - + -
81A GLU 5.5 0.7 - - - +
82A VAL* 4.2 13.5 - - + -
119A PHE* 3.9 40.2 - - + -
359A ALA* 3.0 21.3 + - + +
360A THR 3.8 3.4 - - - +
362A LEU* 1.3 75.8 - - - +
364A LEU* 1.3 61.5 + - - +
365A GLY 3.3 0.5 + - - -
366A ARG* 3.4 16.5 - - - +
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Residues in contact with LEU 364 (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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78A THR* 3.3 21.3 - - - +
80A ARG* 3.5 25.8 + - - +
331A ARG* 3.7 27.9 - - + +
334A ILE* 3.9 28.3 - - + -
335A MET* 3.8 29.8 - - + -
338A MET* 4.0 13.2 - - + -
360A THR* 3.0 16.1 + - + +
361A TYR* 3.5 9.6 - - - +
362A LEU 3.1 0.2 - - - -
363A LEU* 1.3 78.7 - - - +
365A GLY* 1.3 58.5 + - - +
366A ARG 3.2 2.6 + - - -
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Residues in contact with GLY 365 (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* 3.6 21.1 - - - -
361A TYR 3.4 4.8 + - - -
362A LEU 2.8 15.6 + - - -
364A LEU* 1.3 77.0 - - - +
366A ARG* 1.3 57.4 + - - -
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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