Contacts of the helix formed by residues 327 - 343 (chain S) in PDB entry 1I84
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 GLN 327 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325S ALA 4.3 0.2 + - - -
326S GLN* 1.3 74.2 - - - +
328S ASP* 1.3 66.5 + - - +
329S ASP* 3.2 39.3 + - + +
330S GLU* 3.0 37.4 + - + +
331S MET* 2.9 24.9 + - - +
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Residues in contact with ASP 328 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285S ARG* 3.1 35.8 + - - -
291S TYR* 4.1 9.1 - - - +
292S TYR* 3.5 26.4 - - + +
295S ALA* 5.1 5.8 - - + -
310S PHE* 5.9 1.2 - - + -
320S HIS* 4.7 11.7 + - - +
321S VAL 4.8 0.2 - - - +
322S PRO* 5.2 0.5 - - - +
323S ILE* 3.7 7.9 + - - +
326S GLN* 3.0 25.8 + - - -
327S GLN* 1.3 71.1 - - - +
329S ASP* 1.3 72.1 + - - +
331S MET* 3.1 7.8 - - - +
332S PHE* 3.1 21.1 + - - +
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Residues in contact with ASP 329 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295S ALA* 4.8 15.6 - - - +
296S GLY* 4.1 7.5 - - - +
327S GLN* 3.2 35.8 + - + +
328S ASP* 1.3 82.7 + - - +
330S GLU* 1.3 62.6 + - - +
332S PHE* 3.4 15.2 - - - +
333S GLN* 4.5 0.7 + - - +
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Residues in contact with GLU 330 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327S GLN* 3.0 50.6 + - + +
329S ASP* 1.3 71.3 - - - +
331S MET* 1.3 73.6 + - + +
332S PHE 2.6 5.1 + - - -
333S GLN* 2.7 21.8 + - + +
334S GLU* 3.2 21.0 + - - +
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Residues in contact with MET 331 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292S TYR* 3.4 35.9 - - + +
326S GLN* 3.4 37.0 - - + +
327S GLN 2.9 21.3 + - - +
328S ASP* 3.1 15.0 - - - +
330S GLU* 1.3 81.9 - - - +
332S PHE* 1.3 55.8 + - - +
334S GLU* 3.3 33.0 + - - +
335S THR* 2.7 35.5 + - - +
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Residues in contact with PHE 332 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S ILE* 4.9 4.3 - - + -
292S TYR* 3.1 31.8 - - + -
293S LEU* 3.3 42.6 - - + -
296S GLY* 3.2 30.5 - - - -
297S ALA* 4.2 2.0 - - - -
301S MET* 4.6 9.2 - - - -
328S ASP 3.1 8.0 + - - +
329S ASP 3.4 14.1 - - - +
330S GLU 2.6 3.8 + - - -
331S MET* 1.3 75.6 - - - +
333S GLN* 1.3 60.7 + - - +
335S THR* 2.9 5.5 + - - -
336S LEU* 2.6 62.3 + - + +
353S LEU* 3.6 17.7 - - + -
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Residues in contact with GLN 333 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329S ASP 4.5 0.6 + - - +
330S GLU* 2.7 15.9 + - + +
332S PHE* 1.3 81.9 - - - +
334S GLU* 1.3 55.0 + - - +
336S LEU* 3.7 13.3 - - - +
337S GLU* 2.3 63.7 + - + +
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Residues in contact with GLU 334 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226S GLN* 4.9 2.4 - - - +
330S GLU* 3.2 17.7 + - - +
331S MET* 3.3 44.1 - - - +
333S GLN* 1.3 77.0 - - - +
335S THR* 1.3 60.2 + - + +
337S GLU* 3.2 15.2 + - - +
338S ALA* 2.8 26.4 + - - +
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Residues in contact with THR 335 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229S PRO* 4.6 14.8 - - - +
230S ILE* 4.7 1.7 - - - +
233S ALA* 4.7 12.9 - - + +
289S ILE* 5.3 5.5 - - - +
292S TYR* 3.4 28.4 - - + -
331S MET* 2.7 20.4 - - - +
332S PHE* 2.9 6.1 + - - -
334S GLU* 1.3 73.8 - - + +
336S LEU* 1.3 74.0 + - - +
338S ALA* 3.3 9.1 - - - +
339S MET* 2.8 39.6 + - - +
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Residues in contact with LEU 336 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332S PHE* 2.6 60.2 + - + +
333S GLN* 3.2 21.1 - - - +
335S THR* 1.3 77.4 + - - +
337S GLU* 1.3 65.0 + - - +
339S MET* 3.2 30.6 + - + +
340S THR* 3.2 14.7 + - + +
349S GLN* 3.1 33.8 - - + +
353S LEU* 4.9 8.3 - - + -
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Residues in contact with GLU 337 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226S GLN* 5.4 0.7 - - - +
333S GLN* 2.3 65.3 + - + +
334S GLU* 3.2 13.3 + - - +
336S LEU* 1.3 68.8 - - - +
338S ALA* 1.3 62.2 + - - +
340S THR* 2.3 27.3 + - - -
341S ILE* 3.1 15.2 - - + +
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Residues in contact with ALA 338 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226S GLN* 3.4 35.1 + - + +
229S PRO* 4.4 9.0 - - + -
230S ILE* 3.7 18.6 - - + -
334S GLU 2.8 14.6 + - - +
335S THR* 3.3 12.8 - - - +
337S GLU* 1.3 74.3 - - - +
339S MET* 1.3 57.3 - - - +
341S ILE* 2.6 26.7 + - - +
342S MET* 2.8 10.9 + - - +
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Residues in contact with MET 339 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230S ILE* 3.6 21.9 - - + +
234S PHE* 4.4 25.1 - - + -
289S ILE* 5.6 2.7 - - + -
335S THR* 2.8 23.2 + - - +
336S LEU* 3.4 48.0 - - + +
338S ALA* 1.3 71.5 - - - +
340S THR* 1.3 56.7 + - - +
342S MET* 3.3 3.3 - - - +
343S GLY 2.9 23.6 + - - -
344S PHE* 3.1 39.2 + - + +
349S GLN* 3.6 23.1 - - + +
352S ILE* 4.7 7.4 - - + -
353S LEU* 5.0 10.5 - - + -
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Residues in contact with THR 340 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336S LEU* 3.2 10.3 + - + +
337S GLU* 2.3 35.0 + - - -
338S ALA 2.8 2.0 + - - -
339S MET* 1.3 71.5 - - - +
341S ILE* 1.3 68.4 + - - +
343S GLY* 3.0 15.2 + - - -
344S PHE 4.5 6.1 - - - +
346S GLU* 6.0 0.2 - - - -
349S GLN* 3.5 24.2 - - - +
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Residues in contact with ILE 341 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222S LYS* 4.2 26.9 - - + +
223S GLN* 3.4 15.4 - - + +
226S GLN* 3.5 36.1 - - + +
337S GLU* 3.1 18.8 - - + +
338S ALA 2.6 11.0 + - - +
340S THR* 1.3 75.7 + - - +
342S MET* 1.3 64.6 + - - +
343S GLY* 4.4 0.2 - - - -
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Residues in contact with MET 342 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223S GLN* 3.6 29.8 - - - +
226S GLN* 4.2 8.3 - - - +
227S ALA* 4.4 4.9 - - - -
230S ILE* 3.3 28.0 - - + -
338S ALA 2.8 7.7 + - - +
339S MET* 3.3 10.1 - - - +
341S ILE* 1.3 81.7 - - - +
343S GLY* 1.3 59.0 + - - +
344S PHE* 4.8 8.3 - - + +
445S ARG* 4.3 5.1 + - - +
446S VAL* 3.7 34.3 - - + +
449S ALA* 3.5 28.6 - - + +
450S LEU* 3.6 21.8 - - - -
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Residues in contact with GLY 343 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339S MET 2.9 7.5 + - - -
340S THR 3.0 10.3 + - - -
341S ILE 4.4 0.4 - - - -
342S MET* 1.3 76.1 - - - +
344S PHE* 1.3 66.9 + - - +
345S THR* 3.0 7.4 + - - -
348S GLU* 4.5 0.2 - - - +
445S ARG* 3.6 19.5 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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