Contacts of the helix formed by residues 327 - 343 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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325V ALA 4.3 0.4 + - - -
326V GLN* 1.3 73.1 - - - +
328V ASP* 1.3 66.5 + - - +
329V ASP* 3.2 39.3 + - + +
330V GLU* 3.0 35.1 + - + +
331V MET* 2.9 25.2 + - - +
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Residues in contact with ASP 328 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285V ARG* 3.1 35.8 + - - -
291V TYR* 4.1 9.8 - - - +
292V TYR* 3.5 25.7 - - + +
295V ALA* 5.1 6.1 - - + -
310V PHE* 5.9 0.8 - - + -
320V HIS* 4.7 11.9 + - - +
322V PRO* 5.2 0.5 - - - +
323V ILE* 3.7 7.5 + - - +
326V GLN* 3.0 25.2 + - - -
327V GLN* 1.3 71.4 - - - +
329V ASP* 1.3 71.4 + - - +
331V MET* 3.1 7.8 - - - +
332V PHE* 3.1 20.8 + - - +
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Residues in contact with ASP 329 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295V ALA* 4.8 16.3 - - + +
296V GLY* 4.1 8.0 - - - +
327V GLN* 3.2 35.5 + - + +
328V ASP* 1.3 81.5 + - - +
330V GLU* 1.3 60.2 + - - +
332V PHE* 3.4 14.7 - - - +
333V GLN* 4.4 0.9 + - - +
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Residues in contact with GLU 330 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327V GLN* 3.0 49.5 + - + +
329V ASP* 1.3 71.4 - - - +
331V MET* 1.3 72.4 + - + +
332V PHE 2.6 5.5 + - - -
333V GLN* 2.7 20.8 + - + +
334V GLU* 3.2 22.5 + - - +
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Residues in contact with MET 331 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292V TYR* 3.4 36.1 - - + +
326V GLN* 3.4 38.1 - - + +
327V GLN 2.9 20.9 + - - +
328V ASP* 3.1 14.6 - - - +
330V GLU* 1.3 81.7 - - - +
332V PHE* 1.3 56.2 + - - +
334V GLU* 3.3 34.5 + - - +
335V THR* 2.7 35.2 + - - +
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Residues in contact with PHE 332 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289V ILE* 4.9 4.0 - - + -
292V TYR* 3.1 31.6 - - + -
293V LEU* 3.3 43.1 - - + -
296V GLY* 3.2 30.5 - - - -
297V ALA* 4.2 2.2 - - - -
301V MET* 4.6 8.7 - - - -
328V ASP 3.1 7.8 + - - +
329V ASP 3.4 15.0 - - - +
330V GLU 2.6 3.6 + - - -
331V MET* 1.3 75.5 - - - +
333V GLN* 1.3 60.2 + - - +
335V THR* 2.9 4.9 + - - -
336V LEU* 2.6 61.8 + - + +
353V LEU* 3.6 18.6 - - + -
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Residues in contact with GLN 333 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329V ASP 4.4 0.8 + - - +
330V GLU* 2.7 16.5 + - + +
332V PHE* 1.3 82.5 - - - +
334V GLU* 1.3 54.7 + - - +
336V LEU* 3.7 12.7 - - - +
337V GLU* 2.3 63.5 + - + +
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Residues in contact with GLU 334 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226V GLN* 4.9 2.1 - - - +
229V PRO* 6.5 0.2 - - - -
330V GLU* 3.2 17.3 + - - +
331V MET* 3.3 44.7 - - - +
333V GLN* 1.3 77.2 - - - +
335V THR* 1.3 59.5 + - + +
337V GLU* 3.2 15.7 + - - +
338V ALA* 2.8 27.3 + - - +
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Residues in contact with THR 335 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229V PRO* 4.6 15.5 - - - +
230V ILE* 4.7 2.4 - - - +
233V ALA* 4.7 13.4 - - + +
289V ILE* 5.3 5.0 - - - +
292V TYR* 3.4 28.1 - - + -
331V MET* 2.7 20.6 - - - +
332V PHE* 2.9 6.8 + - - -
334V GLU* 1.3 74.3 - - + +
336V LEU* 1.3 73.5 + - - +
338V ALA* 3.3 8.5 - - - +
339V MET* 2.8 39.2 + - - +
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Residues in contact with LEU 336 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289V ILE* 6.3 0.9 - - + -
332V PHE* 2.6 59.7 + - + +
333V GLN* 3.2 21.3 - - - +
335V THR* 1.3 77.2 + - - +
337V GLU* 1.3 65.0 + - - +
339V MET* 3.2 29.9 + - + +
340V THR* 3.2 14.4 + - + +
349V GLN* 3.1 34.2 - - + +
353V LEU* 4.9 8.5 - - + -
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Residues in contact with GLU 337 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226V GLN* 5.9 0.4 - - - +
333V GLN* 2.3 64.8 + - + +
334V GLU* 3.2 13.9 + - - +
336V LEU* 1.3 68.4 - - - +
338V ALA* 1.3 60.8 + - - +
340V THR* 2.3 28.5 + - - -
341V ILE* 3.1 15.1 - - + +
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Residues in contact with ALA 338 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226V GLN* 3.4 33.8 + - + +
229V PRO* 4.4 9.2 - - + -
230V ILE* 3.7 19.1 - - + -
334V GLU 2.8 14.6 + - - +
335V THR* 3.3 13.2 - - - +
337V GLU* 1.3 75.4 - - - +
339V MET* 1.3 56.3 + - - +
341V ILE* 2.6 27.2 + - - +
342V MET* 2.8 10.4 + - - +
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Residues in contact with MET 339 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230V ILE* 3.6 20.8 - - + +
234V PHE* 4.4 25.8 - - + -
289V ILE* 5.6 2.9 - - + -
335V THR* 2.8 22.6 + - - +
336V LEU* 3.4 47.8 - - + +
338V ALA* 1.3 71.5 - - - +
340V THR* 1.3 57.3 + - - +
342V MET* 3.3 3.0 - - - +
343V GLY 2.9 24.3 + - - -
344V PHE* 3.1 39.3 + - + +
349V GLN* 3.6 23.6 - - + +
352V ILE* 4.7 7.2 - - + -
353V LEU* 5.0 10.3 - - + -
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Residues in contact with THR 340 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336V LEU* 3.2 9.3 + - + +
337V GLU* 2.3 34.7 + - - -
338V ALA 2.8 2.0 + - - -
339V MET* 1.3 71.4 - - - +
341V ILE* 1.3 68.5 + - - +
343V GLY* 3.0 15.1 + - - +
344V PHE 4.5 6.5 - - - +
346V GLU* 6.0 0.4 - - - -
349V GLN* 3.5 24.0 - - - +
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Residues in contact with ILE 341 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222V LYS* 4.2 26.7 - - + +
223V GLN* 3.4 15.7 - - + +
226V GLN* 3.5 37.2 - - + +
337V GLU* 3.1 19.7 - - + +
338V ALA 2.6 10.5 + - - +
340V THR* 1.3 76.3 + - - +
342V MET* 1.3 63.8 + - - +
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Residues in contact with MET 342 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223V GLN* 3.6 30.7 - - + +
226V GLN 4.2 8.1 - - - +
227V ALA* 4.4 3.8 - - - -
230V ILE* 3.3 26.9 - - + -
338V ALA 2.8 8.2 + - - +
339V MET* 3.3 9.4 - - - +
341V ILE* 1.3 81.8 - - - +
343V GLY* 1.3 58.0 + - - +
344V PHE* 4.8 9.2 - - + +
445V ARG* 4.3 5.2 - - - +
446V VAL* 3.7 34.3 - - + +
449V ALA* 3.5 28.8 - - + +
450V LEU* 3.6 21.3 - - - -
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Residues in contact with GLY 343 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339V MET 2.9 7.2 + - - -
340V THR 3.0 10.8 + - - -
341V ILE 4.4 0.4 - - - -
342V MET* 1.3 76.4 - - - +
344V PHE* 1.3 67.8 + - - +
345V THR* 3.0 7.8 + - - -
445V ARG* 3.5 19.2 + - - -
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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