Contacts of the helix formed by residues 326 - 341 (chain G) in PDB entry 1O1F
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 326 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324G SER 4.4 0.4 + - - -
325G ILE* 1.3 73.0 - - - +
327G ASP* 1.3 65.6 + - - +
328G GLN* 3.0 21.6 + - - +
329G GLU* 2.9 51.2 + - + +
330G GLU* 2.9 19.7 + - + +
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Residues in contact with ASP 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ARG* 3.2 33.9 + - - -
286G HIS* 5.0 1.9 - - - +
289G TYR* 3.7 30.3 - - - +
290G GLN* 3.3 16.7 + - - +
293G SER* 3.9 10.2 + - - -
320G ILE 4.7 1.9 - - - +
321G THR* 4.5 10.9 + - - -
322G VAL 5.3 1.4 + - - +
325G ILE* 4.5 13.4 - - - +
326G ASP* 1.3 73.1 + - - +
328G GLN* 1.3 63.0 + - + +
330G GLU* 4.0 6.6 - - - +
331G LEU* 3.1 21.1 + - - +
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Residues in contact with GLN 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293G SER* 3.8 32.2 + - - +
294G ASN 4.5 1.2 - - - +
295G MLY 3.7 48.1 - - + +
326G ASP* 3.8 18.9 + - - +
327G ASP* 1.3 82.3 - - + +
329G GLU* 1.3 59.6 + - - +
331G LEU* 3.7 6.8 + - - +
332G MET* 3.4 17.5 - - - +
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Residues in contact with GLU 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295G MLY 5.7 0.2 - - - -
326G ASP* 2.9 34.8 + - + +
328G GLN* 1.3 76.6 - - - +
330G GLU* 1.3 75.1 + - + +
332G MET* 3.2 12.3 + - - +
333G ALA* 3.0 18.8 + - - +
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Residues in contact with GLU 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G GLN* 3.5 20.4 - - + +
325G ILE* 4.4 17.4 - - + +
326G ASP* 2.9 26.7 + - - +
327G ASP* 3.9 4.9 - - - +
329G GLU* 1.3 84.0 - - - +
331G LEU* 1.3 51.7 + - - +
333G ALA* 2.7 15.4 + - + +
334G THR* 2.6 41.1 + - - +
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Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G GLN* 2.8 51.8 - - + +
291G ILE* 3.1 19.3 - - + +
293G SER* 3.8 7.0 - - - +
295G MLY 4.9 7.6 - - + +
296G MLY 3.8 30.5 - - + +
299G LEU* 4.2 9.2 - - + -
327G ASP 3.1 15.3 + - - +
328G GLN* 3.7 8.3 - - - +
329G GLU 3.3 0.2 - - - -
330G GLU* 1.3 75.1 - - - +
332G MET* 1.3 59.6 + - + +
334G THR* 3.3 3.3 - - + +
335G ASP* 2.8 28.8 + - - +
352G TYR* 4.0 17.4 + - + +
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Residues in contact with MET 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295G MLY 3.0 56.1 - - + +
296G MLY 4.8 24.0 - - - -
328G GLN 3.4 11.4 - - - +
329G GLU* 3.4 9.6 - - - +
331G LEU* 1.3 76.4 - - - +
333G ALA* 1.3 56.8 + - - +
335G ASP* 3.8 6.1 - - - -
336G SER* 2.3 47.3 + - - +
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Residues in contact with ALA 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G PRO* 4.9 15.1 - - + +
329G GLU 3.0 10.5 + - - +
330G GLU* 2.7 26.2 + - - +
332G MET* 1.3 74.7 - - - +
334G THR* 1.3 66.0 + - - +
336G SER* 3.8 4.5 - - - -
337G ALA* 2.8 25.5 + - - +
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Residues in contact with THR 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G PRO 3.8 18.2 + - - -
228G LEU* 4.2 18.4 - - + -
231G ALA* 3.8 8.4 - - + +
287G ILE* 4.5 11.4 - - + -
290G GLN* 2.4 33.5 + - - +
330G GLU* 2.6 15.9 + - - +
331G LEU* 3.3 6.5 - - + +
333G ALA* 1.3 73.9 - - - +
335G ASP* 1.3 67.9 - - - +
337G ALA* 3.0 15.4 + - - +
338G ILE* 3.0 19.0 + - + +
352G TYR* 4.9 4.3 - - + +
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Residues in contact with ASP 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296G MLY 2.8 46.1 + - - +
331G LEU* 2.8 15.9 + - + +
332G MET* 3.3 6.1 - - - +
334G THR* 1.3 80.0 - - - +
336G SER* 1.3 58.7 + - - +
338G ILE* 2.9 32.0 + - - +
339G ASP* 3.2 6.6 - - - +
348G MLY 2.5 36.1 + - - -
352G TYR* 2.7 25.2 + - - +
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Residues in contact with SER 336 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214G MET* 4.7 18.8 - - - +
215G GLN* 2.2 36.9 + - - +
296G MLY 5.2 2.7 - - - -
332G MET* 2.3 35.1 + - - +
333G ALA* 3.9 4.2 - - - -
335G ASP* 1.3 74.9 + - - +
337G ALA* 1.3 52.5 + - - +
339G ASP* 3.4 7.3 - - - +
340G ILE* 3.1 5.9 + - - +
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Residues in contact with ALA 337 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G SER* 3.7 35.0 - - - +
227G PRO* 4.8 4.7 - - + -
228G LEU* 4.6 9.9 - - + +
333G ALA 2.8 19.3 + - - +
334G THR* 3.1 8.7 - - - +
336G SER* 1.3 74.0 - - - +
338G ILE* 1.3 57.6 + - - +
340G ILE* 3.2 2.7 + - - +
341G LEU* 2.7 44.4 + - + +
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Residues in contact with ILE 338 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 3.5 26.5 - - + -
232G PHE* 5.5 0.9 - - + -
334G THR* 3.0 19.6 + - + +
335G ASP* 2.9 16.7 + - - +
337G ALA* 1.3 76.2 - - - +
339G ASP* 1.3 66.1 + - - +
341G LEU* 3.0 12.7 + - - -
342G GLY 3.3 6.4 + - - -
343G PHE* 3.3 38.6 + - + +
348G MLY 3.6 32.8 - - + -
351G ILE* 4.7 23.8 - - + -
352G TYR* 4.7 10.3 - - + +
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Residues in contact with ASP 339 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G GLN* 1.4 64.8 - - - +
296G MLY 5.5 0.5 - - - -
335G ASP* 3.2 14.4 - - - +
336G SER* 3.4 5.9 - - - +
338G ILE* 1.3 76.6 - - - +
340G ILE* 1.3 48.3 + - - +
342G GLY* 2.5 28.2 + - - -
343G PHE 4.0 9.1 + - - +
345G ALA* 6.0 0.2 - - - -
348G MLY 2.8 47.4 + - - +
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Residues in contact with ILE 340 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213G LYS 3.3 9.4 - - - +
214G MET* 2.8 32.5 - - + +
215G GLN* 1.0 199.1 - - + +
216G GLY 3.9 3.9 + - - +
217G THR 4.2 11.4 - - - +
221G GLN* 3.6 22.7 - - - +
224G SER* 3.8 20.4 - - - +
336G SER* 3.5 12.6 - - - +
337G ALA* 3.6 6.1 - - - +
339G ASP 1.3 25.9 - - - +
341G LEU* 1.3 60.0 + - - +
342G GLY* 3.0 5.4 + - - -
448G GLN* 5.1 0.5 - - - +
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Residues in contact with LEU 341 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221G GLN* 3.4 35.0 - - + +
224G SER* 3.4 36.1 - - - +
225G ALA* 3.6 6.7 - - - +
228G LEU* 4.5 12.1 - - + -
337G ALA* 2.7 24.7 + - + +
338G ILE 3.3 4.5 - - - +
339G ASP 2.9 0.8 - - - -
340G ILE* 1.3 80.4 - - - +
342G GLY* 1.3 49.0 + - - +
343G PHE* 3.4 20.8 + - + -
444G ARG 5.0 1.0 - - - +
445G ILE* 3.9 28.1 - - + -
448G GLN* 2.6 38.3 + - + +
449G LEU* 4.5 5.4 - - + -
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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