Contacts of the helix formed by residues 323 - 347 (chain F) in PDB entry 4DEM
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 323 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320F GLU 3.1 16.5 + - - +
321F GLU 3.2 3.2 - - - +
322F LEU* 1.3 79.2 - - - +
324F LEU* 1.3 64.7 + - - +
325F PRO* 3.3 6.5 - - - -
326F ALA* 3.0 30.7 + - - -
327F VAL* 3.1 15.1 + - + +
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Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F TYR* 5.1 1.1 - - - -
263F PHE* 5.0 0.2 - - + -
283F TRP* 4.7 3.4 - - + -
284F LEU* 3.6 42.3 - - + +
287F GLN* 4.1 17.3 - - + -
288F CYS* 4.0 7.9 - - + +
291F ARG* 4.0 20.9 - - - -
319F TYR* 3.0 47.0 + - + +
322F LEU* 3.8 16.8 - - + +
323F ASP* 1.3 76.8 - - - +
325F PRO* 1.3 63.5 - - + +
327F VAL* 3.2 9.9 + - + +
328F PHE* 2.8 29.5 + - - +
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Residues in contact with PRO 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F TYR* 3.9 25.0 + - + +
263F PHE* 4.0 32.8 - - + -
319F TYR 4.1 5.8 - - - +
320F GLU* 4.4 9.6 - - + -
323F ASP* 3.4 6.5 - - - -
324F LEU* 1.3 92.3 - - + +
326F ALA* 1.3 55.2 + - - +
328F PHE* 3.2 5.7 + - - +
329F LEU* 2.9 27.4 + - - +
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Residues in contact with ALA 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323F ASP* 3.0 29.4 + - + +
325F PRO* 1.3 76.9 - - - +
327F VAL* 1.3 65.8 + - + +
329F LEU* 3.3 7.4 + - - +
330F GLN* 3.1 23.2 + - - +
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Residues in contact with VAL 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F TRP* 3.9 18.6 - - + -
287F GLN* 4.2 6.7 - - + +
291F ARG* 3.4 46.9 - - - +
322F LEU 4.5 2.2 - - - +
323F ASP* 3.1 19.1 + - + +
324F LEU* 3.6 13.9 - - + +
326F ALA* 1.3 75.9 - - + +
328F PHE* 1.3 58.1 + - - +
330F GLN* 3.4 6.8 + - - +
331F TYR* 2.9 27.6 + - + +
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Residues in contact with PHE 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F PHE* 4.2 12.6 - + - -
255F ILE* 3.9 21.8 - - + -
256F GLN* 3.9 33.9 - - + -
259F TYR* 3.6 58.1 - + + -
283F TRP* 3.8 17.0 - + + -
324F LEU 2.8 13.3 + - - +
325F PRO 3.5 7.6 - - - +
327F VAL* 1.3 75.3 - - - +
329F LEU* 1.3 66.4 + - + +
331F TYR* 3.2 3.2 + + - +
332F GLU* 2.8 50.8 + - - +
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Residues in contact with LEU 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325F PRO 2.9 15.8 + - - +
326F ALA* 3.3 8.5 + - - +
328F PHE* 1.3 82.6 - - + +
330F GLN* 1.3 66.3 + - - +
332F GLU* 3.4 19.3 + - - +
333F GLU* 3.3 24.3 + - + +
364F LYS* 4.6 18.7 + - - +
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Residues in contact with GLN 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326F ALA 3.1 17.0 + - - +
327F VAL* 3.7 6.5 - - - +
329F LEU* 1.3 79.4 - - - +
331F TYR* 1.3 65.1 + - - +
333F GLU* 3.2 25.7 + - - +
334F ASP* 3.0 57.5 + - - +
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Residues in contact with TYR 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F LYS* 5.7 1.1 + - - -
251F GLU* 3.6 15.4 + - - +
252F PHE* 4.0 14.2 + + - -
255F ILE* 3.0 51.6 - - + +
283F TRP* 4.0 22.4 - + + -
327F VAL* 2.9 19.6 + - + +
328F PHE* 3.5 5.4 - + - +
330F GLN* 1.3 76.7 - - - +
332F GLU* 1.3 59.3 + - - +
334F ASP* 3.3 9.2 + - + +
335F SER* 2.8 54.9 + - - -
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Residues in contact with GLU 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F PHE* 3.6 39.6 - - + -
256F GLN* 4.2 2.5 - - - +
328F PHE* 2.8 38.4 + - + +
329F LEU* 3.6 18.0 - - - +
330F GLN 3.3 0.2 - - - -
331F TYR* 1.3 71.7 - - - +
333F GLU* 1.3 58.2 + - - +
336F TYR* 3.0 30.3 + - - +
363F TYR* 3.6 8.1 - - + -
364F LYS* 2.6 55.6 + - - +
365F ARG 5.7 0.6 - - - +
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Residues in contact with GLU 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F LEU* 3.3 14.1 + - + +
330F GLN* 3.2 31.9 + - - +
332F GLU* 1.3 80.9 - - - +
334F ASP* 1.3 69.0 + - - +
336F TYR* 3.4 6.9 + - - +
337F SER* 3.1 28.3 + - - +
364F LYS* 5.0 10.9 - - - +
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Residues in contact with ASP 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330F GLN* 3.0 49.0 + - - +
331F TYR* 3.8 8.5 + - + +
333F GLU* 1.3 81.6 - - - +
335F SER* 1.3 58.5 + - - +
337F SER* 3.4 7.2 + - - -
338F HIS* 3.0 27.7 + - - +
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Residues in contact with SER 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F GLU 5.3 0.3 + - - -
252F PHE* 3.4 18.1 - - - +
331F TYR* 2.8 44.2 + - - -
332F GLU 3.8 3.1 - - - -
334F ASP* 1.3 75.1 - - - +
336F TYR* 1.3 59.7 + - - +
338F HIS* 3.1 10.5 + - - +
339F ILE* 2.8 33.4 + - - +
363F TYR* 2.7 24.6 + - - -
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Residues in contact with TYR 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332F GLU* 3.0 19.7 + - + +
333F GLU* 3.6 6.3 - - - +
335F SER* 1.3 76.2 + - - +
337F SER* 1.3 72.3 + - - +
339F ILE* 3.3 1.8 + - - +
340F MET* 3.0 67.0 + - + +
359F ALA* 4.7 4.0 - - + -
360F ARG* 5.9 1.7 - - - -
363F TYR* 3.6 47.1 - + + -
364F LYS* 6.1 2.0 - - - +
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Residues in contact with SER 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333F GLU* 3.1 19.3 + - - +
334F ASP* 3.7 10.1 - - - -
335F SER 3.2 0.2 - - - -
336F TYR* 1.3 84.5 - - - +
338F HIS* 1.3 57.0 + - - +
340F MET* 3.3 7.3 + - - +
341F ALA* 3.0 27.7 + - - +
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Residues in contact with HIS 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F GLU* 3.0 28.9 + - + -
334F ASP 3.0 14.0 + - - +
335F SER* 3.1 13.0 + - - +
337F SER* 1.3 72.9 - - - +
339F ILE* 1.3 71.5 + - + +
341F ALA* 3.2 10.5 + - - +
342F LEU* 3.0 47.9 + - + +
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Residues in contact with ILE 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ILE* 4.9 2.5 - - + +
248F GLU* 3.9 15.7 - - + +
249F MET* 3.5 65.7 - - + +
335F SER* 2.8 19.7 + - - +
336F TYR 3.8 3.8 - - - +
338F HIS* 1.3 75.7 - - + +
340F MET* 1.3 60.1 + - + +
342F LEU* 3.2 10.1 + - + +
343F ILE* 2.9 34.1 + - + +
359F ALA* 4.8 4.5 - - + -
363F TYR* 2.5 37.9 - - + +
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Residues in contact with MET 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336F TYR* 3.0 68.3 + - + +
337F SER* 3.7 7.0 - - - +
338F HIS 3.2 0.2 - - - -
339F ILE* 1.3 78.0 - - + +
341F ALA* 1.3 61.7 + - - +
343F ILE* 3.2 11.5 + - + +
344F GLU* 3.0 30.6 + - - +
356F LEU* 3.6 30.3 - - + +
359F ALA* 3.3 28.7 - - + -
360F ARG 5.3 0.2 - - - +
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Residues in contact with ALA 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337F SER 3.0 13.2 + - - +
338F HIS* 3.5 13.9 - - - +
340F MET* 1.3 75.4 - - - +
342F LEU* 1.3 58.6 + - + +
344F GLU* 3.2 17.9 + - - +
345F GLN* 3.0 28.6 + - - +
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Residues in contact with LEU 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F LYS* 4.0 9.4 - - + +
245F ILE* 3.7 16.1 - - + +
248F GLU* 3.5 38.4 - - + -
338F HIS* 3.0 39.6 + - + +
339F ILE* 3.2 11.0 + - + +
341F ALA* 1.3 74.8 - - + +
343F ILE* 1.3 58.6 + - - +
345F GLN* 3.2 10.5 + - - +
346F TYR* 2.8 60.3 + - + +
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Residues in contact with ILE 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245F ILE* 4.0 15.7 - - + -
249F MET* 3.9 12.8 - - + -
339F ILE* 2.9 19.3 + - + +
340F MET* 3.2 19.7 + - + +
342F LEU* 1.3 74.1 - - - +
344F GLU* 1.3 66.3 + - + +
347F ALA* 3.0 42.4 + - + +
352F PRO* 4.3 16.8 - - + -
355F PHE* 3.5 42.0 - - + +
356F LEU* 4.0 23.8 - - + -
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Residues in contact with GLU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340F MET* 3.0 22.8 + - - +
341F ALA* 3.2 18.1 + - - +
343F ILE* 1.3 77.6 - - + +
345F GLN* 1.3 62.6 + - - +
347F ALA* 4.8 0.7 + - - +
348F ALA* 5.5 3.1 + - - +
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Residues in contact with GLN 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341F ALA 3.0 16.5 + - - +
342F LEU* 3.7 13.4 - - - +
343F ILE 3.2 0.2 - - - -
344F GLU* 1.3 80.6 - - - +
346F TYR* 1.3 104.8 + - + +
348F ALA* 5.1 4.6 + - - +
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Residues in contact with TYR 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F ASN* 3.4 60.0 - - + +
242F ALA 4.9 0.5 + - - -
244F LYS* 3.7 42.2 + - + +
245F ILE* 3.7 9.2 - - + +
342F LEU* 2.8 43.3 + - + +
345F GLN* 1.3 115.0 + - + +
347F ALA* 1.3 66.1 + - - +
348F ALA 3.3 10.4 + - - +
355F PHE* 5.2 0.5 - - - -
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Residues in contact with ALA 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F ILE* 3.8 2.3 - - - +
343F ILE* 3.0 29.2 + - + +
344F GLU 4.8 0.2 + - - -
345F GLN 3.8 0.2 - - - -
346F TYR* 1.3 78.3 - - - +
348F ALA* 1.3 64.8 + - - +
350F LEU* 2.9 36.0 + - - +
352F PRO* 4.2 15.0 - - + -
355F PHE* 3.9 30.6 - - + -
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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