Contacts of the helix formed by residues 269 - 294 (chain R) in PDB entry 6DDE
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 LYS 269 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268R SER* 1.3 68.2 - - - +
270R GLU* 1.3 53.4 + - - +
271R LYS 3.3 0.7 - - - -
272R ASP* 3.4 17.1 - - + +
273R ARG* 2.6 32.9 + - - +
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Residues in contact with GLU 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP* 3.4 40.7 - - - +
268R SER 2.6 7.7 + - - +
269R LYS* 1.3 74.0 - - - +
271R LYS* 1.3 57.5 + - - +
273R ARG* 3.2 15.4 + - + +
274R ASN* 2.9 53.5 + - - +
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Residues in contact with LYS 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS 3.3 21.2 + - - -
315A ASP* 3.4 30.9 - - - +
317A LYS 4.8 4.9 + - - -
318A GLU* 5.5 5.3 - - - +
263R ARG* 4.8 8.4 + - - +
264R MET* 3.3 39.4 + - + +
265R LEU* 3.3 19.0 - - + +
267R GLY 3.5 11.7 - - - +
268R SER* 2.7 34.6 + - - +
270R GLU* 1.3 76.0 - - - +
272R ASP* 1.3 57.8 + - - +
274R ASN* 3.1 10.3 + - - +
275R LEU 2.9 22.9 + - - -
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Residues in contact with ASP 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265R LEU 3.9 6.1 - - - -
266R SER 3.8 20.1 - - - +
267R GLY* 3.7 5.4 + - - +
269R LYS* 3.2 21.6 + - + +
271R LYS* 1.3 77.3 - - - +
273R ARG* 1.3 56.7 + - - +
275R LEU* 3.4 14.6 + - - +
276R ARG* 2.9 39.8 + - - +
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Residues in contact with ARG 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269R LYS 2.6 17.8 + - - +
270R GLU* 3.2 17.4 + - - +
272R ASP* 1.3 71.5 - - - +
274R ASN* 1.3 60.6 + - - +
276R ARG* 3.3 15.6 + - + +
277R ARG* 2.9 27.0 + - + +
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Residues in contact with ASN 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASP 5.4 1.2 + - - -
354A PHE* 4.5 25.3 - - + +
265R LEU* 3.8 14.0 - - + +
270R GLU* 2.9 46.1 + - - +
271R LYS* 3.1 14.8 + - - +
273R ARG* 1.3 75.8 - - - +
275R LEU* 1.3 60.0 + - - +
277R ARG* 3.1 17.2 + - - +
278R ILE* 3.0 32.2 + - - +
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Residues in contact with LEU 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256R ILE 5.7 0.2 - - - +
259R LEU* 3.6 48.5 - - + +
260R LYS* 4.4 20.0 - - + +
265R LEU* 3.5 40.9 - - + +
266R SER* 5.1 3.4 - - - +
271R LYS 2.9 6.6 + - - +
272R ASP* 3.6 17.0 - - - +
274R ASN* 1.3 75.6 - - - +
276R ARG* 1.3 57.6 + - - +
278R ILE* 3.3 8.7 + - + +
279R THR* 3.0 44.4 + - + +
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Residues in contact with ARG 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272R ASP* 2.9 27.8 + - - +
273R ARG* 3.4 18.1 - - + +
274R ASN 3.2 0.2 - - - -
275R LEU* 1.3 75.7 - - - +
277R ARG* 1.3 57.8 + - - +
279R THR* 2.7 21.2 + - - +
280R ARG* 2.8 51.4 + - + +
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Residues in contact with ARG 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLY 4.8 2.8 + - - -
353A LEU* 3.4 24.7 + - - +
354A PHE 4.7 3.8 + - - -
273R ARG* 2.9 15.1 + - + +
274R ASN* 3.1 19.9 + - - +
276R ARG* 1.3 75.2 - - - +
278R ILE* 1.3 60.9 + - - +
280R ARG* 3.3 8.2 + - - +
281R MET* 2.9 36.4 + - + +
339R LEU* 3.9 30.5 + - - +
340R ASP* 4.5 11.1 + - - +
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Residues in contact with ILE 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 4.4 13.7 - - + -
353A LEU* 4.2 31.9 - - + +
354A PHE* 3.1 38.6 - - - +
255R MET* 5.3 0.9 - - + -
256R ILE* 6.1 1.8 - - + -
259R LEU* 3.9 25.8 - - + -
265R LEU* 4.8 6.7 - - + -
274R ASN 3.0 17.8 + - - +
275R LEU* 3.3 14.6 + - + +
277R ARG* 1.3 78.7 - - + +
279R THR* 1.3 57.7 - - + +
281R MET* 3.3 6.4 + - - +
282R VAL* 3.0 35.0 + - + +
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Residues in contact with THR 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256R ILE* 3.9 33.4 - - + -
259R LEU* 6.5 0.4 - - + -
260R LYS* 4.9 10.5 - - + +
275R LEU* 3.0 26.4 + - + +
276R ARG* 2.7 27.5 + - - +
278R ILE* 1.3 77.0 - - + +
280R ARG* 1.3 63.0 + - - +
282R VAL* 3.9 5.2 - - - +
283R LEU* 2.9 42.3 + - - +
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Residues in contact with ARG 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276R ARG* 2.8 59.4 + - + +
277R ARG* 3.7 7.6 - - + +
278R ILE 3.3 0.2 - - - -
279R THR* 1.3 83.6 + - - +
281R MET* 1.3 56.9 + - - +
283R LEU* 3.4 29.9 - - - +
284R VAL* 2.9 41.2 + - + +
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Residues in contact with MET 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLY 5.3 1.3 - - - +
353A LEU* 3.7 28.3 - - + -
165R ARG* 4.6 8.7 - - - +
277R ARG* 2.9 27.5 + - + +
278R ILE* 3.3 6.0 + - - +
280R ARG* 1.3 76.0 - - - +
282R VAL* 1.3 59.1 + - + +
284R VAL* 3.4 6.5 + - - +
285R VAL* 3.0 31.2 + - + +
335R LEU* 4.1 21.7 - - + +
336R TYR* 4.3 19.1 - - + -
339R LEU* 3.4 37.0 - - + +
340R ASP* 3.7 13.7 - - - +
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Residues in contact with VAL 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 5.1 9.0 - - + -
165R ARG* 5.3 4.0 - - - +
252R TYR* 3.7 37.5 - - + -
255R MET* 3.8 24.5 - - + -
256R ILE* 3.7 23.6 - - + -
278R ILE* 3.0 23.5 + - + +
279R THR 3.9 3.4 - - - +
281R MET* 1.3 77.5 - - + +
283R LEU* 1.3 62.7 + - + +
285R VAL* 3.2 10.1 - - + +
286R VAL* 3.0 25.9 + - + +
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Residues in contact with LEU 283 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256R ILE* 5.0 14.1 - - + -
279R THR* 2.9 23.9 + - - +
280R ARG* 3.4 33.0 - - - +
282R VAL* 1.3 76.3 - - + +
284R VAL* 1.3 59.1 + - + +
286R VAL* 4.1 5.9 - - + +
287R ALA* 2.9 32.7 + - - +
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Residues in contact with VAL 284 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280R ARG* 2.9 28.0 + - + +
281R MET* 3.9 4.7 - - - +
282R VAL 3.3 0.2 - - - -
283R LEU* 1.3 77.5 - - + +
285R VAL* 1.3 57.8 + - - +
287R ALA* 3.8 4.9 - - - +
288R VAL* 2.8 32.0 + - + +
335R LEU* 3.8 29.4 - - + -
339R LEU* 6.1 0.2 - - + -
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Residues in contact with VAL 285 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R LEU* 5.5 2.7 - - + -
165R ARG* 5.1 4.7 - - - +
248R ILE* 5.6 1.7 - - + +
252R TYR* 4.3 19.7 - - + -
281R MET* 3.0 19.5 + - + +
282R VAL* 3.2 20.6 - - - +
284R VAL* 1.3 76.5 - - - +
286R VAL* 1.3 62.4 + - + +
288R VAL* 3.3 3.8 - - + +
289R PHE* 3.0 24.5 + - + +
332R ASN* 4.8 4.7 - - - +
335R LEU* 3.7 19.7 - - + -
336R TYR* 3.3 40.4 - - + +
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Residues in contact with VAL 286 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R VAL* 6.2 1.1 - - + -
248R ILE* 4.0 23.8 - - + +
249R THR* 4.8 19.7 - - - +
252R TYR* 3.8 27.4 - - + -
282R VAL* 3.0 20.8 + - + +
283R LEU* 4.1 7.2 - - + +
285R VAL* 1.3 77.1 - - + +
287R ALA* 1.3 58.3 + - - +
289R PHE* 3.3 6.4 + - - +
290R ILE* 3.0 46.5 + - + +
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Residues in contact with ALA 287 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283R LEU 2.9 20.9 + - - +
284R VAL* 3.9 5.2 - - - +
286R VAL* 1.3 78.5 - - - +
288R VAL* 1.3 56.6 + - - +
290R ILE* 3.4 7.3 + - - +
291R VAL* 2.8 32.1 + - - +
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Residues in contact with VAL 288 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284R VAL* 2.8 24.1 + - + +
285R VAL* 3.3 15.9 - - + +
287R ALA* 1.3 74.0 - - - +
289R PHE* 1.3 63.9 + - - +
291R VAL* 4.4 5.6 - - + +
292R CYS* 2.9 37.9 + - + +
327R THR 6.0 0.7 - - - +
328R ASN* 5.0 11.4 - - - +
331R LEU* 5.1 23.1 - - + +
332R ASN* 6.4 1.3 - - - -
335R LEU* 3.8 16.6 - - + -
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Residues in contact with PHE 289 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R ILE* 5.0 4.3 - - + -
158R LEU* 3.6 26.5 - - + -
240R ALA 5.1 1.1 - - - -
241R PHE* 4.8 6.5 - + - -
244R PRO* 4.2 21.3 - - + -
245R VAL* 3.6 38.6 - - + -
248R ILE* 4.1 20.9 - - + -
285R VAL* 3.0 19.7 + - + +
286R VAL* 3.5 7.4 - - - +
288R VAL* 1.3 79.0 - - + +
290R ILE* 1.3 64.2 + - + +
292R CYS* 3.9 0.7 - - - +
293R TRP* 3.0 59.4 + + - +
328R ASN* 3.3 23.6 - - - +
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Residues in contact with ILE 290 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R PHE* 5.0 9.9 - - + -
245R VAL* 4.5 28.5 - - + -
249R THR* 6.2 0.9 - - - -
286R VAL* 3.0 35.1 + - + +
287R ALA* 3.9 6.5 - - - +
289R PHE* 1.3 77.7 - - + +
291R VAL* 1.3 59.1 + - - +
294R THR* 3.0 44.2 + - - +
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Residues in contact with VAL 291 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287R ALA 2.8 20.3 + - - +
288R VAL* 4.2 6.3 - - + +
290R ILE* 1.3 77.9 - - - +
292R CYS* 1.3 61.3 + - - +
294R THR* 5.2 1.6 - - - -
295R PRO* 4.0 12.6 - - - +
324R LEU* 4.0 7.3 - - - +
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Residues in contact with CYS 292 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288R VAL* 2.9 23.6 + - + +
289R PHE 4.0 1.1 - - - +
291R VAL* 1.3 79.1 - - - +
293R TRP* 1.3 63.9 + - - +
295R PRO* 3.7 1.4 - - - +
296R ILE* 4.6 0.7 - - - +
324R LEU* 2.9 47.5 - - - +
325R GLY* 3.8 1.0 - - - -
327R THR* 4.8 2.9 - - - -
328R ASN* 3.7 31.2 - - + +
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Residues in contact with TRP 293 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114R ASP* 5.9 0.2 - - - -
151R MET* 4.6 17.5 - - + +
154R SER* 4.2 19.7 - - - -
155R ILE* 3.5 36.3 - - + -
158R LEU* 5.1 0.7 - - + -
240R ALA 5.2 2.7 - - - -
241R PHE* 3.2 18.0 - + + -
289R PHE* 3.0 35.3 + + + +
292R CYS* 1.3 75.7 - - + +
294R THR* 1.3 63.0 + - - +
295R PRO* 4.0 0.2 - - - -
296R ILE* 3.6 14.9 - - + +
297R HIS* 3.1 34.3 - + + -
325R GLY* 2.6 44.1 + - - -
326R TYR* 5.7 3.6 - + - -
328R ASN* 3.3 32.5 - - + -
329R SER* 5.1 7.9 - - - -
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Residues in contact with THR 294 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R PHE* 3.9 16.8 - - - -
290R ILE* 3.0 25.8 + - - -
291R VAL* 5.1 1.1 - - - -
293R TRP* 1.3 77.3 - - - +
295R PRO* 1.4 68.2 - - - +
297R HIS* 3.1 6.1 + - - +
298R ILE* 2.9 35.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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