Contacts of the helix formed by residues 261 - 283 (chain C) in PDB entry 6I53
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 ALA 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 3.9 6.5 - - + -
258C ASN* 3.6 28.8 + - - +
259C LYS 3.1 3.0 + - - -
260C ASP* 1.3 75.2 - - - +
262C VAL* 1.3 59.0 + - - +
263C PRO* 3.6 4.9 - - - -
264C ALA* 3.1 4.1 + - - -
265C ARG* 2.9 30.5 + - - +
314C TYR* 4.5 0.4 + - - -
252D VAL* 3.8 29.6 - - + -
253D PRO* 5.5 2.7 - - - -
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 4.4 4.0 - - + -
246B ALA* 3.8 17.7 - - + -
249B ALA* 3.7 19.3 - - + -
260C ASP* 3.2 23.1 + - - +
261C ALA* 1.3 70.8 - - - +
263C PRO* 1.3 69.4 - - + +
266C THR* 2.7 33.2 + - - +
314C TYR* 3.3 24.5 - - + +
318C HIS* 3.6 28.0 - - + +
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Residues in contact with PRO 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 5.8 2.5 - - + -
248B ALA* 3.7 41.3 - - + +
249B ALA* 4.3 10.5 - - + +
252B ALA* 5.6 0.2 - - - +
261C ALA 3.9 1.3 - - - -
262C VAL* 1.3 92.9 - - + +
264C ALA* 1.3 58.4 + - - +
266C THR* 4.1 0.7 - - - -
267C SER* 2.9 30.3 + - - -
253D PRO* 3.7 30.5 - - + -
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ILE* 4.9 4.7 - - + -
261C ALA* 3.1 6.3 + - + +
263C PRO* 1.3 77.3 - - - +
265C ARG* 1.3 65.8 + - - +
266C THR 3.2 1.6 - - - -
267C SER* 3.7 5.9 + - - -
268C LEU* 3.2 27.5 + - - +
252D VAL* 3.4 45.8 - - + +
253D PRO* 3.8 5.7 - - + +
256D THR* 3.4 17.3 - - + +
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C SER* 2.9 45.5 + - - -
255C PHE* 4.6 1.4 - - - -
257C ILE* 3.0 35.1 + - + -
258C ASN 3.5 18.2 + - - +
259C LYS* 4.1 1.6 - - - +
261C ALA 2.9 20.0 + - - +
264C ALA* 1.3 77.4 - - - +
266C THR* 1.3 62.1 + - - +
268C LEU* 4.3 3.5 - - - +
269C GLY* 3.7 10.4 + - - -
311C LEU* 4.3 7.1 - - - +
313C GLU* 3.7 19.6 + - - -
314C TYR* 3.3 60.5 - - + +
317C LEU* 4.9 1.6 - - - +
411C ASP* 3.7 25.1 + - - -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ILE* 4.4 6.3 - - + +
249B ALA* 3.7 34.2 - - + +
252B ALA* 5.1 1.8 - - + -
253B LEU* 3.7 17.5 - - + -
262C VAL* 2.7 23.0 + - - +
263C PRO 4.1 2.5 - - - -
264C ALA 3.2 0.4 - - - -
265C ARG* 1.3 76.7 - - - +
267C SER* 1.3 60.6 + - - +
269C GLY* 2.9 19.6 + - - -
270C ILE* 3.2 32.0 - - + +
311C LEU* 4.0 11.1 - - + +
314C TYR* 3.9 13.3 - - - -
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 4.7 13.0 - - - -
263C PRO 2.9 20.4 + - - -
264C ALA* 3.7 7.8 + - - -
266C THR* 1.3 78.5 - - - +
268C LEU* 1.3 61.7 + - - +
269C GLY 3.2 0.4 + - - -
270C ILE* 4.1 10.7 - - - +
271C THR* 3.4 27.0 + - - -
253D PRO 5.6 0.3 + - - -
256D THR* 4.7 4.3 - - - +
257D VAL* 4.6 16.6 - - - +
260D VAL* 4.4 3.0 - - - +
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C LEU* 3.4 23.8 - - + +
251C SER* 3.9 11.0 - - - +
253C VAL* 4.3 11.2 - - + -
254C SER* 3.7 27.8 - - - +
257C ILE* 3.9 20.4 - - + -
264C ALA 3.2 17.7 + - - +
265C ARG 4.3 3.1 - - - +
267C SER* 1.3 78.0 + - - +
269C GLY* 1.3 55.5 + - - +
270C ILE 3.4 0.4 + - - -
272C THR* 2.6 32.2 + - - +
256D THR* 3.8 22.0 - - + -
260D VAL* 3.8 25.7 - - + +
301D LEU* 4.6 3.8 - - + -
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Residues in contact with GLY 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C SER* 5.9 3.6 - - - -
265C ARG 3.7 4.2 + - - -
266C THR 2.9 9.1 + - - -
268C LEU* 1.3 81.2 - - - +
270C ILE* 1.3 60.0 + - - +
272C THR* 4.5 6.3 - - - -
273C VAL* 3.3 20.0 - - - +
307C VAL 4.9 2.2 - - - +
310C ALA* 5.9 2.2 - - - -
311C LEU* 3.4 32.8 - - - +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 6.2 3.6 - - + -
252B ALA* 3.3 24.7 - - + +
253B LEU* 3.7 29.6 - - + -
256B THR* 3.7 27.8 - - + +
257B THR* 4.7 11.4 - - - +
260B THR* 5.7 1.6 - - - +
266C THR* 3.2 30.7 + - + +
267C SER* 3.8 8.0 + - - +
268C LEU 3.4 0.2 - - - -
269C GLY* 1.3 80.3 - - - +
271C THR* 1.3 57.2 + - - +
272C THR 3.2 1.1 - - - -
273C VAL* 3.0 10.6 + - + +
274C LEU* 2.7 33.2 + - - +
311C LEU* 4.2 4.3 - - + -
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 4.8 7.7 - - - +
250C LEU* 6.0 1.3 - - + -
267C SER* 3.4 13.4 + - - -
270C ILE* 1.3 76.0 - - - +
272C THR* 1.3 54.9 + - - +
274C LEU* 3.2 12.2 + - + +
275C THR* 2.6 41.1 + - - +
260D VAL* 3.7 30.6 - - + +
261D THR* 5.4 2.9 - - - +
264D LEU* 3.8 32.8 - - + -
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Residues in contact with THR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ILE* 3.3 37.0 - - + +
250C LEU* 4.0 17.9 - - + +
251C SER* 3.7 19.9 - - - +
268C LEU* 2.6 25.5 + - - +
269C GLY* 4.6 4.7 - - - -
270C ILE 3.2 0.2 - - - -
271C THR* 1.3 79.0 - - - +
273C VAL* 1.3 58.3 + - - +
275C THR* 3.7 4.7 + - - -
276C MET* 3.3 24.3 + - - +
307C VAL* 3.6 20.0 - - + -
260D VAL* 5.1 1.1 - - - +
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 6.5 0.7 - - + -
232B ILE* 4.3 22.0 - - + -
235B LEU* 3.7 33.2 - - + -
260B THR* 5.5 1.3 - - + -
269C GLY 3.3 23.3 - - - +
270C ILE* 3.0 12.8 + - + +
272C THR* 1.3 75.4 - - - +
274C LEU* 1.3 63.8 + - - +
276C MET* 3.3 6.4 + - + +
277C THR* 3.2 25.4 + - - +
304C PHE* 5.2 6.2 - - + -
307C VAL* 3.7 25.8 - - + +
308C PHE* 5.2 0.4 - - - +
311C LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 4.1 18.8 - - + -
259B LEU* 4.8 14.4 - - + -
260B THR* 3.3 40.4 + - + +
263B THR* 4.6 11.7 - - + +
270C ILE 2.7 19.2 + - - +
271C THR* 3.2 12.3 + - + +
273C VAL* 1.3 73.2 - - - +
275C THR* 1.3 60.1 + - - +
277C THR* 3.5 6.7 + - - -
278C THR* 3.2 26.4 + - - +
264D LEU* 4.6 22.2 - - + -
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Residues in contact with THR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C ILE* 3.7 34.8 - - + +
250C LEU* 5.9 1.4 - - - +
271C THR* 2.6 25.0 + - - +
272C THR* 4.2 4.6 - - - -
273C VAL 3.2 0.2 - - - -
274C LEU* 1.3 73.3 - - - +
276C MET* 1.3 61.6 + - - +
277C THR 3.2 0.4 - - - -
278C THR* 3.1 9.6 + - + -
279C LEU* 2.9 30.7 + - + +
264D LEU* 3.3 33.2 - - + +
267D THR* 4.0 15.7 - - + -
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Residues in contact with MET 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C CYS* 4.2 20.2 - - - +
247C ILE* 3.8 26.9 - - + -
272C THR 3.3 13.4 + - - +
273C VAL* 3.3 11.3 + - - +
275C THR* 1.3 75.9 - - - +
277C THR* 1.3 62.3 + - - +
279C LEU* 3.7 27.5 - - + +
280C SER* 3.1 26.7 + - - -
300C VAL* 5.1 5.7 - - - +
303C CYS* 3.5 33.7 - - - +
304C PHE* 3.5 22.2 - - + -
307C VAL* 3.8 20.2 - - + -
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 5.2 6.2 - - + +
232B ILE* 3.4 20.6 - - + +
260B THR* 3.6 15.2 - - + +
263B THR* 4.7 6.7 - - - +
264B ILE* 3.9 30.3 - - + -
273C VAL* 3.2 14.1 + - - +
274C LEU* 3.6 10.3 - - - -
275C THR 3.2 0.4 - - - -
276C MET* 1.3 75.8 - - - +
278C THR* 1.3 57.4 + - - +
280C SER* 4.3 1.8 - - - -
281C THR* 2.7 36.3 + - - +
304C PHE* 4.3 10.0 - - - -
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LEU* 3.2 17.2 + - - +
275C THR* 3.1 15.4 + - + -
277C THR* 1.3 79.2 - - - +
279C LEU* 1.3 62.5 + - + +
281C THR* 3.3 5.2 + - - -
282C ILE* 3.2 43.5 + - + +
264D LEU* 5.5 4.6 - - + +
267D THR* 6.5 0.2 - - + -
268D THR* 5.9 3.4 - - - +
271D ILE* 4.7 8.5 - - + -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLN 4.8 6.3 - - - +
240C THR* 5.4 1.8 - - + +
243C PRO* 3.9 19.5 - - + +
244C CYS* 4.0 20.5 - - - -
247C ILE* 3.7 29.4 - - + -
275C THR* 2.9 18.3 + - + +
276C MET* 3.7 22.2 - - + +
278C THR* 1.3 74.6 - - + +
280C SER* 1.3 65.8 + - - +
282C ILE* 4.1 3.7 - - + +
283C ALA* 3.2 25.5 + - - +
300C VAL* 5.2 1.5 - - - +
267D THR* 4.0 9.9 - - + -
271D ILE* 3.7 29.4 - - + -
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU 4.4 12.0 + - - -
224B GLN* 4.5 3.2 + - - +
276C MET 3.1 20.8 + - - -
277C THR* 4.3 2.9 - - - -
279C LEU* 1.3 76.1 - - - +
281C THR* 1.3 62.4 + - - +
283C ALA* 3.8 5.9 + - - +
284C ARG* 3.8 20.4 - - - +
297C ASP* 5.7 0.9 + - - -
300C VAL* 3.7 19.0 - - - +
304C PHE* 3.7 24.3 - - - -
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Residues in contact with THR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B GLN* 3.9 18.1 + - - +
264B ILE* 6.1 0.2 - - - +
267B HIS* 3.4 49.7 + - + +
277C THR* 2.7 26.7 + - - +
278C THR* 3.3 7.3 + - - -
279C LEU 3.2 0.4 - - - -
280C SER* 1.3 78.5 - - - +
282C ILE* 1.3 65.5 + - + +
283C ALA 3.4 0.5 + - - -
284C ARG* 3.5 15.1 + - - +
285C LYS* 4.1 7.1 + - - +
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Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C GLN* 3.6 27.9 + - + +
278C THR* 3.2 30.5 + - + +
279C LEU* 4.4 4.0 - - + +
281C THR* 1.3 76.6 - - + +
283C ALA* 1.3 60.8 + - - +
284C ARG 3.1 6.3 + - - -
285C LYS* 3.3 50.8 + - + +
271D ILE* 3.7 43.5 - - + -
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C PHE* 4.8 1.7 - - - -
236C PHE* 5.3 3.1 - - - -
239C GLN* 5.8 2.2 - - - +
240C THR* 4.1 20.0 - - + +
279C LEU 3.2 20.6 + - - +
280C SER* 4.1 8.3 - - - +
281C THR 3.3 0.6 - - - -
282C ILE* 1.3 75.9 - - - +
284C ARG* 1.3 64.9 + - + +
285C LYS 3.5 0.8 + - - -
286C SER* 4.8 4.9 + - - -
287C LEU* 4.4 6.9 - - - +
296C MET* 3.9 31.6 - - + +
297C ASP* 5.8 1.3 - - - +
300C VAL* 5.0 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
------------------------------------------------------------
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