Contacts of the helix formed by residues 279 - 306 (chain C) in PDB entry 6D6U
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 279 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU 3.9 11.9 - - - +
141C ARG* 4.0 8.5 - - - -
143C TYR* 4.2 25.4 - - + +
272C LEU* 4.6 14.2 - - - +
273C PRO* 4.6 9.0 - - + -
275C ILE* 3.5 44.4 - - + -
277C TYR 3.5 2.9 + - - +
278C VAL* 1.3 92.6 - - - +
280C ALA* 1.3 62.7 + - - +
281C ILE* 3.9 17.4 - - + +
282C ASP* 2.8 44.4 + - - +
283C MET* 3.5 12.1 + - - +
225D TYR* 5.2 3.4 + - - -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ARG 3.5 15.4 + - - +
142C ARG* 5.0 2.7 - - - -
143C TYR 4.0 11.1 + - - +
226C TYR* 5.6 0.2 - - - +
279C LYS* 1.3 73.6 - - - +
281C ILE* 1.3 66.7 + - - +
282C ASP 3.2 2.0 - - - -
283C MET* 3.1 8.1 + - - +
284C TYR 2.9 18.5 + - - -
335C TYR* 3.4 23.9 + - - +
339C TYR* 3.6 30.3 - - + -
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Residues in contact with ILE 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C TYR* 4.4 9.4 + - + +
144C PRO* 4.9 9.2 - - + -
225C THR* 3.8 35.2 - - + +
226C TYR* 4.4 23.8 + - + +
268C LEU* 4.0 14.6 - - + -
272C LEU* 4.2 17.7 - - + -
279C LYS* 3.9 28.9 - - + +
280C ALA* 1.3 78.8 - - - +
282C ASP* 1.3 64.1 + - - +
284C TYR* 3.3 6.1 + - + +
285C LEU* 2.9 47.6 + - + +
335C TYR* 4.1 2.9 + - - -
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Residues in contact with ASP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ARG* 3.0 43.3 + - - +
272C LEU* 5.5 2.3 - - - +
279C LYS* 2.8 42.0 + - - +
280C ALA* 3.2 1.0 - - - +
281C ILE* 1.3 79.9 - - - +
283C MET* 1.3 61.3 + - - +
285C LEU* 3.3 9.3 + - - +
286C MET* 2.9 30.2 + - - +
225D TYR* 3.8 15.1 + - - -
228D ILE* 4.1 19.0 - - + +
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Residues in contact with MET 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C VAL* 4.3 9.2 - - + -
279C LYS 3.5 16.8 - - - +
280C ALA* 3.1 10.6 + - - +
282C ASP* 1.3 76.4 - - - +
284C TYR* 1.3 58.1 + - - +
286C MET* 3.4 8.0 + - + +
287C GLY* 2.9 25.6 + - - -
331C PHE* 5.3 0.9 - - - -
335C TYR* 5.6 3.8 - - + -
339C TYR* 6.1 1.3 - - + -
408C Y01 3.5 65.5 - - + +
228D ILE* 4.2 28.5 - - - -
406D Y01 4.4 22.4 - - + -
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Residues in contact with TYR 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TYR* 3.4 43.6 - + + -
229C SER* 4.7 4.0 - - - -
230C ILE* 3.3 30.7 - - - +
280C ALA 2.9 12.7 + - - +
281C ILE* 3.5 11.9 - - + +
282C ASP 3.2 0.2 - - - -
283C MET* 1.3 75.8 - - - +
285C LEU* 1.3 73.5 + - + +
287C GLY* 3.1 3.4 + - - -
288C CYS* 3.0 41.4 + - - -
328C PHE* 4.9 1.3 - + - -
331C PHE* 4.8 14.6 - + - -
332C ASN* 3.4 28.2 + - - -
335C TYR* 4.1 36.2 - + + +
336C TRP* 4.6 9.0 + - - -
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Residues in contact with LEU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C THR 5.4 4.0 - - - +
226C TYR* 6.3 0.7 - - - -
229C SER* 3.1 29.6 - - - +
261C MET* 3.8 14.8 - - + +
264C ILE* 5.7 2.0 - - + -
265C ASN* 3.6 37.4 + - - +
268C LEU* 3.7 32.1 - - + -
269C ARG* 5.6 0.9 - - + -
272C LEU* 6.2 0.4 - - + -
281C ILE* 2.9 27.3 + - + +
282C ASP* 3.8 12.8 - - - +
284C TYR* 1.3 83.5 - - + +
286C MET* 1.3 58.1 + - - +
288C CYS* 3.2 4.4 + - - +
289C PHE* 2.9 27.7 + - - +
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Residues in contact with MET 286 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASN* 5.5 6.0 - - - +
269C ARG* 5.8 3.1 - - - +
282C ASP 2.9 17.8 + - - +
283C MET* 3.8 11.0 - - + +
285C LEU* 1.3 77.1 - - - +
287C GLY* 1.3 58.5 + - - +
289C PHE* 3.3 36.6 + - + +
290C VAL* 2.9 51.8 + - + +
228D ILE* 4.9 23.8 - - + +
232D LEU* 3.6 39.5 - - + +
233D PRO* 5.2 8.5 - - - -
236D MET* 4.4 6.3 - - + -
406D Y01 5.4 7.4 - - + -
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Residues in contact with GLY 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C MET 2.9 15.9 + - - -
284C TYR 3.1 4.4 + - - -
286C MET* 1.3 76.3 - - - +
288C CYS* 1.3 56.6 + - - +
290C VAL* 3.1 9.2 + - - +
291C PHE* 2.9 41.2 + - - -
331C PHE* 4.9 6.3 - - - -
408C Y01 4.7 16.3 - - - +
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Residues in contact with CYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER* 3.9 23.6 - - - -
233C THR* 4.0 17.4 + - - +
261C MET* 4.0 17.7 - - + -
284C TYR* 3.0 36.6 + - - -
285C LEU 3.2 6.5 + - - +
287C GLY* 1.3 75.1 - - - +
289C PHE* 1.3 63.8 + - - +
291C PHE* 3.1 11.4 + - - +
292C VAL* 3.0 28.4 + - + +
328C PHE* 4.6 13.5 - - - -
331C PHE* 5.8 1.3 - - - -
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 4.2 20.4 - - + -
261C MET* 4.4 19.4 - - + +
262C THR* 3.5 26.9 - - - -
265C ASN* 6.2 2.2 - - - +
285C LEU 2.9 15.1 + - - +
286C MET* 3.5 33.9 - - + +
288C CYS* 1.3 76.8 - - - +
290C VAL* 1.3 62.6 + - + +
292C VAL* 3.1 13.0 - - + +
293C PHE* 3.0 32.2 + + + +
233D PRO* 4.9 14.4 - - + -
236D MET* 3.6 37.5 - - + -
237D THR* 5.2 4.7 - - - -
265D THR* 6.2 1.1 - - + -
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C MET* 2.9 40.3 + - + +
287C GLY* 3.1 10.7 + - - +
289C PHE* 1.3 75.5 - - + +
291C PHE* 1.3 65.7 + - + +
293C PHE* 3.8 7.6 - - + +
294C MET* 2.9 37.6 + - + +
406C Y01 6.2 1.3 - - + -
236D MET* 5.7 5.6 - - - -
406D Y01 4.5 24.5 - - + -
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Residues in contact with PHE 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C THR* 4.7 13.7 - - + -
236C SER* 5.8 0.2 - - - -
237C TRP* 6.1 2.7 - - - +
287C GLY* 2.9 33.7 + - - -
288C CYS* 3.1 12.1 + - - +
290C VAL* 1.3 79.2 - - + +
292C VAL* 1.3 62.5 + - - +
294C MET* 3.2 5.5 + - - +
295C ALA* 3.0 23.1 + - - +
324C PHE* 4.7 15.3 - + + -
327C VAL* 4.3 10.8 - - + -
328C PHE* 3.8 39.7 - + + -
331C PHE* 4.0 37.9 - + + -
406C Y01 4.1 27.8 - - + -
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ILE* 4.5 13.9 - - + -
233C THR* 4.4 14.6 - - - +
236C SER* 3.8 29.1 - - - +
254C GLY 5.4 0.2 - - - +
257C THR* 4.6 9.9 + - - +
258C VAL* 4.3 24.3 - - + +
261C MET* 4.8 6.7 - - + -
288C CYS* 3.0 12.9 + - + +
289C PHE* 3.1 26.7 - - + +
291C PHE* 1.3 76.2 - - + +
293C PHE* 1.3 62.9 + - + +
295C ALA* 3.3 7.9 + - - +
296C LEU* 3.0 23.6 + - - +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C VAL* 4.9 6.1 - - + -
289C PHE* 3.0 28.7 + + + +
290C VAL* 3.8 7.6 - - + +
292C VAL* 1.3 80.8 - - + +
294C MET* 1.3 69.1 + - - +
296C LEU* 3.3 4.4 + - - +
297C LEU* 3.0 51.8 + - + +
236D MET* 3.8 39.5 - - + -
239D ILE* 3.8 28.5 - - + -
240D LEU* 3.6 46.2 - - + -
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Residues in contact with MET 294 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C VAL* 2.9 35.2 + - + +
291C PHE* 3.6 6.3 - - - +
293C PHE* 1.3 81.2 - - + +
295C ALA* 1.3 58.3 + - - +
297C LEU* 3.4 19.5 + - + +
298C GLU* 2.9 29.9 + - - +
324C PHE* 4.7 6.9 - - + -
406C Y01 3.7 51.8 - - + -
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C SER* 5.1 12.3 - - - +
237C TRP* 5.8 1.3 - - + -
240C PHE* 4.0 24.7 - - + -
291C PHE 3.0 14.2 + - - +
292C VAL* 3.3 12.5 + - - +
294C MET* 1.3 76.6 - - - +
296C LEU* 1.3 61.7 + - - +
298C GLU* 3.2 6.8 + - - +
299C TYR* 3.0 22.2 + - - +
324C PHE* 4.1 17.2 - - + -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C ARG 5.2 1.3 - - - +
251C VAL* 4.9 7.9 - - + +
254C GLY* 3.4 44.0 - - - +
255C ILE* 4.4 6.3 - - + +
258C VAL* 4.2 8.3 - - + -
292C VAL 3.0 16.3 + - - +
293C PHE* 3.3 5.8 + - - +
295C ALA* 1.3 77.7 - - - +
297C LEU* 1.3 62.0 + - - +
299C TYR* 3.3 16.6 + - + -
300C ALA* 3.0 23.2 + - + +
240D LEU* 3.6 32.1 - - + -
243D VAL* 6.1 2.0 - - + -
258D PHE* 4.3 14.8 - - + -
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C PHE* 3.0 55.5 + - + +
294C MET* 3.8 18.6 - - + +
296C LEU* 1.3 76.8 - - - +
298C GLU* 1.3 63.9 + - - +
300C ALA* 3.2 5.3 + - + +
301C LEU* 2.9 23.0 + - - +
239D ILE* 5.2 5.2 - - + -
240D LEU* 5.2 1.3 - - + -
243D VAL* 3.6 33.4 - - + -
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 3.2 28.3 - - - -
250C ARG* 5.9 0.2 + - - -
294C MET 2.9 17.6 + - - +
295C ALA* 3.2 6.8 + - - +
297C LEU* 1.3 76.1 - - - +
299C TYR* 1.3 68.0 + - - +
301C LEU* 3.3 10.2 + - + +
302C VAL* 3.0 54.8 + - + +
316C ILE* 3.3 17.9 - - + +
317C ASP* 4.6 4.9 - - - +
320C SER* 3.6 16.8 + - - +
324C PHE* 4.5 10.1 - - + -
406C Y01 5.0 10.1 - - + -
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Residues in contact with TYR 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C PHE* 5.8 2.5 - - + -
244C TYR* 4.7 13.2 + - + +
247C SER* 3.1 34.3 - - - -
250C ARG* 3.3 56.3 - - + +
251C VAL* 3.6 32.3 - - + -
295C ALA 3.0 13.9 + - - +
296C LEU* 3.3 17.0 + - + +
298C GLU* 1.3 84.6 + - - +
300C ALA* 1.3 60.6 + - - +
302C VAL* 4.3 11.0 - - + -
303C ASN* 2.9 44.6 + - + +
247D LEU* 6.1 2.2 - - + -
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Residues in contact with ALA 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C LEU* 3.0 15.3 + - + +
297C LEU* 3.2 11.0 + - + +
299C TYR* 1.3 80.3 - - - +
301C LEU* 1.3 62.3 + - - +
303C ASN* 3.3 6.3 + - - +
304C TYR* 3.0 23.7 + - - +
243D VAL* 3.7 29.4 - - + -
246D TRP* 5.1 10.0 - - + +
247D LEU* 5.3 11.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU 2.9 12.7 + - - +
298C GLU* 3.3 13.7 + - + +
300C ALA* 1.3 76.8 - - - +
302C VAL* 1.3 65.7 + - + +
304C TYR* 3.2 7.7 + - + -
305C ILE* 2.9 54.2 + - + +
316C ILE* 5.8 5.8 - - + -
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Residues in contact with VAL 302 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C TYR* 5.9 6.1 - - + -
250C ARG* 5.6 0.7 - - - +
298C GLU* 3.0 43.0 + - + +
299C TYR* 3.3 17.0 + - + +
301C LEU* 1.3 78.5 - - + +
303C ASN* 1.3 64.2 + - - +
305C ILE* 3.6 7.4 - - - +
306C PHE* 3.2 25.9 + - + +
313C ALA* 3.7 23.3 - - + -
316C ILE* 3.8 23.6 - - + -
317C ASP* 4.3 16.4 - - - +
----------------------------------------------------------
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Residues in contact with ASN 303 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C TYR 5.9 0.6 + - - -
247C SER* 3.9 15.0 + - - -
251C VAL* 4.9 1.9 - - - +
299C TYR* 2.9 46.6 + - + +
300C ALA* 3.7 6.1 - - - +
302C VAL* 1.3 78.7 - - - +
304C TYR* 1.3 62.0 + - - +
306C PHE* 4.0 10.6 + - - +
307C PHE* 4.9 2.3 + - - +
246D TRP 5.6 0.9 - - - +
247D LEU* 4.8 15.4 - - + +
248D ASN* 5.8 9.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 304 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C ALA 3.0 16.3 + - - +
301C LEU* 3.8 8.5 - - + +
303C ASN* 1.3 81.1 - - - +
305C ILE* 1.3 74.5 + - + +
306C PHE 3.5 0.7 + - - -
307C PHE* 4.2 8.8 + - - +
308C SER 5.2 0.7 + - - -
246D TRP* 3.6 64.1 + + + +
326D ARG* 3.8 19.6 + - - -
----------------------------------------------------------
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU* 2.9 44.7 + - + +
302C VAL* 3.6 12.1 - - - +
304C TYR* 1.3 87.5 - - + +
306C PHE* 1.3 67.5 + - - +
307C PHE 3.4 0.7 - - - -
308C SER* 3.0 23.5 + - - +
309C GLN* 3.5 13.8 + - - +
312C ARG* 3.6 30.7 - - + -
313C ALA* 5.0 4.7 - - + +
316C ILE* 4.0 15.5 - - + -
----------------------------------------------------------
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C TYR* 3.2 57.2 - + + -
302C VAL* 3.2 20.1 + - + +
303C ASN* 4.3 8.7 - - - +
304C TYR 3.3 1.4 - - - -
305C ILE* 1.3 78.6 - - - +
307C PHE* 1.3 71.6 + + + +
308C SER 3.1 1.4 + - - -
309C GLN 3.1 22.1 + - - +
310C PRO* 3.5 38.3 - - + +
313C ALA* 3.5 22.0 - - + -
314C ALA* 5.3 1.8 - - + -
----------------------------------------------------------
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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