Contacts of the helix formed by residues 283 - 316 (chain C) in PDB entry 4GQS
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 THR 283 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C PHE* 5.1 2.9 - - - -
267C PHE* 3.4 10.5 - - - -
271C MET* 4.2 4.5 - - - -
280C SER 3.9 15.9 - - - +
281C GLU 3.2 9.8 + - - +
282C PHE* 1.3 80.6 - - - +
284C ILE* 1.3 66.9 + - - +
285C GLU* 3.6 12.0 - - - +
286C ASN* 2.9 17.8 + - - +
287C LEU 2.9 18.2 + - - -
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Residues in contact with ILE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C LEU* 3.5 31.4 - - + -
248C VAL* 4.6 14.8 - - + -
252C GLN* 4.3 17.9 - - - +
267C PHE* 4.6 0.9 - - - -
271C MET* 3.9 24.2 - - + -
283C THR* 1.3 71.3 - - - +
285C GLU* 1.3 64.0 + - - +
287C LEU* 3.8 8.3 - - - -
288C VAL* 3.0 27.5 + - + +
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Residues in contact with GLU 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG* 4.6 10.4 + - - -
110C PHE* 3.3 39.7 - - + -
283C THR* 2.9 12.0 + - - +
284C ILE* 1.3 82.1 - - - +
286C ASN* 1.3 60.5 + - - +
288C VAL* 3.7 2.4 + - - +
289C ILE* 2.8 40.5 + - - +
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Residues in contact with ASN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C GLY 5.1 0.2 + - - -
110C PHE* 3.7 23.4 - - + +
111C GLY* 3.1 23.8 + - - +
119C ARG* 3.8 17.8 - - - +
123C ILE* 3.6 29.2 - - + +
267C PHE* 4.7 1.3 - - + -
281C GLU* 3.8 21.9 + - - +
283C THR* 2.9 13.7 + - - +
285C GLU* 1.3 74.4 - - - +
287C LEU* 1.3 56.5 + - - +
289C ILE* 3.8 0.6 - - - +
290C THR* 2.7 45.7 + - - -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C VAL* 3.6 39.3 - - + -
263C PHE* 4.2 20.6 - - + -
264C ILE* 4.4 14.4 - - + -
267C PHE* 3.3 60.3 - - + -
268C LEU* 4.8 0.4 - - + -
271C MET* 4.5 7.9 - - + -
283C THR 2.9 5.4 + - - +
284C ILE* 3.1 10.7 + - - +
286C ASN* 1.3 73.5 - - - +
288C VAL* 1.3 59.0 + - - +
290C THR* 2.8 7.0 + - - -
291C ALA* 2.7 38.1 + - + +
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C GLU* 3.3 43.0 - - + +
244C ILE* 3.7 20.7 - - + +
245C LEU* 3.8 35.4 - - + -
248C VAL* 4.6 7.6 - - + -
284C ILE* 3.0 19.2 + - + +
285C GLU* 4.2 4.7 - - - +
287C LEU* 1.3 74.8 - - + +
289C ILE* 1.3 63.8 + - + +
291C ALA* 3.5 2.6 + - - +
292C ALA* 3.2 22.2 + - - +
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ALA 5.5 1.1 - - - +
107C ASN* 4.1 25.4 - - - +
110C PHE* 3.3 23.8 - - + +
111C GLY* 3.1 31.6 - - - +
241C GLU* 3.9 23.6 - - - +
285C GLU* 2.8 44.2 - - - +
286C ASN 3.8 1.3 - - - +
287C LEU 3.1 1.2 - - - -
288C VAL* 1.3 80.0 - - + +
290C THR* 1.3 59.4 + - - +
292C ALA* 3.2 7.5 + - - +
293C ASP* 3.0 25.8 + - - +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLY* 3.6 11.9 - - - -
112C ILE* 4.8 8.3 - - + -
123C ILE* 3.7 13.9 - - + +
127C SER* 4.1 12.1 - - - +
263C PHE* 4.1 27.6 - - + -
267C PHE* 5.7 2.9 - - + -
286C ASN* 2.7 36.4 + - - -
287C LEU* 2.8 7.0 + - - -
289C ILE* 1.3 75.2 - - - +
291C ALA* 1.3 65.4 + - - +
293C ASP* 3.0 14.1 + - - +
294C LEU* 3.1 20.6 + - + +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ILE* 3.3 33.2 - - + +
183C PHE* 6.1 0.2 - - + -
244C ILE* 3.6 33.0 - - + -
263C PHE* 5.1 3.8 - - + -
264C ILE* 6.0 1.3 - - + -
287C LEU* 2.7 24.2 + - + +
288C VAL* 3.7 1.1 - - - +
290C THR* 1.3 75.5 - - - +
292C ALA* 1.3 61.2 + - - +
294C LEU* 3.8 2.9 + - - -
295C LEU* 3.2 24.3 + - - +
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU* 6.2 3.8 - - + -
240C MET* 5.0 11.4 - - - +
241C GLU* 4.6 13.5 - - + -
244C ILE* 3.9 13.9 - - + +
288C VAL 3.2 13.6 + - - +
289C ILE* 3.4 12.1 - - - +
290C THR 3.0 0.4 - - - -
291C ALA* 1.3 76.9 - - - +
293C ASP* 1.3 67.5 + - - +
295C LEU* 3.1 16.4 + - - +
296C GLY* 3.2 11.3 + - - -
502C 0XV 5.6 0.3 - - - +
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Residues in contact with ASP 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ASN* 2.9 32.8 + - - +
111C GLY* 3.4 1.6 - - - -
112C ILE* 2.9 40.2 + - + -
113C VAL* 3.2 19.5 + - + +
289C ILE 3.0 15.9 + - - +
290C THR 3.0 9.8 + - - +
292C ALA* 1.3 78.1 - - - +
294C LEU* 1.3 56.5 + - - +
296C GLY* 3.4 0.5 + - - -
297C ALA* 2.9 34.0 + - - +
502C 0XV 3.6 15.2 - - - +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ILE* 4.7 10.5 - - + -
127C SER* 5.5 2.5 - - - +
131C LEU* 4.9 14.6 - - + -
178C ILE* 4.0 18.7 - - + +
181C ILE* 5.8 1.6 - - + -
182C ILE* 4.3 15.7 - - + -
263C PHE* 3.9 37.2 - - + -
290C THR* 3.1 18.7 + - + +
291C ALA 4.0 3.6 - - - +
293C ASP* 1.3 77.1 - - - +
295C LEU* 1.3 62.0 + - - +
297C ALA* 3.9 4.0 - - - -
298C GLY* 3.1 21.8 + - - -
436C VAL* 5.2 0.4 - - + -
501C HEM 4.1 44.0 - - + +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C CYS* 4.9 6.3 - - - +
178C ILE* 3.7 26.0 - - + +
179C CYS* 4.5 19.7 - - - +
182C ILE* 4.2 7.4 - - + -
183C PHE* 5.5 7.9 - - + -
197C LEU* 4.0 27.6 - - + -
201C LEU* 4.5 13.9 - - + +
240C MET* 4.5 6.5 - - - -
244C ILE* 4.0 23.6 - - + -
291C ALA 3.2 16.1 + - - +
292C ALA* 3.1 9.3 + - - +
294C LEU* 1.3 80.3 - - - +
296C GLY* 1.3 59.3 + - - +
299C THR* 2.6 31.1 + - - -
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Residues in contact with GLY 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C LEU* 4.5 12.3 - - - +
292C ALA 3.2 9.0 + - - -
293C ASP 3.8 2.0 - - - -
295C LEU* 1.3 78.4 - - - +
297C ALA* 1.3 61.0 + - - +
298C GLY 3.4 0.4 + - - -
299C THR* 4.4 5.3 + - - -
300C GLU* 4.8 4.9 + - - +
502C 0XV 3.8 32.5 - - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C VAL* 4.6 1.3 - - + -
293C ASP 2.9 22.6 + - - +
294C LEU* 4.0 2.2 - - - +
295C LEU 3.3 0.2 - - - -
296C GLY* 1.3 78.0 - - - +
298C GLY* 1.3 58.2 + - - +
301C THR* 2.8 20.8 + - - +
501C HEM 3.0 45.6 + - + -
502C 0XV 3.2 27.2 - - + +
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Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C PRO* 4.0 7.1 - - - +
178C ILE* 4.7 8.7 - - - -
294C LEU 3.1 13.0 + - - -
295C LEU 4.3 0.2 - - - -
297C ALA* 1.3 78.9 - - - +
299C THR* 1.3 59.3 + - - +
301C THR* 3.4 4.7 - - - -
302C THR* 2.7 25.3 + - - -
444C GLU* 4.9 0.5 - - - +
501C HEM 3.3 27.8 - - - +
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Residues in contact with THR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLY* 3.9 22.7 - - - +
174C PRO* 4.1 6.8 - - - +
175C CYS* 3.9 21.7 - - + +
178C ILE* 5.3 1.2 - - - +
198C MET* 5.3 4.3 - - + -
201C LEU* 3.9 24.6 - - + +
295C LEU* 2.6 24.6 + - - -
296C GLY* 4.4 2.6 - - - -
297C ALA 3.8 0.6 - - - -
298C GLY* 1.3 76.1 - - - +
300C GLU* 1.3 67.6 + - + +
301C THR 3.2 1.0 + - - -
302C THR* 3.3 2.1 + - - -
303C SER* 2.8 33.7 + - - -
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN* 4.6 11.1 + - - -
205C ILE* 3.7 33.8 - - + +
296C GLY 4.8 4.6 + - - +
299C THR* 1.3 82.5 - - + +
301C THR* 1.3 58.3 + - - +
303C SER* 4.2 6.3 + - - -
304C THR* 2.6 59.0 + - - +
307C ARG* 4.5 10.0 + - - -
479C VAL* 5.2 5.9 - - - +
502C 0XV 3.6 33.0 - - + -
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ALA 2.8 26.6 + - - +
298C GLY* 3.4 10.7 - - - -
300C GLU* 1.3 79.7 - - - +
302C THR* 1.3 60.5 + - - -
305C THR* 2.7 30.0 + - - -
361C LEU* 3.5 13.6 - - + +
501C HEM 3.4 35.4 - - + +
502C 0XV 3.6 42.4 - - + +
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Residues in contact with THR 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C PRO* 3.9 8.5 - - + -
298C GLY 2.7 21.4 + - - -
299C THR 3.3 1.2 + - - -
301C THR* 1.3 75.3 + - - +
303C SER* 1.3 56.4 + - - +
305C THR* 3.2 2.4 + - - -
306C LEU* 2.8 57.8 + - + +
441C ALA* 4.8 2.4 - - - +
444C GLU* 4.0 29.9 + - + +
445C LEU* 4.5 10.1 - - + -
501C HEM 3.5 31.4 - - + +
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Residues in contact with SER 303 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C THR 4.1 6.9 + - - -
170C LEU* 3.4 21.8 + - - +
171C GLY* 3.3 24.9 + - - -
174C PRO* 4.0 2.6 - - - +
299C THR* 2.8 26.0 + - - -
300C GLU* 3.7 8.9 + - - -
302C THR* 1.3 73.2 - - - +
304C THR* 1.3 52.7 + - - +
306C LEU* 3.1 4.7 + - - +
307C ARG* 2.8 43.1 + - - +
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Residues in contact with THR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C GLU* 2.6 48.3 + - - +
303C SER* 1.3 72.6 - - - +
305C THR* 1.3 57.0 + - - +
307C ARG* 3.2 20.4 + - - +
308C TYR* 2.9 30.1 + - + +
361C LEU* 3.4 28.7 - - + -
478C SER 4.1 8.7 - - - +
479C VAL* 4.7 1.6 - - + +
480C PRO* 3.8 24.5 - - + +
502C 0XV 6.4 0.2 - - - -
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Residues in contact with THR 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C THR 2.7 21.1 + - - -
302C THR 3.2 3.8 + - - -
304C THR* 1.3 77.8 - - - +
306C LEU* 1.3 56.9 + - - +
308C TYR* 3.3 3.2 + - - +
309C ALA* 3.1 26.0 + - - +
355C VAL* 4.1 8.6 - - + +
356C GLN* 4.2 15.5 + - + +
359C ILE* 3.8 24.3 - - + +
361C LEU* 3.5 12.3 - - - +
445C LEU* 3.6 28.0 - - + -
501C HEM 3.2 14.0 - - - +
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Residues in contact with LEU 306 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C LEU* 5.8 1.6 - - + -
170C LEU* 4.2 23.8 - - + +
173C ALA* 5.9 0.2 - - + -
174C PRO* 4.1 20.2 - - + -
302C THR* 2.8 22.6 + - + +
303C SER* 3.5 4.9 - - - +
305C THR* 1.3 74.5 - - - +
307C ARG* 1.3 65.3 + - - +
308C TYR 3.4 0.3 + - - -
309C ALA* 3.5 3.6 + - - +
310C LEU* 3.4 27.5 + - - +
445C LEU* 3.5 30.5 - - + -
448C PHE* 3.9 33.2 - - + -
449C LEU* 4.0 29.3 - - + +
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Residues in contact with ARG 307 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASP* 4.8 1.3 - - - -
166C PRO* 4.9 1.6 - - + -
167C THR* 3.2 47.7 + - - +
170C LEU* 3.5 21.1 - - + +
300C GLU* 4.5 6.3 + - - -
303C SER* 2.8 24.5 + - - +
304C THR* 3.2 27.7 + - - +
306C LEU* 1.3 77.1 - - - +
308C TYR* 1.3 61.7 + - - +
311C LEU 3.6 0.7 + - - -
479C VAL* 3.5 32.1 - - - +
480C PRO* 3.7 19.6 + - + +
481C PRO 5.9 0.4 + - - -
483C TYR* 2.6 46.9 + - + +
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Residues in contact with TYR 308 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C THR* 2.9 16.7 + - + +
305C THR* 3.5 7.2 - - - +
306C LEU 3.1 0.2 - - - -
307C ARG* 1.3 77.0 - - - +
309C ALA* 1.3 66.5 + - - +
311C LEU* 2.8 16.7 + - + +
312C LEU* 2.8 42.7 + - + +
355C VAL* 4.7 0.7 - - + -
358C TYR* 4.6 1.3 - + - -
359C ILE* 3.3 44.6 - - + -
361C LEU* 5.6 0.9 - - + -
469C THR 2.9 28.9 + - - -
470C THR 3.8 0.9 - - - -
471C PRO* 3.0 32.0 - - + +
478C SER* 5.3 1.6 - - - -
479C VAL* 4.1 4.9 - - - -
480C PRO* 3.4 47.9 - - + +
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Residues in contact with ALA 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C THR 3.1 14.5 + - - +
306C LEU* 3.7 9.9 - - + +
308C TYR* 1.3 75.8 - - - +
310C LEU* 1.3 57.5 + - - +
312C LEU* 2.8 21.2 + - - +
313C LEU* 2.8 21.9 + - + +
351C VAL* 6.5 0.2 - - + -
355C VAL* 4.1 26.8 - - + +
445C LEU* 6.2 0.7 - - + -
449C LEU* 3.9 30.5 - - + -
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Residues in contact with LEU 310 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C PRO* 4.9 1.1 - - + -
170C LEU* 3.3 43.5 - - + -
306C LEU 3.4 7.9 + - - +
308C TYR 3.3 0.8 - - - -
309C ALA* 1.3 78.2 - - - +
311C LEU* 1.3 56.9 + - - +
313C LEU* 3.5 23.9 - - + +
314C LEU* 3.2 29.3 + - - +
449C LEU* 4.3 13.7 - - + -
452C ILE* 4.2 16.8 - - + -
453C LEU* 5.4 1.1 - - + -
458C LEU* 3.8 24.3 - - + +
483C TYR* 3.6 13.7 - - - +
485C LEU* 4.3 6.2 - - + +
487C PHE* 4.0 19.1 - - + -
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Residues in contact with LEU 311 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C ARG 3.7 2.5 - - - +
308C TYR* 2.8 19.9 + - + +
310C LEU* 1.3 77.2 - - - +
312C LEU* 1.3 59.9 + - - +
313C LEU 3.0 5.4 + - - -
314C LEU* 3.3 11.4 + - - +
315C LYS* 3.3 11.6 + - - +
467C LEU* 4.3 21.0 - - + +
468C ASP 4.3 8.5 - - - +
469C THR* 4.5 8.7 - - + -
480C PRO* 3.7 28.3 - - + -
481C PRO* 3.9 20.4 - - + +
483C TYR* 3.5 51.2 + - + -
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Residues in contact with LEU 312 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C TYR* 2.8 27.4 + - + +
309C ALA* 2.8 5.8 + - - +
311C LEU* 1.3 75.9 - - - +
313C LEU* 1.3 60.9 + - + +
315C LYS* 3.8 0.9 - - - -
316C HIS* 2.9 31.6 + - + +
355C VAL* 3.7 31.2 - - + -
358C TYR* 3.7 26.5 - - + -
359C ILE* 4.4 0.9 - - + -
407C PHE* 3.7 42.9 - - + -
469C THR* 3.5 35.2 - - + +
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Residues in contact with LEU 313 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ALA* 2.8 20.4 + - + +
310C LEU* 3.5 27.1 - - + +
312C LEU* 1.3 76.8 - - + +
314C LEU* 1.3 65.4 + - - +
315C LYS 3.1 1.1 - - - -
316C HIS* 3.0 16.9 + - - +
317C PRO* 3.5 2.8 - - - +
319C VAL* 5.3 5.6 - - + -
320C THR* 3.0 40.6 + - + +
323C VAL* 5.7 1.6 - - + -
351C VAL* 4.9 17.7 - - + -
407C PHE* 6.0 3.1 - - + -
449C LEU* 4.8 10.3 - - + -
453C LEU* 4.5 17.7 - - + -
458C LEU* 3.4 31.4 - - + -
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Residues in contact with LEU 314 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU 3.2 17.5 - - - +
311C LEU* 3.6 8.3 - - - +
313C LEU* 1.3 79.4 - - - +
315C LYS* 1.3 61.0 + - - +
317C PRO* 3.8 7.0 - - - +
458C LEU* 3.6 30.1 - - + +
459C LYS* 3.7 4.9 - - - +
460C SER* 3.6 30.0 + - - +
464C PRO* 3.3 24.8 - - - +
467C LEU* 3.7 22.3 - - + +
483C TYR* 3.6 33.2 - - + -
484C GLN 4.6 0.4 - - - +
485C LEU* 3.8 13.9 - - + -
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU 3.3 10.0 + - - +
312C LEU 3.8 3.4 - - - +
313C LEU 3.1 0.4 - - - -
314C LEU* 1.3 80.7 - - - +
316C HIS* 1.3 89.0 + - + +
317C PRO* 3.7 5.9 - - - +
464C PRO* 3.3 27.1 + - - +
465C LYS* 3.5 29.9 + - - +
467C LEU* 2.9 34.7 - - + +
469C THR* 4.0 17.3 - - + +
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Residues in contact with HIS 316 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LEU* 2.9 24.5 + - - +
313C LEU* 3.0 6.9 + - - +
315C LYS* 1.3 108.4 + - + +
317C PRO* 1.3 59.3 - - - +
318C GLU* 2.8 41.7 + - + +
319C VAL* 3.1 19.5 + - + +
320C THR* 3.2 12.0 + - - -
407C PHE* 3.6 40.4 + + + +
469C THR* 5.1 6.3 - - + -
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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