Contacts of the helix formed by residues 287 - 318 (chain D) in PDB entry 4EJJ
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 TYR 287 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.5 18.7 - + - -
123D ARG* 3.4 23.6 + - - -
271D PHE* 3.6 3.0 - - - -
275D MET* 3.5 15.1 - - - +
284D THR* 3.1 31.6 - - + -
285D GLU* 3.4 10.3 + - - -
286D PHE* 1.3 72.3 - - - +
288D LEU* 1.3 68.2 + - - +
289D LYS* 3.4 16.8 - - + -
290D ASN* 3.2 38.9 + - - -
291D LEU 3.1 18.2 + - - -
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D VAL* 3.9 21.1 - - + -
256D GLN* 3.7 27.8 - - - +
275D MET* 3.6 16.6 - - + +
287D TYR* 1.3 72.7 - - - +
289D LYS* 1.3 57.4 + - - +
291D LEU* 3.3 7.4 + - + +
292D VAL* 2.8 44.5 + - + +
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL 4.7 2.6 + - - -
111D PHE 4.8 1.1 - - - -
112D LYS* 4.8 14.4 - - - +
114D TYR* 3.6 44.2 - - + -
245D GLU* 4.0 8.5 + - - -
287D TYR* 3.3 18.1 + - + -
288D LEU* 1.3 79.3 - - - +
290D ASN* 1.3 60.2 + - - +
292D VAL* 4.2 3.9 - - + -
293D MET* 3.2 60.3 + - + +
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Residues in contact with ASN 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TYR* 3.7 8.8 - - - +
115D GLY* 3.0 22.6 + - - +
123D ARG* 3.7 10.6 - - - +
127D LEU* 3.6 16.1 - - + +
271D PHE* 3.8 8.1 - - + -
285D GLU* 2.7 40.9 + - - +
287D TYR* 3.2 34.6 + - + +
289D LYS* 1.3 72.9 - - - +
291D LEU* 1.3 53.9 + - - +
294D THR* 2.7 41.8 + - - -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D VAL* 3.9 22.7 - - + -
267D PHE* 4.9 2.2 - - + -
268D ILE* 4.2 14.8 - - + -
271D PHE* 3.4 52.2 - - + -
272D LEU* 3.9 32.8 - - + -
275D MET* 4.1 4.7 - - - -
287D TYR 3.1 7.8 + - - +
288D LEU* 3.4 11.4 - - + +
290D ASN* 1.3 73.7 - - - +
292D VAL* 1.3 66.6 + - - +
294D THR* 3.8 0.6 - - - -
295D THR* 2.9 46.2 + - - +
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Residues in contact with VAL 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D GLU* 4.1 31.9 - - + +
248D ILE* 3.6 20.1 - - + +
249D ALA* 4.3 17.5 - - + +
252D VAL* 4.2 19.1 - - + -
288D LEU* 2.8 40.0 + - + +
289D LYS* 4.2 5.2 - - + +
291D LEU* 1.3 73.4 - - - +
293D MET* 1.3 67.8 + - + +
296D LEU* 2.9 30.4 + - + +
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Residues in contact with MET 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D VAL* 3.4 23.6 - - + +
111D PHE* 3.6 24.8 - - + +
114D TYR* 3.6 19.1 - - + +
115D GLY* 3.6 20.0 - - - +
245D GLU* 3.5 24.7 - - + +
289D LYS* 3.2 44.9 + - + +
292D VAL* 1.3 85.0 - - + +
294D THR* 1.3 60.0 + - - +
296D LEU* 3.4 9.6 + - - -
297D ASN* 2.9 32.9 + - - -
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Residues in contact with THR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D GLY* 3.6 1.8 - - - -
116D VAL* 3.3 27.2 + - + +
127D LEU* 3.9 12.3 - - + +
131D SER* 3.2 27.1 - - - +
267D PHE* 3.7 21.1 - - + -
271D PHE* 4.4 4.9 - - + -
290D ASN 2.7 29.4 + - - -
291D LEU* 3.9 3.1 - - - -
293D MET* 1.3 67.6 - - - +
295D THR* 1.3 67.5 + - - +
297D ASN* 3.1 12.7 + - - +
298D LEU* 2.8 24.8 + - + +
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Residues in contact with THR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D VAL* 4.0 22.8 - - + +
187D PHE* 4.1 5.8 - - + -
248D ILE* 3.8 29.6 - - + -
252D VAL* 5.1 0.3 - - - +
267D PHE* 4.2 10.8 - - + -
268D ILE* 4.0 15.4 - - + +
291D LEU* 2.9 41.2 + - - +
292D VAL 3.7 3.4 - - - -
294D THR* 1.3 76.9 - - - +
296D LEU* 1.3 56.7 + - - +
298D LEU* 3.2 5.7 + - - +
299D PHE* 3.0 26.9 + - - +
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Residues in contact with LEU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 4.3 14.4 - - + -
111D PHE* 3.8 20.9 - - + -
241D LEU* 4.7 2.9 - - + +
244D LEU* 3.8 25.4 - - + +
245D GLU* 4.2 23.6 - - + +
248D ILE* 3.9 20.8 - - + +
292D VAL* 2.9 19.4 + - + +
293D MET* 3.6 12.1 - - - +
295D THR* 1.3 74.3 - - - +
297D ASN* 1.4 65.2 + - - +
299D PHE* 3.3 8.1 + - + -
300D ILE* 2.9 49.4 + - + +
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Residues in contact with ASN 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D PHE* 3.1 38.1 - - - -
115D GLY* 3.5 3.5 - - - -
116D VAL* 3.1 20.3 + - + +
117D VAL* 3.0 51.7 + - + +
118D PHE* 4.4 1.0 + - - -
293D MET 2.9 16.6 + - - +
294D THR* 3.1 7.8 + - - +
296D LEU* 1.4 74.5 - - - +
298D LEU* 1.4 62.1 + - + +
301D GLY* 2.8 29.5 + - - -
501D NCT 3.7 14.3 + - - -
502D HEM 5.2 1.4 - - - +
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Residues in contact with LEU 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 5.0 2.0 - - + -
131D SER* 4.7 1.3 - - - +
135D LEU* 4.2 15.9 - - + -
182D ILE* 3.5 12.7 - - + +
186D VAL* 4.2 15.7 - - + -
267D PHE* 3.8 43.5 - - + -
294D THR* 2.8 20.6 + - + +
295D THR* 3.9 3.4 - - - +
296D LEU 3.2 0.2 - - - -
297D ASN* 1.4 77.2 - - + +
299D PHE* 1.3 60.2 + - - +
301D GLY 4.5 0.2 - - - +
302D GLY* 2.9 27.9 + - - -
440D PHE* 4.3 13.9 - - + -
502D HEM 3.9 43.8 - - + +
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Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D SER* 3.6 14.8 - - - -
182D ILE* 4.3 9.4 - - + +
183D SER* 3.3 26.7 - - - -
186D VAL* 4.7 5.6 - - + +
187D PHE* 3.9 20.4 - + + -
191D PHE* 4.5 4.5 - + - -
198D PHE* 5.5 2.0 - + - -
201D LEU* 4.2 27.6 - - + -
202D LEU* 5.8 1.6 - - + -
205D MET* 3.2 25.1 - - + +
244D LEU* 3.9 17.5 - - + -
247D PHE* 4.8 2.7 - + - -
248D ILE* 3.8 25.4 - - + -
295D THR 3.0 17.0 + - - +
296D LEU* 3.8 6.3 - - + +
298D LEU* 1.3 77.3 - - - +
300D ILE* 1.4 60.1 + - - +
302D GLY 4.1 0.2 - - - -
303D THR* 2.8 36.4 + - - -
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Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D PHE* 5.0 8.5 - - + -
111D PHE* 4.4 13.0 - - + -
205D MET* 3.4 31.6 - - + -
208D ILE* 5.6 2.5 - - + -
209D PHE* 3.8 29.1 - - + -
241D LEU* 5.0 9.9 - - + -
244D LEU* 4.5 8.1 - - + -
296D LEU* 2.9 44.0 + - + +
297D ASN 4.0 2.0 - - - +
299D PHE* 1.4 73.6 - - - +
301D GLY* 1.3 65.2 - - - +
303D THR 3.3 0.5 + - - -
304D GLU* 2.9 28.2 + - + +
305D THR 4.5 0.3 + - - -
501D NCT 4.2 17.7 - - + +
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Residues in contact with GLY 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ASN 2.8 21.0 + - - -
298D LEU 4.0 0.2 - - - -
300D ILE* 1.3 73.9 - - - +
302D GLY* 1.3 59.9 - - - +
303D THR 3.6 0.2 + - - -
305D THR* 2.9 25.5 + - - -
306D VAL 5.0 0.2 + - - -
501D NCT 3.5 30.1 - - - -
502D HEM 3.4 17.7 - - - +
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Residues in contact with GLY 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D VAL* 3.4 18.4 - - - +
182D ILE* 3.6 22.4 - - - +
298D LEU 2.9 17.2 + - - -
301D GLY* 1.3 74.7 - - - +
303D THR* 1.3 57.3 + - - +
306D VAL* 4.9 2.2 - - - +
444D LEU* 5.3 0.2 - - - -
448D GLU* 4.3 5.5 - - - +
502D HEM 3.2 27.9 - - - +
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Residues in contact with THR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D SER* 4.3 6.3 - - - +
178D VAL* 3.4 10.1 - - - +
179D SER* 2.9 39.6 + - - +
182D ILE* 4.0 3.6 - - - +
202D LEU* 3.8 17.9 - - + -
205D MET* 3.9 12.1 - - - -
299D PHE* 2.8 26.7 + - - -
302D GLY* 1.3 80.1 - - - +
304D GLU* 1.3 76.2 + - - +
305D THR 3.4 1.7 + - - -
306D VAL 4.0 1.0 + - - -
307D SER* 3.2 23.7 + - - -
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D SER* 4.2 7.6 - - - -
202D LEU* 4.8 2.9 - - - +
205D MET* 4.2 17.0 - - + +
206D LEU* 3.0 41.6 + - - +
209D PHE* 3.7 42.8 - - + +
300D ILE* 2.9 18.6 + - + +
303D THR* 1.3 88.1 - - + +
305D THR* 1.3 59.1 + - - +
307D SER* 4.2 9.8 + - - -
308D THR* 2.9 41.6 + - - +
311D ARG* 4.4 3.5 + - - -
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Residues in contact with THR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PHE* 3.7 14.1 - - + -
300D ILE 4.5 0.2 + - - -
301D GLY 2.9 21.9 + - - -
303D THR 3.4 0.2 - - - -
304D GLU* 1.3 74.8 - - - +
306D VAL* 1.3 60.6 + - - +
308D THR* 3.3 7.1 + - - -
309D THR* 2.8 32.4 + - - -
365D VAL* 4.2 6.3 - - + +
366D ILE* 3.6 25.6 - - + -
501D NCT 3.4 25.0 - - - -
502D HEM 3.5 26.3 - - + +
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Residues in contact with VAL 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D VAL* 3.9 16.2 - - + -
301D GLY 5.5 0.2 - - - +
302D GLY 4.9 1.3 - - - +
303D THR 4.0 1.2 + - - +
305D THR* 1.3 77.8 + - - +
307D SER* 1.3 61.1 + - - +
309D THR* 3.3 6.4 + - - -
310D LEU* 3.2 35.2 + - + +
445D ALA* 3.7 37.7 - - + +
448D GLU* 3.7 28.0 - - + +
449D LEU* 3.8 15.3 - - + -
452D PHE* 5.0 0.7 - - + -
502D HEM 3.7 20.6 - - + -
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Residues in contact with SER 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D THR* 4.4 2.9 + - - +
174D LEU* 4.2 4.1 - - - +
175D SER* 3.2 41.3 + - - +
178D VAL* 4.1 10.7 - - - +
303D THR 3.2 21.0 + - - -
304D GLU* 3.9 10.5 + - - -
305D THR 3.2 0.2 - - - -
306D VAL* 1.3 78.0 - - - +
308D THR* 1.3 57.4 + - - +
310D LEU* 4.0 4.1 + - - +
311D ARG* 3.0 35.0 + - - +
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Residues in contact with THR 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D PHE* 4.5 6.8 - - + -
304D GLU* 2.9 32.3 + - - +
305D THR 3.6 4.9 - - - -
306D VAL 3.2 0.2 - - - -
307D SER* 1.3 73.2 - - - +
309D THR* 1.3 55.6 + - - +
311D ARG* 3.2 21.4 + - - +
312D TYR* 2.7 34.5 + - + +
365D VAL* 3.7 27.6 - - + -
482D THR 3.7 17.0 - - - +
483D ILE* 5.0 5.5 - - + +
484D PRO* 3.9 15.7 - - + +
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Residues in contact with THR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D THR 2.8 22.1 + - - -
306D VAL 3.6 5.6 - - - -
308D THR* 1.3 74.1 - - - +
310D LEU* 1.3 56.0 + - - +
312D TYR* 3.1 7.5 + - - +
313D GLY* 2.7 32.7 + - - -
359D ILE* 3.6 21.4 - - + +
360D GLN* 4.2 20.9 + - + -
365D VAL* 3.5 21.0 - - + +
449D LEU* 3.7 23.1 - - + -
453D PHE* 4.3 3.4 - - + -
502D HEM 3.9 8.8 - - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D LEU* 4.0 25.1 - - + +
178D VAL* 3.8 25.1 - - + -
306D VAL* 3.3 21.3 - - + +
307D SER* 4.1 2.5 - - - +
309D THR* 1.3 75.8 - - - +
311D ARG* 1.3 64.1 + - - +
313D GLY 2.9 10.4 + - - -
314D PHE* 3.1 22.4 + - + -
449D LEU* 3.8 14.8 - - + -
452D PHE* 4.1 28.9 - - + -
453D PHE* 3.4 45.5 - - + -
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Residues in contact with ARG 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ASP* 5.1 1.1 - - - -
170D PRO* 5.1 1.8 - - + -
171D THR* 3.3 42.2 + - - +
174D LEU* 3.7 15.0 - - + +
206D LEU* 4.1 18.0 - - - +
210D GLN* 6.1 0.6 - - - -
304D GLU* 4.4 6.1 + - - -
307D SER* 3.0 24.2 + - - +
308D THR* 3.2 29.2 + - - +
310D LEU* 1.3 74.7 - - - +
312D TYR* 1.4 62.3 + - - +
315D LEU* 3.6 2.9 + - - +
483D ILE* 4.1 20.2 - - - +
484D PRO* 4.0 28.2 + - + +
485D ARG 5.7 1.0 + - - -
487D TYR* 2.8 46.7 + - + +
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Residues in contact with TYR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D THR* 2.7 17.3 + - + +
309D THR* 3.5 9.2 - - - +
311D ARG* 1.4 72.5 - - - +
313D GLY* 1.3 53.0 - - - +
315D LEU* 3.2 12.6 + - + +
316D LEU* 2.8 54.9 + - + +
359D ILE* 4.8 6.1 - - + -
362D PHE* 4.4 11.8 - + - -
363D GLY* 4.4 20.4 - - - -
365D VAL* 5.8 2.0 - - + -
473D VAL* 2.5 36.1 + - + -
475D PRO* 3.7 21.8 - - - +
482D THR* 4.2 19.7 - - + -
483D ILE 4.5 0.2 - - - -
484D PRO* 3.5 46.1 - - + +
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Residues in contact with GLY 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D THR 2.7 17.6 + - - -
310D LEU 2.9 5.4 + - - -
312D TYR* 1.3 70.1 - - - +
314D PHE* 1.3 60.6 + - - -
316D LEU* 3.7 3.3 - - - +
317D LEU* 3.1 32.1 + - - +
359D ILE* 3.4 32.9 - - - +
453D PHE* 3.8 5.6 - - - -
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Residues in contact with PHE 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PRO* 6.0 0.2 - - + -
174D LEU* 3.7 36.1 - - + -
310D LEU* 3.1 25.4 + - + -
313D GLY* 1.3 74.2 - - - +
315D LEU* 1.3 65.5 + - - +
316D LEU 3.1 1.8 - - - -
317D LEU* 4.1 3.1 - - + +
318D MET* 3.1 31.7 + - - +
452D PHE 4.7 3.1 - - - -
453D PHE* 3.7 30.5 - + - -
456D VAL* 3.7 30.7 - - + -
457D MET* 3.6 24.2 - - + -
462D LEU* 3.7 28.1 - - + +
487D TYR* 4.0 10.3 - - - +
489D MET* 4.3 9.0 - - + -
491D PHE* 4.9 9.9 - + - -
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Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D ARG 3.6 5.4 + - - +
312D TYR* 3.2 16.7 + - + +
314D PHE* 1.3 79.3 - - - +
316D LEU* 1.3 57.3 + - - +
318D MET* 3.9 13.4 + - + +
319D LYS* 3.5 18.4 + - - +
466D GLN* 6.1 1.6 - - - +
471D ILE* 3.9 18.9 - - + +
472D ASP 4.0 12.3 - - - +
473D VAL* 4.0 23.5 - - + +
484D PRO* 4.6 15.3 - - + -
485D ARG* 4.8 7.6 - - + +
487D TYR* 3.5 51.6 + - + -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D TYR* 2.8 28.9 + - + +
313D GLY 3.9 5.6 - - - +
315D LEU* 1.3 77.3 - - - +
317D LEU* 1.3 58.8 + - - +
319D LYS* 3.1 18.3 + - - +
320D HIS* 3.2 19.8 + - + +
359D ILE* 3.8 28.9 - - + +
362D PHE* 3.4 39.7 - - + -
411D PHE* 3.7 45.4 - - + -
473D VAL* 4.1 15.9 - - + -
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Residues in contact with LEU 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D GLY 3.1 22.8 + - - +
314D PHE* 3.3 10.5 + - + +
316D LEU* 1.3 78.2 - - + +
318D MET* 1.3 56.5 + - - +
320D HIS* 3.1 27.2 - - - +
321D PRO* 3.5 5.9 - - - +
323D VAL* 3.8 30.1 - - + -
324D GLU* 3.9 27.6 - - + +
327D VAL* 4.1 9.4 - - + -
355D VAL* 4.6 8.5 - - + -
359D ILE* 4.8 10.8 - - + -
411D PHE* 5.3 4.0 - - + -
453D PHE* 5.2 3.1 - - + -
457D MET* 3.4 35.0 - - + -
462D LEU* 4.2 9.4 - - + -
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Residues in contact with MET 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D PHE 3.1 16.8 + - - +
315D LEU* 4.1 15.0 - - + +
317D LEU* 1.3 73.9 - - - +
319D LYS* 1.3 60.1 + - - +
320D HIS 3.4 0.2 - - - -
321D PRO* 4.5 7.0 - - - +
324D GLU* 5.6 1.6 - - - -
462D LEU* 3.6 22.9 - - + -
463D LYS 3.7 27.6 - - - +
464D SER* 3.7 15.1 + - - +
468D PRO* 4.4 12.3 - - - +
471D ILE* 3.3 21.8 - - + +
487D TYR* 3.8 32.3 - - + -
488D THR 5.1 1.3 - - - +
489D MET* 3.5 25.1 - - + -
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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) + - + + + + + -
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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