Contacts of the helix formed by residues 294 - 320 (chain E) 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 THR 294 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.8 1.8 - - - -
224A GLN* 3.7 1.8 + - - -
292E TYR* 3.6 32.7 + - + +
293E VAL* 1.3 83.3 - - - +
295E ALA* 1.3 64.7 + - - +
296E MET* 3.9 9.1 + - - +
297E ASP* 2.7 44.7 + - - +
298E LEU 3.6 7.1 + - - -
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Residues in contact with ALA 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 5.0 4.9 + - - +
224A GLN* 3.4 20.4 - - - +
241E TYR* 5.4 0.9 - - - +
293E VAL 3.8 0.8 + - - -
294E THR* 1.3 74.5 - - - +
296E MET* 1.3 62.1 + - - +
298E LEU* 3.5 9.0 + - - +
299E PHE 3.8 3.3 + - - -
350E TYR* 2.8 34.2 + - + +
354E TYR* 5.7 10.3 - - + -
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Residues in contact with MET 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E THR* 4.9 17.7 - - - -
240E THR* 5.0 13.5 - - + -
241E TYR* 3.5 37.3 + - + +
283E ALA* 4.7 20.4 - - + +
286E SER* 4.7 17.5 - - - +
294E THR* 3.2 8.2 + - - +
295E ALA* 1.3 80.6 - - - +
297E ASP* 1.3 68.9 + - - +
298E LEU 3.4 0.2 + - - -
299E PHE* 3.7 9.9 + - - +
300E VAL* 3.7 14.0 + - + +
350E TYR* 4.3 0.4 - - - -
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Residues in contact with ASP 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 3.7 27.7 + - - +
271A THR* 4.7 9.8 - - + +
283E ALA* 4.6 12.8 - - - +
284E ARG* 4.7 12.8 + - - +
293E VAL* 4.7 7.6 - - + -
294E THR* 2.7 37.1 + - - +
296E MET* 1.3 85.8 - - - +
298E LEU* 1.3 64.0 + - - +
300E VAL* 3.2 21.2 - - + +
301E SER* 4.0 3.3 + - - -
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Residues in contact with LEU 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU 4.6 5.8 - - - +
224A GLN* 4.0 52.5 - - - +
228A PRO* 4.6 16.6 - - + -
267A HIS* 5.9 0.4 - - - -
293E VAL* 5.0 5.8 - - + +
294E THR 3.6 2.9 + - - +
295E ALA 3.5 9.3 + - - +
296E MET 3.2 0.8 - - - -
297E ASP* 1.3 78.2 - - - +
299E PHE* 1.3 64.6 + - - +
301E SER* 2.9 28.5 + - - +
302E VAL* 3.6 15.7 + - + +
346E PHE* 5.3 8.1 - - + -
350E TYR* 4.9 13.9 - - + -
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Residues in contact with PHE 299 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E TYR* 4.2 33.7 - + + -
244E CYS* 4.1 20.0 - - + -
245E THR* 3.4 25.8 - - - -
295E ALA 3.8 2.0 + - - -
296E MET 3.7 7.0 + - - +
297E ASP 3.5 0.2 - - - -
298E LEU* 1.3 79.3 - - - +
300E VAL* 1.3 64.7 + - + +
301E SER 3.3 0.7 + - - -
302E VAL* 3.4 10.0 + - - +
303E CYS* 3.5 19.7 + - - -
343E PHE* 4.7 7.9 - + - -
346E PHE* 3.4 35.9 - + - -
347E ASN* 3.9 18.6 - - - -
350E TYR* 4.1 35.8 - + + +
351E TRP* 5.2 6.5 - + - -
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Residues in contact with VAL 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E CYS* 3.8 20.0 - - + -
276E MET* 4.9 3.5 - - - +
279E LEU* 4.5 18.8 - - + -
280E SER* 4.6 9.1 - - - +
283E ALA* 4.7 10.5 - - + -
284E ARG* 3.2 32.7 + - - +
296E MET* 3.7 9.5 + - + +
297E ASP* 3.2 26.5 - - - +
299E PHE* 1.3 80.8 - - + +
301E SER* 1.3 59.4 + - - +
303E CYS* 3.5 14.1 - - - +
304E PHE* 3.7 5.9 + - - +
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Residues in contact with SER 301 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 6.0 1.1 - - - +
267A HIS* 4.3 21.1 - - - -
284E ARG* 4.6 8.3 - - - +
297E ASP 4.1 7.3 + - - -
298E LEU* 2.9 27.0 + - - +
300E VAL* 1.3 80.8 - - - +
302E VAL* 1.3 63.2 + - - +
303E CYS 3.2 0.4 - - - -
304E PHE* 3.1 11.1 + - - +
305E ILE* 2.9 37.1 + - - +
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Residues in contact with VAL 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E LEU* 3.8 17.7 - - + +
299E PHE 3.4 5.9 + - - +
301E SER* 1.3 77.4 - - - +
303E CYS* 1.3 65.8 + - - +
305E ILE* 3.6 17.6 - - + +
306E PHE* 2.9 52.1 + - + -
343E PHE* 6.2 0.7 - - + -
346E PHE* 3.5 47.6 - - + -
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Residues in contact with CYS 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E CYS* 2.0 53.2 - - - -
245E THR 4.3 0.2 - - - -
248E VAL* 3.5 22.4 - - + -
276E MET* 3.5 14.1 - - + -
299E PHE* 3.5 20.7 + - - -
300E VAL 3.5 4.0 - - - +
302E VAL* 1.3 78.8 - - - +
304E PHE* 1.3 63.5 + - - +
306E PHE* 3.3 2.3 + - - +
307E VAL* 3.0 29.7 + - - +
343E PHE* 5.7 1.6 - - - -
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Residues in contact with PHE 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR* 3.9 32.5 - - + -
264B LEU* 4.6 18.8 - - + -
273E VAL* 3.8 31.4 - - + -
276E MET* 3.7 26.8 - - + +
277E THR* 4.6 7.6 - - - -
300E VAL 3.7 5.3 + - - +
301E SER* 3.1 15.8 + - - +
303E CYS* 1.3 77.7 - - - +
305E ILE* 1.3 68.1 + - + +
307E VAL* 3.3 9.2 - - + +
308E PHE* 2.9 47.1 + + + +
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Residues in contact with ILE 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 5.9 0.4 - - + -
260A THR* 3.8 30.0 + - + +
263A THR* 4.2 15.3 - - - +
264A ILE* 4.0 28.9 - - + -
301E SER* 2.9 26.4 + - - +
302E VAL* 3.2 24.7 + - + +
304E PHE* 1.3 82.5 - - + +
306E PHE* 1.3 66.8 + - + +
308E PHE* 3.9 3.6 - - - +
309E SER* 2.9 31.2 + - - -
401E Y01 4.9 10.5 - - + -
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Residues in contact with PHE 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E VAL* 4.3 14.8 - - + -
252E TRP* 5.4 7.6 + + - +
302E VAL* 2.9 38.9 + - + +
303E CYS 3.8 3.4 - - - +
305E ILE* 1.3 81.8 - - + +
307E VAL* 1.3 58.3 + - - +
309E SER* 2.7 23.4 + - - -
310E ALA* 3.0 18.2 + - - +
339E PHE* 4.5 15.1 - + + -
342E ALA* 4.4 20.6 - - + -
343E PHE* 3.7 42.8 - + + -
346E PHE* 4.7 7.9 - + + -
401E Y01 3.9 33.0 - - + -
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Residues in contact with VAL 307 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247E ILE* 4.2 2.5 - - + +
248E VAL* 3.9 22.4 - - + -
251E SER* 3.5 33.3 - - - +
269E GLY* 5.5 0.7 - - - -
272E THR* 4.3 16.7 + - - +
273E VAL* 4.3 9.4 - - + +
276E MET* 3.5 34.8 - - + -
303E CYS 3.0 20.5 + - - +
304E PHE* 3.3 13.2 - - + +
306E PHE* 1.3 76.2 - - + +
308E PHE* 1.3 58.2 + - - +
310E ALA* 4.1 5.2 + - - +
311E LEU* 3.9 15.1 + - - +
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Residues in contact with PHE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.5 39.0 - - + -
260A THR* 6.1 1.3 - - - -
263A THR* 5.6 6.7 - - + -
257B VAL* 4.5 10.8 - - + -
260B VAL* 5.6 4.5 - - + -
261B THR* 3.0 41.1 - - + -
273E VAL* 4.3 23.8 - - + -
304E PHE* 2.9 41.5 + + + +
305E ILE* 3.9 4.5 - - - +
307E VAL* 1.3 77.1 - - - +
309E SER* 1.3 66.0 + - - +
310E ALA 3.2 1.8 - - - -
311E LEU* 3.2 9.0 + - + +
312E VAL* 3.0 37.5 + - + +
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Residues in contact with SER 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 3.9 17.8 + - - -
260A THR* 5.6 0.2 - - - -
305E ILE* 2.9 17.8 + - - -
306E PHE* 2.7 25.6 + - - -
308E PHE* 1.3 78.9 - - - +
310E ALA* 1.3 57.9 + - - +
312E VAL* 3.3 9.9 + - - +
313E GLU* 2.9 29.1 + - - +
339E PHE* 3.9 7.6 - - - -
401E Y01 3.8 33.4 - - - +
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E SER* 5.2 10.1 - - - +
252E TRP* 5.3 2.0 - - + -
254E SER* 6.4 1.6 - - - -
255E PHE* 3.7 31.1 - - + -
306E PHE 3.0 16.5 + - - +
307E VAL* 4.2 7.9 - - - +
308E PHE 3.2 0.2 - - - -
309E SER* 1.3 78.9 + - - +
311E LEU* 1.3 62.2 + - - +
313E GLU* 3.1 5.7 + - - +
314E TYR* 3.0 22.3 + - - +
339E PHE* 4.3 12.1 - - + -
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B VAL* 3.4 36.6 - - + +
260B VAL* 5.7 5.6 - - + -
265E ARG 4.3 11.2 - - - +
266E THR* 4.3 13.7 - - + -
269E GLY* 3.7 39.7 - - - +
270E ILE* 4.1 11.7 - - + +
273E VAL* 4.5 9.4 - - + -
307E VAL 3.9 9.3 + - - +
308E PHE* 3.2 14.5 + - + +
310E ALA* 1.3 77.8 - - - +
312E VAL* 1.3 58.2 + - - +
314E TYR* 3.3 12.0 + - + +
315E GLY 2.9 23.4 + - - -
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Residues in contact with VAL 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 4.8 2.0 - - - +
255A ILE* 3.8 28.0 - - + -
256A THR* 3.8 22.0 - - - +
259A LEU* 4.2 6.1 - - + -
257B VAL* 3.8 20.4 - - + -
308E PHE* 3.0 41.3 + - + +
309E SER* 3.6 10.1 - - - +
310E ALA 3.2 0.2 - - - -
311E LEU* 1.3 74.8 - - - +
313E GLU* 1.3 62.5 + - - +
315E GLY* 3.2 2.5 + - - +
316E THR* 3.0 26.9 + - - +
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Residues in contact with GLU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 5.3 4.5 - - + -
256A THR* 5.3 0.6 + - - -
255E PHE* 3.6 9.8 - - - -
309E SER 2.9 13.5 + - - +
310E ALA 3.1 8.0 + - - +
312E VAL* 1.3 78.4 - - - +
314E TYR* 1.3 57.3 + - - +
316E THR* 3.2 8.8 + - - -
317E LEU* 2.9 38.4 + - + +
331E MET* 3.9 18.0 - - + +
332E ASP* 5.3 0.5 - - - +
335E ALA* 3.2 23.6 - - - +
339E PHE* 3.0 31.2 - - - -
401E Y01 3.4 33.8 + - + +
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Residues in contact with TYR 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 3.7 29.6 - - + +
254E SER* 5.5 1.6 - - - +
255E PHE* 6.2 0.6 - - + -
259E LYS* 3.7 27.2 + - + -
261E ALA 4.0 9.0 + - - -
262E VAL* 4.0 8.8 - - - +
265E ARG* 3.1 56.8 - - + +
266E THR* 3.9 14.8 - - + -
310E ALA 3.0 12.8 + - - +
311E LEU* 3.3 15.4 + - + +
313E GLU* 1.3 73.6 - - - +
315E GLY* 1.3 67.2 + - - +
317E LEU* 3.2 19.5 + - + -
318E HIS* 2.9 37.1 + - + +
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Residues in contact with GLY 315 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 4.3 6.5 - - - -
254B ALA* 3.6 35.8 - - - +
257B VAL* 4.8 1.6 - - - -
311E LEU 2.9 14.6 + - - -
312E VAL* 3.2 4.2 + - - -
314E TYR* 1.3 78.5 - - - +
316E THR* 1.3 60.6 + - - +
318E HIS* 3.3 1.6 + - - +
319E TYR* 3.0 24.3 + - - +
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Residues in contact with THR 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 3.8 27.8 - - + +
251A VAL* 5.1 1.2 - - + +
252A ALA* 3.6 38.6 + - + +
255A ILE* 4.7 9.0 - - - +
312E VAL* 3.0 16.2 + - - +
313E GLU* 3.2 8.7 + - - -
315E GLY* 1.3 75.9 - - - +
317E LEU* 1.3 63.5 + - + +
319E TYR* 3.2 5.0 + - - +
320E PHE* 2.9 33.9 + - + +
331E MET* 5.3 5.6 - - + -
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Residues in contact with LEU 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA* 6.3 1.1 - - + -
255E PHE* 6.1 1.3 - - + -
259E LYS* 5.3 9.4 - - + -
265E ARG* 4.8 5.6 - - - +
313E GLU* 2.9 31.0 + - + +
314E TYR* 3.2 29.4 + - + +
316E THR* 1.3 77.2 - - + +
318E HIS* 1.3 62.6 + - - +
320E PHE* 3.7 1.7 - - - -
321E VAL* 3.2 27.4 + - - +
328E ALA* 4.0 22.8 - - + +
331E MET* 3.5 39.0 - - + -
332E ASP* 3.6 24.0 - - - +
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Residues in contact with HIS 318 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B GLU* 3.8 16.4 + - - +
251B SER* 3.6 18.0 + - - -
252B VAL* 4.1 1.0 + - - +
253B PRO* 3.3 41.6 - - + +
254B ALA 5.3 0.4 - - - +
259E LYS 5.6 1.6 + - - -
262E VAL* 4.5 19.4 - - + +
314E TYR* 2.9 30.5 + - + +
315E GLY 4.0 3.1 - - - +
317E LEU* 1.3 76.7 - - - +
319E TYR* 1.3 64.3 + - - +
321E VAL* 3.2 27.0 - - + +
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Residues in contact with TYR 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 6.0 0.7 - - + -
247B LEU* 4.5 20.9 - - + +
248B ASN* 3.6 40.1 + - + +
251B SER* 3.0 32.9 + - - +
254B ALA* 4.5 8.3 - - + -
315E GLY 3.0 17.4 + - - +
316E THR* 3.2 6.3 + - - +
318E HIS* 1.3 79.6 - - - +
320E PHE* 1.3 100.7 + + + +
321E VAL* 3.2 5.1 + - - +
322E SER* 4.4 5.7 + - - -
----------------------------------------------------------
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Residues in contact with PHE 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 3.0 27.8 - - - -
248A ALA* 3.5 30.5 - - + -
251A VAL* 3.8 41.7 - - + -
303A ASN* 5.9 2.7 - - - -
316E THR* 2.9 21.4 + - + +
317E LEU* 3.7 4.5 - - - -
319E TYR* 1.3 111.8 - + + +
321E VAL* 1.3 60.6 + - - +
322E SER 3.3 2.4 + - - -
323E SER* 4.0 21.3 + - - +
324E GLN* 4.0 12.1 + - - +
327E ARG* 5.6 2.6 - - - +
328E ALA* 5.8 1.7 + - - +
----------------------------------------------------------
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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