Contacts of the helix formed by residues 290 - 316 (chain D) in PDB entry 1U3Q
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 290 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 4.3 8.1 - - + +
289D PHE* 1.3 79.3 - - - +
291D GLU* 1.3 68.9 + - - +
292D ALA* 2.8 9.8 + - - +
293D SER* 2.9 35.0 + - - +
294D MET* 3.1 11.8 + - - +
369D CYS* 4.3 5.2 - - - -
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D THR* 1.3 73.5 - - - +
292D ALA* 1.3 61.1 + - - +
295D MET* 3.3 24.3 + - - +
369D CYS* 3.1 25.9 + - - +
370D VAL* 4.0 15.5 - - + +
371D GLU* 3.1 35.0 + - - +
479D MET* 4.3 6.5 - - - +
482D LYS* 5.7 0.3 + - - -
484D VAL* 3.7 32.5 - - + +
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Residues in contact with ALA 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D THR* 2.8 9.4 + - - +
291D GLU* 1.3 77.9 - - - +
293D SER* 1.3 60.1 + - - +
295D MET* 3.3 3.7 + - - +
296D MET* 2.9 31.3 + - - +
484D VAL* 4.1 24.3 - - + +
485D VAL* 5.0 0.5 - - - +
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Residues in contact with SER 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D PRO* 4.9 9.9 - - - +
288D PRO 4.2 3.2 + - - -
289D PHE* 3.4 15.7 - - - -
290D THR* 2.9 41.0 + - - +
292D ALA* 1.3 73.5 - - - +
294D MET* 1.3 56.4 + - - +
296D MET* 3.4 10.5 + - - +
297D SER* 2.9 30.8 + - - -
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Residues in contact with MET 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D PHE* 3.6 37.5 - - + -
290D THR 3.1 13.1 + - - +
293D SER* 1.3 75.1 + - - +
295D MET* 1.3 59.2 + - - +
297D SER* 2.8 22.6 + - - -
298D LEU* 2.8 23.6 + - + +
360D LEU* 6.1 0.2 - - + -
362D LEU* 4.3 14.1 - - + -
366D GLU* 3.5 22.4 - - - +
369D CYS* 4.9 2.2 - - + -
370D VAL* 3.3 30.3 - - + -
373D ILE* 3.7 19.1 - - + -
377D PHE* 3.5 32.1 - - + -
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Residues in contact with MET 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLU 3.3 20.1 + - - +
292D ALA 3.3 3.7 + - - +
294D MET* 1.3 78.3 - - - +
296D MET* 1.3 57.6 + - - +
298D LEU* 3.3 21.5 + - + +
299D THR* 3.0 35.2 + - - +
370D VAL* 3.7 21.8 - - + -
373D ILE* 3.3 34.3 - - + -
475D HIS* 4.3 0.2 - - - -
476D LEU* 5.0 2.9 - - - -
479D MET* 3.6 35.0 - - + -
484D VAL* 4.3 4.7 - - + -
485D VAL* 3.9 21.8 - - + -
501D 272 4.0 16.6 - - + +
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Residues in contact with MET 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D ALA 2.9 18.8 + - - +
293D SER* 3.5 11.0 - - - +
295D MET* 1.3 77.3 - - - +
297D SER* 1.3 65.9 + - - +
299D THR* 3.2 8.4 + - - +
300D LYS* 3.0 56.0 + - + +
485D VAL* 3.9 12.3 - - + +
486D PRO* 5.3 8.5 - - + -
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Residues in contact with SER 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ILE* 2.8 39.3 - - - +
283D SER 4.7 1.6 + - - -
285D PRO* 4.4 8.5 - - - +
289D PHE* 3.7 15.2 - - - -
293D SER 2.9 20.0 + - - -
294D MET* 2.8 13.9 + - - -
296D MET* 1.3 82.3 - - - +
298D LEU* 1.3 62.7 + - - -
300D LYS* 4.5 1.6 - - - -
301D LEU* 3.2 13.9 + - - +
360D LEU* 4.2 12.1 - - - -
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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
----------------------------------------------------------
294D MET* 2.8 27.4 + - + +
295D MET* 3.4 32.1 - - + +
297D SER* 1.3 79.5 - - - +
299D THR* 1.3 57.6 + - - +
301D LEU* 3.2 8.5 + - + +
302D ALA* 2.9 27.9 + - - +
356D PHE* 3.5 45.5 - - + -
360D LEU* 4.8 3.8 - - + -
362D LEU* 4.4 7.4 - - + -
373D ILE* 3.6 16.6 - - + -
377D PHE* 4.9 2.9 - - + -
501D 272 4.0 29.4 - - + -
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Residues in contact with THR 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D MET* 3.0 18.9 + - - +
296D MET* 3.2 15.6 + - - +
298D LEU* 1.3 73.1 - - + +
300D LYS* 1.3 64.2 + - - +
302D ALA* 4.3 1.8 - - - -
303D ASP* 2.9 32.4 + - - +
476D LEU* 3.7 30.1 - - + -
485D VAL* 3.8 21.4 - - + +
486D PRO 4.2 9.6 + - - +
487D VAL* 5.0 2.9 - - + -
491D LEU* 3.7 21.3 - - + +
501D 272 5.5 0.9 - - + -
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Residues in contact with LYS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ILE* 4.6 15.2 - - + +
296D MET* 3.0 46.6 + - + +
297D SER 3.7 4.5 - - - +
299D THR* 1.3 81.1 + - - +
301D LEU* 1.3 60.1 + - - +
303D ASP* 4.0 4.5 - - - +
304D LYS* 3.0 41.8 + - + +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 3.6 37.5 - - + +
282D ILE* 4.1 19.2 - - + +
297D SER 3.2 9.9 + - - +
298D LEU* 3.4 9.4 - - + +
299D THR 3.2 0.4 - - - -
300D LYS* 1.3 77.7 - - - +
302D ALA* 1.3 59.0 + - - +
304D LYS* 3.4 2.3 + - - +
305D GLU* 2.9 57.4 + - - +
356D PHE* 3.6 47.3 - - + +
360D LEU* 4.5 2.9 - - + -
501D 272 3.8 17.5 - - + +
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU 2.9 16.3 + - - +
299D THR* 3.7 4.5 - - - +
301D LEU* 1.3 76.7 - - - +
303D ASP* 1.3 51.5 + - - +
305D GLU* 3.3 3.5 + - - +
306D LEU* 2.7 41.7 + - + +
335D TRP* 5.0 1.3 - - + -
336D MET* 6.3 0.7 - - + -
339D LEU* 4.0 25.7 - - + +
476D LEU* 6.1 0.9 - - + -
491D LEU* 4.2 21.1 - - + -
501D 272 4.2 12.3 - - + -
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Residues in contact with ASP 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR 2.9 20.7 + - - +
300D LYS* 4.0 4.9 - - - +
302D ALA* 1.3 73.0 - - - +
304D LYS* 1.3 67.1 + - + +
306D LEU* 3.4 11.7 + - - +
307D VAL* 3.3 28.9 + - - +
488D TYR* 5.5 1.4 + - - -
489D ASP* 2.8 31.1 + - - +
490D LEU* 3.5 4.9 + - - +
491D LEU* 3.3 29.4 + - + +
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Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 3.8 31.4 - - + +
281D LEU 5.0 9.8 + - - +
282D ILE* 6.5 0.9 - - + -
300D LYS* 3.0 28.6 + - + +
303D ASP* 1.3 80.7 - - + +
305D GLU* 1.3 63.1 + - - +
307D VAL* 3.2 22.4 + - - +
308D HIS* 3.4 18.4 + - + +
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Residues in contact with GLU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D VAL* 3.3 25.8 + - + +
301D LEU* 2.9 41.3 + - + +
302D ALA 3.6 3.4 - - - +
304D LYS* 1.3 74.5 - - - +
306D LEU* 1.3 67.1 + - - +
308D HIS* 2.9 9.0 + - - +
309D MET* 2.8 22.8 + - - +
339D LEU* 3.7 19.0 - - + +
346D ARG* 4.0 17.8 + - - -
501D 272 2.3 36.9 - - - +
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D ALA 2.7 28.0 + - - +
303D ASP* 3.6 5.4 - - - +
305D GLU* 1.3 71.5 - - - +
307D VAL* 1.3 63.2 + - - +
309D MET* 3.0 26.5 + - + +
310D ILE* 3.3 17.0 + - - +
335D TRP* 3.9 27.4 - - + -
339D LEU* 5.2 2.5 - - + -
490D LEU* 3.6 15.5 - - + -
491D LEU* 3.5 50.5 - - + +
494D MET* 3.7 33.7 - - + -
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Residues in contact with VAL 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ASP* 3.3 24.9 - - - +
304D LYS* 3.2 11.6 + - - +
305D GLU 3.1 0.4 - - - -
306D LEU* 1.3 76.3 - - - +
308D HIS* 1.3 69.4 + - + +
310D ILE* 3.7 10.4 + - - +
311D SER* 3.6 14.5 + - - +
489D ASP* 5.8 0.4 - - - +
490D LEU* 3.6 20.4 - - + -
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Residues in contact with HIS 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D PRO* 3.9 23.0 - - + +
278D PRO* 4.2 29.3 + - + +
279D HIS 5.5 0.8 + - - -
280D VAL* 3.7 25.2 - - + +
304D LYS* 3.4 24.2 + - - +
305D GLU* 2.9 7.0 + - - +
307D VAL* 1.3 84.2 - - + +
309D MET* 1.3 64.9 + - - +
311D SER* 3.1 10.8 + - - -
312D TRP* 3.0 20.9 + - - +
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Residues in contact with MET 309 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D PRO* 5.3 2.4 - - - +
305D GLU 2.8 14.7 + - - +
306D LEU* 3.0 19.3 + - + +
308D HIS* 1.3 72.9 - - - +
310D ILE* 1.3 52.4 + - + +
312D TRP* 3.1 30.6 - - + +
313D ALA* 2.8 32.1 + - - +
331D LEU* 4.1 18.2 - - + -
334D CYS* 5.7 0.2 - - - -
335D TRP* 3.2 50.5 - - + +
338D VAL* 3.5 23.1 - - + -
339D LEU* 3.9 20.4 - - + -
494D MET* 5.2 1.8 - - - -
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LEU 3.5 6.7 - - - +
307D VAL* 3.9 7.9 - - - +
308D HIS 3.2 0.6 - - - -
309D MET* 1.3 76.3 - - + +
311D SER* 1.3 63.1 + - - +
313D ALA* 3.5 6.6 + - - +
314D LYS* 2.8 45.0 + - + +
319D PHE* 6.4 0.2 - - + -
331D LEU* 4.4 22.9 - - + -
490D LEU* 3.5 41.1 - - + -
494D MET* 5.5 9.4 - - + -
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Residues in contact with SER 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D VAL 3.6 12.0 + - - -
308D HIS* 3.1 9.8 + - - -
310D ILE* 1.3 76.0 - - - +
312D TRP* 1.3 68.0 + - - +
314D LYS* 3.3 18.1 + - - +
315D LYS* 3.3 34.0 + - - +
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Residues in contact with TRP 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LEU* 5.1 6.5 + - - +
275D ALA* 3.7 39.3 - - + +
276D GLU* 4.1 8.1 + - - -
277D PRO* 4.3 17.9 - - + -
308D HIS 3.0 13.0 + - - +
309D MET* 3.1 37.5 - - + +
311D SER* 1.3 76.8 - - - +
313D ALA* 1.3 64.1 + - + +
315D LYS* 2.8 27.8 + - - +
316D ILE* 3.5 25.3 + - + +
331D LEU* 5.3 0.2 - - + -
338D VAL* 3.9 23.3 - - + -
398D LEU* 5.4 1.4 + - - +
401D LYS* 3.5 44.3 - - + +
402D ALA* 3.8 13.0 - - + -
405D LEU* 3.9 26.9 - - + -
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Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D MET 2.8 19.4 + - - +
310D ILE 3.8 5.4 - - - +
311D SER 3.4 0.2 - - - -
312D TRP* 1.3 73.7 - - + +
314D LYS* 1.3 62.3 + - - +
316D ILE* 3.0 25.7 + - - +
319D PHE* 3.2 33.2 - - + +
331D LEU* 3.9 17.9 - - + -
405D LEU* 3.7 21.8 - - + -
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Residues in contact with LYS 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D ILE* 2.8 36.3 + - + +
311D SER* 3.5 12.1 - - - +
312D TRP 3.1 0.4 - - - -
313D ALA* 1.3 76.3 - - - +
315D LYS* 1.3 61.5 + - + +
316D ILE 3.5 4.2 + - - +
319D PHE* 3.9 15.9 - - + +
320D VAL* 3.7 37.4 - - + +
327D GLN* 4.9 7.0 - - - +
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Residues in contact with LYS 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D THR* 3.9 12.2 - - + +
274D GLU 4.8 4.0 - - - +
275D ALA* 3.8 38.4 + - + +
311D SER* 3.3 34.4 + - - +
312D TRP 2.8 9.7 + - - +
314D LYS* 1.3 77.4 - - + +
316D ILE* 1.3 64.9 + - - +
317D PRO* 3.2 10.2 - - - +
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Residues in contact with ILE 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D LEU* 5.8 0.4 - - + -
272D LEU* 4.2 20.0 - - + -
275D ALA* 5.8 0.4 - - + -
312D TRP* 3.8 31.0 - - + +
313D ALA* 3.0 15.5 + - - +
314D LYS 4.1 2.9 - - - +
315D LYS* 1.3 76.9 - - - +
317D PRO* 1.3 81.8 - - + +
318D GLY 3.2 0.7 + - - -
319D PHE* 2.9 24.7 + - + +
320D VAL* 4.7 0.3 + - - +
402D ALA* 4.3 9.6 - - + +
405D LEU* 3.4 34.5 - - + -
406D LEU* 4.3 12.1 - - + -
429D LEU* 4.2 13.0 - - + -
433D 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