Contacts of the helix formed by residues 290 - 314 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PRO 4.4 6.7 - - - +
289B PHE* 1.3 77.5 - - - +
291B GLU* 1.3 69.7 + - - +
292B ALA* 3.6 7.9 + - - +
293B SER* 2.6 39.1 + - - +
294B MET* 3.0 7.1 + - - +
369B CYS* 4.3 2.7 - - - -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR* 1.3 70.6 - - - +
292B ALA* 1.3 61.8 + - - +
294B MET 3.5 0.3 + - - -
295B MET* 3.2 31.7 + - + +
369B CYS* 3.1 25.4 + - - +
370B VAL* 3.7 18.1 - - + +
371B GLU* 2.9 39.4 + - - +
479B MET* 5.1 7.1 - - - +
484B VAL* 4.9 18.2 - - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR* 2.8 10.4 + - - +
291B GLU* 1.3 77.6 - - - +
293B SER* 1.3 56.5 + - - +
295B MET* 4.2 3.9 - - - +
296B MET* 3.1 28.6 + - - +
484B VAL* 5.7 17.0 - - + +
485B VAL* 5.1 4.1 - - - +
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Residues in contact with SER 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 4.6 9.4 - - - +
288B PRO 4.2 2.5 + - - -
289B PHE* 3.4 14.9 - - - -
290B THR* 2.6 49.0 + - - +
292B ALA* 1.3 71.4 - - - +
294B MET* 1.3 58.3 + - - -
296B MET* 3.4 23.0 - - - +
297B SER* 3.0 29.5 + - - -
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Residues in contact with MET 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.5 35.0 - - + -
290B THR 3.0 10.0 + - - +
293B SER* 1.3 75.3 + - - +
295B MET* 1.3 61.9 + - - +
296B MET 3.0 1.3 - - - -
297B SER* 3.0 3.5 + - - -
298B LEU* 2.8 41.9 + - + +
362B LEU* 3.7 24.0 - - + -
366B GLU* 3.9 22.4 - - - +
369B CYS* 4.5 0.9 - - + -
370B VAL* 3.3 34.5 - - + +
373B ILE* 3.6 28.3 - - + -
377B PHE* 4.0 10.5 - - + -
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 3.2 18.6 + - + +
292B ALA* 4.2 2.5 - - - +
294B MET* 1.3 79.3 - - + +
296B MET* 1.3 57.6 + - - +
298B LEU* 3.8 13.4 - - + +
299B THR* 2.9 36.2 + - - +
370B VAL* 3.4 28.3 - - + -
373B ILE* 3.1 33.4 - - + -
476B LEU* 5.1 2.5 - - - -
479B MET* 3.9 24.0 - - + -
484B VAL* 5.8 3.1 - - + -
485B VAL* 3.6 30.5 - - + -
501B 272 3.7 20.4 - - - +
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Residues in contact with MET 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 4.9 9.4 - - + -
292B ALA 3.1 21.8 + - - +
293B SER* 3.4 28.9 - - - +
295B MET* 1.3 77.9 - - - +
297B SER* 1.3 63.8 + - - +
299B THR* 2.7 19.7 + - - -
300B LYS* 3.0 26.1 + - - +
485B VAL* 4.0 8.3 - - + +
488B TYR* 4.0 12.6 + - - +
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 3.5 21.5 - - - +
283B SER 4.4 4.3 + - - -
285B PRO* 4.0 13.7 - - - +
289B PHE* 3.8 21.4 - - - -
293B SER 3.0 15.8 + - - -
294B MET* 3.0 6.9 + - - -
296B MET* 1.3 83.2 - - - +
298B LEU* 1.3 59.7 + - - +
300B LYS* 3.3 2.3 + - - -
301B LEU* 2.9 30.5 + - - +
360B LEU* 4.6 9.1 - - - +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B MET* 2.8 30.2 + - + +
295B MET* 3.9 13.5 - - + +
297B SER* 1.3 75.0 - - - +
299B THR* 1.3 57.3 + - - +
301B LEU* 3.7 6.7 + - + +
302B ALA* 3.2 25.8 + - - +
356B PHE* 3.5 43.3 - - + -
360B LEU* 5.0 4.7 - - + -
362B LEU* 4.7 4.7 - - + -
373B ILE* 3.9 28.5 - - + -
377B PHE* 4.5 11.2 - - + -
501B 272 3.9 32.2 - - + -
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 2.9 22.6 + - - +
296B MET* 2.7 24.9 + - - -
298B LEU* 1.3 75.9 - - + +
300B LYS* 1.3 66.1 + - - +
302B ALA 3.5 0.2 + - - -
303B ASP* 3.0 23.9 + - - +
476B LEU* 4.1 20.0 - - + -
485B VAL* 3.5 23.4 - - + +
487B VAL* 4.9 6.3 - - + -
488B TYR* 3.3 19.3 - - - -
491B LEU* 3.7 28.3 - - + +
501B 272 5.9 0.2 - - - -
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Residues in contact with LYS 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 4.3 21.8 - - + +
296B MET* 3.0 23.0 + - - +
297B SER* 3.6 5.2 - - - +
299B THR* 1.3 82.8 + - - +
301B LEU* 1.3 62.4 + - - +
303B ASP* 3.3 4.1 + - + +
304B LYS* 3.1 46.0 + - + +
488B TYR* 3.5 24.5 - - + +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 3.6 29.4 - - + -
282B ILE* 4.0 15.2 - - + +
297B SER 2.9 17.1 + - - +
298B LEU* 3.9 7.0 - - + +
299B THR 3.2 0.2 - - - -
300B LYS* 1.3 77.7 - - - +
302B ALA* 1.3 61.6 + - - +
304B LYS* 3.2 6.7 + - - +
305B GLU* 3.1 52.0 + - - +
356B PHE* 3.4 44.9 - - + +
357B ALA* 4.2 4.5 - - + -
360B LEU* 3.9 12.1 - - + -
501B 272 4.2 8.7 - - + -
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU 3.2 15.3 + - - +
299B THR* 3.9 4.5 - - - +
300B LYS 3.4 0.2 - - - -
301B LEU* 1.3 79.0 - - - +
303B ASP* 1.3 53.7 + - - +
305B GLU* 3.2 8.8 + - - +
306B LEU* 2.7 41.4 + - - +
335B TRP* 5.0 1.1 - - + -
336B MET* 6.1 0.7 - - + -
339B LEU* 4.0 19.3 - - + -
476B LEU* 5.9 1.1 - - + -
491B LEU* 4.1 21.8 - - + -
501B 272 4.1 11.4 - - + -
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Residues in contact with ASP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR 3.0 18.4 + - - +
300B LYS* 3.5 5.4 - - + +
301B LEU 3.2 0.2 - - - -
302B ALA* 1.3 79.1 - - - +
304B LYS* 1.3 61.1 + - + +
306B LEU* 4.5 1.8 - - - -
307B VAL* 3.2 8.7 + - - +
488B TYR* 3.5 25.1 - - + +
489B ASP* 3.2 16.3 - - - +
490B LEU* 2.8 55.6 - - - +
491B LEU* 3.2 17.2 + - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 3.3 34.1 - - + +
281B LEU* 3.9 22.2 + - - +
282B ILE* 4.2 5.6 - - + +
300B LYS* 3.1 37.7 + - + +
301B LEU* 3.2 7.4 + - - +
303B ASP* 1.3 78.8 - - + +
305B GLU* 1.3 62.5 + - - +
307B VAL* 3.5 9.1 - - - +
308B HIS* 3.4 31.6 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B VAL* 3.7 20.0 - - + +
301B LEU* 3.1 37.3 + - - +
302B ALA 3.7 2.0 - - - +
304B LYS* 1.3 74.7 - - - +
306B LEU* 1.3 57.0 + - - +
307B VAL 2.9 2.2 + - - -
308B HIS* 3.1 8.6 + - + +
309B MET* 2.7 37.2 + - - +
339B LEU* 3.4 24.6 - - + +
346B ARG* 4.0 18.1 + - - -
356B PHE 5.0 0.7 - - - -
501B 272 2.5 32.8 - - - +
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Residues in contact with LEU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 5.2 1.5 - - + -
302B ALA 2.7 27.6 + - - +
303B ASP 3.6 0.2 + - - -
304B LYS 3.5 0.2 - - - -
305B GLU* 1.3 72.7 - - - +
307B VAL* 1.3 61.0 + - - +
309B MET* 3.7 13.4 + - + +
310B ILE* 3.3 26.2 + - - +
335B TRP* 3.4 37.5 - - + -
339B LEU* 4.1 9.4 - - + -
490B LEU* 3.3 17.7 - - + -
491B LEU* 3.5 38.8 - - + +
494B MET* 3.4 34.9 - - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ASP* 3.2 18.8 - - - +
304B LYS* 3.5 11.7 - - - +
305B GLU 2.9 0.4 - - - -
306B LEU* 1.3 76.0 - - - +
308B HIS* 1.3 75.6 + - + +
310B ILE* 3.1 26.5 + - + +
311B SER* 3.6 9.3 + - - +
490B LEU* 3.3 21.1 - - + -
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Residues in contact with HIS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PRO* 4.0 18.9 - - + +
278B PRO* 3.4 46.6 + - + +
279B HIS 5.2 2.2 + - - -
280B VAL* 4.2 16.7 - - + +
304B LYS* 3.4 20.1 + - - +
305B GLU* 3.1 8.1 + - + +
307B VAL* 1.3 87.0 - - + +
309B MET* 1.3 58.1 + - - +
311B SER* 3.1 12.3 + - - -
312B TRP* 2.9 28.7 + - - +
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Residues in contact with MET 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B PRO* 5.3 1.5 - - - +
305B GLU 2.7 18.7 + - - +
306B LEU* 3.7 16.4 - - + +
307B VAL 3.1 0.2 - - - -
308B HIS* 1.3 71.8 - - - +
310B ILE* 1.3 57.8 + - - +
312B TRP* 3.3 26.0 - - + -
313B ALA* 2.9 25.5 + - - +
331B LEU* 4.1 18.1 - - + +
334B CYS* 6.0 0.4 - - - -
335B TRP* 3.2 46.0 - - - +
338B VAL* 3.8 22.0 - - + -
339B LEU* 3.7 26.0 - - + -
494B MET* 5.3 1.8 - - - -
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A SER* 5.5 7.4 - - - -
324A LEU* 4.7 23.8 - - + +
325A PHE* 3.4 39.0 - - + -
306B LEU 3.3 18.4 - - - +
307B VAL* 3.1 12.7 + - + +
309B MET* 1.3 73.9 - - + +
311B SER* 1.3 64.0 + - - +
312B TRP 3.1 1.6 - - - -
313B ALA* 3.3 5.1 + - - +
314B LYS* 2.9 49.6 + - + +
331B LEU* 4.8 7.2 - - + -
490B LEU* 5.7 3.8 - - + -
494B MET* 6.2 0.2 - - + -
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Residues in contact with SER 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B VAL* 3.6 11.7 + - - +
308B HIS* 3.1 13.7 + - - -
310B ILE* 1.3 79.5 - - - +
312B TRP* 1.3 60.5 + - - +
314B LYS* 3.7 10.3 + - - +
315B LYS* 3.2 43.1 + - - +
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Residues in contact with TRP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LEU* 5.1 7.5 + - - +
275B ALA* 3.6 36.2 - - + +
276B GLU* 4.1 9.0 + - - -
277B PRO* 4.1 19.3 - - + -
308B HIS 2.9 12.9 + - - +
309B MET* 3.3 40.2 - - + +
311B SER* 1.3 76.8 - - - +
313B ALA* 1.3 71.5 + - + +
315B LYS* 3.0 16.5 + - - +
316B ILE* 3.5 33.9 - - + +
338B VAL* 4.2 18.4 - - + -
398B LEU* 5.5 1.9 + - - +
401B LYS* 3.9 44.2 - - + +
402B ALA* 4.1 6.1 - - + -
405B LEU* 4.2 27.1 - - + -
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B MET 2.9 17.8 + - - +
310B ILE* 3.3 5.6 + - - +
312B TRP* 1.3 82.7 - - + +
314B LYS* 1.3 62.8 + - - +
316B ILE* 3.1 21.0 + - - +
319B PHE* 3.1 45.6 - - + +
331B LEU* 4.2 15.5 - - + -
405B LEU* 4.2 9.2 - - + -
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 5.7 6.0 - - + +
310B ILE* 2.9 36.8 + - + +
311B SER* 4.0 9.4 - - - +
312B TRP 3.2 0.2 - - - -
313B ALA* 1.3 78.3 - - - +
315B LYS* 1.3 57.8 + - + +
316B ILE 3.3 4.5 + - - +
319B PHE* 3.9 16.2 - - + -
320B VAL* 3.7 33.3 - - + +
327B GLN* 4.9 6.7 - - - +
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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