Contacts of the helix formed by residues 290 - 315 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 5.9 2.5 - - + -
288A PRO 3.8 11.4 - - - +
289A PHE* 1.3 75.3 - - - +
291A GLU* 1.3 64.9 + - - +
292A ALA* 3.2 8.9 + - - +
293A SER* 2.7 34.7 + - - +
294A MET* 2.9 24.2 + - - +
369A CYS* 4.6 2.0 - - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 1.3 72.4 - - - +
292A ALA* 1.3 61.2 + - - +
294A MET* 3.6 2.3 + - - +
295A MET* 3.2 24.3 + - + +
369A CYS* 3.3 25.0 + - - +
370A VAL* 3.9 18.2 - - + +
371A GLU* 3.2 32.3 + - - +
479A MET* 4.9 4.5 - - - +
482A LYS* 5.7 1.0 + - - +
484A VAL* 3.3 31.7 - - + +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A THR* 3.1 7.0 + - - +
291A GLU* 1.3 76.9 - - - +
293A SER* 1.3 59.8 + - - +
295A MET* 3.3 2.6 + - - +
296A MET* 2.9 29.0 + - - +
484A VAL* 3.9 27.7 - - + +
486A PRO* 5.5 0.5 - - - +
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 4.3 16.2 - - - +
288A PRO 4.4 0.3 + - - -
289A PHE* 3.4 11.8 - - - -
290A THR* 2.7 47.9 + - - +
292A ALA* 1.3 71.2 - - - +
294A MET* 1.3 59.1 + - - +
296A MET* 3.2 12.6 + - - +
297A SER* 2.8 33.6 + - - -
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 3.7 32.5 - - + -
290A THR 2.9 17.5 + - - +
291A GLU 3.9 3.6 - - - +
293A SER* 1.3 77.4 + - - +
295A MET* 1.3 57.8 + - - +
297A SER* 3.3 2.8 + - - -
298A LEU* 3.1 37.3 + - + +
362A LEU* 4.0 23.1 - - + -
366A GLU 2.9 29.6 - - - +
367A GLY* 4.2 6.3 - - - -
369A CYS* 3.6 13.2 - - + -
370A VAL* 3.2 34.5 - - + +
373A ILE* 4.2 5.2 - - + -
377A PHE* 4.4 5.8 - - + -
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Residues in contact with MET 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU 3.2 15.8 + - - +
292A ALA 3.7 4.7 - - - +
293A SER 3.2 0.2 - - - -
294A MET* 1.3 75.1 - - - +
296A MET* 1.3 66.2 + - - +
297A SER 3.1 1.3 - - - -
298A LEU* 3.8 11.9 - - + +
299A THR* 2.9 34.0 + - - +
370A VAL* 3.2 40.6 - - + -
373A ILE* 3.3 28.3 - - + -
475A HIS* 4.1 1.8 - - + -
479A MET* 4.0 7.6 - - - -
484A VAL* 4.4 8.3 - - + +
485A VAL* 3.1 39.7 - - + -
501A 272 3.8 20.4 - - - +
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Residues in contact with MET 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 5.9 0.4 - - + -
285A PRO* 5.6 5.8 - - + -
292A ALA 2.9 17.9 + - - +
293A SER* 3.5 11.9 - - - +
295A MET* 1.3 77.3 - - - +
297A SER* 1.3 66.6 + - - +
299A THR* 3.5 6.5 + - - +
300A LYS* 2.7 72.8 + - + +
486A PRO* 5.1 19.0 - - + +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 3.1 28.1 - - - +
283A SER 4.9 2.4 + - - -
285A PRO* 4.2 7.6 - - - +
289A PHE* 3.5 23.3 - - - -
293A SER 2.8 21.9 + - - -
294A MET 3.4 7.9 - - - -
296A MET* 1.3 89.3 - - - +
298A LEU* 1.3 58.9 + - - +
301A LEU* 3.1 23.4 + - - +
360A LEU* 4.7 9.9 - - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET* 3.1 24.9 + - + +
295A MET* 3.8 12.8 - - + +
297A SER* 1.3 75.5 - - - +
299A THR* 1.3 59.8 + - - +
300A LYS 3.1 1.3 - - - -
301A LEU* 3.3 5.2 + - + +
302A ALA* 2.9 30.2 + - - +
356A PHE* 3.8 40.8 - - + -
360A LEU* 4.8 6.7 - - + -
362A LEU* 4.6 9.0 - - + -
373A ILE* 3.5 33.4 - - + -
377A PHE* 4.7 5.8 - - + -
501A 272 3.7 28.7 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MET* 2.9 23.9 + - - +
296A MET* 3.5 9.0 + - - +
298A LEU* 1.3 74.5 - - - +
300A LYS* 1.3 60.2 + - - +
302A ALA* 4.0 1.1 - - - -
303A ASP* 3.1 30.1 + - - +
476A LEU* 3.9 17.0 - - + -
485A VAL* 4.2 9.9 - - + +
486A PRO* 5.2 3.8 - - - +
487A VAL* 3.6 31.2 + - + +
491A LEU* 3.7 20.4 - - + +
501A 272 4.8 6.1 - - + -
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 4.4 17.7 - - + +
296A MET* 2.7 51.0 + - + +
297A SER 3.7 4.7 - - - +
299A THR* 1.3 77.8 + - - +
301A LEU* 1.3 63.9 + - - +
303A ASP* 3.9 3.9 - - - +
304A LYS* 3.1 49.5 + - + +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.6 41.7 - - + +
282A ILE* 4.4 14.8 - - + +
297A SER 3.1 19.0 + - - +
298A LEU* 3.6 4.5 - - - +
300A LYS* 1.3 74.7 - - - +
302A ALA* 1.3 66.5 + - - +
304A LYS* 3.2 5.5 + - - +
305A GLU* 3.0 39.5 + - - +
356A PHE* 3.4 48.0 - - + +
360A LEU* 4.3 7.2 - - + -
501A 272 4.0 16.2 - - + +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU 2.9 16.7 + - - +
299A THR* 4.1 3.8 - - - +
301A LEU* 1.3 75.8 - - - +
303A ASP* 1.3 64.4 + - - +
305A GLU* 2.8 24.8 + - - +
306A LEU* 2.9 17.1 + - - +
335A TRP* 4.6 2.2 - - + -
336A MET* 6.2 0.4 - - + -
339A LEU* 3.7 21.5 - - + -
476A LEU* 6.4 0.4 - - + -
491A LEU* 4.4 19.3 - - + -
501A 272 4.0 9.8 - - + -
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR 3.1 19.8 + - - +
300A LYS* 3.9 5.6 - - - +
302A ALA* 1.3 79.7 - - - +
304A LYS* 1.3 67.4 + - - +
306A LEU* 3.5 14.2 + - - -
307A VAL* 3.9 4.0 + - - +
489A ASP* 5.2 3.4 - - - +
490A LEU* 3.2 47.1 + - - +
491A LEU* 3.6 14.9 + - + +
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.8 29.3 - - + +
281A LEU 4.1 17.4 + - - -
282A ILE* 6.0 3.2 - - + +
300A LYS* 3.1 39.7 - - + +
301A LEU* 3.2 4.4 + - - +
302A ALA 3.1 0.8 - - - -
303A ASP* 1.3 81.8 - - - +
305A GLU* 1.3 64.2 + - - +
306A LEU 3.5 0.2 + - - -
307A VAL* 3.6 19.1 + - - +
308A HIS* 3.8 8.0 + - - -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.6 24.7 + - + +
301A LEU* 3.0 28.8 + - + +
302A ALA* 2.8 8.5 + - - +
304A LYS* 1.3 74.5 - - - +
306A LEU* 1.3 60.5 + - - +
307A VAL 3.2 0.7 - - - -
308A HIS* 3.0 8.4 + - + +
309A MET* 2.8 28.6 + - - +
339A LEU* 3.7 20.9 - - + +
346A ARG* 3.9 19.4 + - - -
356A PHE 4.9 0.2 - - - +
501A 272 2.4 43.0 - - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ALA 2.9 19.1 + - - +
303A ASP* 3.7 2.7 - - - +
304A LYS 3.3 0.2 - - - -
305A GLU* 1.3 77.8 - - - +
307A VAL* 1.3 59.8 + - - +
309A MET* 3.7 22.6 - - + +
310A ILE* 3.0 34.5 + - + +
335A TRP* 3.7 22.9 - - + -
339A LEU* 4.2 5.2 - - + -
490A LEU* 3.5 21.1 - - + -
491A LEU* 3.8 29.4 - - + -
494A MET* 3.4 45.0 - - + +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASP* 3.9 7.4 - - - +
304A LYS* 3.8 11.0 - - - +
305A GLU 3.2 0.4 - - - -
306A LEU* 1.3 78.9 - - - +
308A HIS* 1.3 68.0 + - + +
310A ILE* 3.6 16.0 + - + +
311A SER* 3.3 17.9 + - - +
490A LEU* 3.8 19.7 - - + -
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Residues in contact with HIS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO* 3.8 24.5 - - + +
278A PRO* 3.8 37.1 + - + +
279A HIS 5.1 1.8 + - - -
280A VAL* 3.4 33.8 - - + +
304A LYS 3.8 7.2 + - - -
305A GLU* 3.0 8.8 + - + +
307A VAL* 1.3 82.2 - - + +
309A MET* 1.3 59.5 + - - +
311A SER* 3.3 9.1 + - - -
312A TRP* 3.0 28.7 + - - +
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Residues in contact with MET 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO* 5.0 1.5 - - - +
305A GLU 2.8 13.6 + - - +
306A LEU* 3.3 17.9 + - + +
308A HIS* 1.3 76.3 - - - +
310A ILE* 1.3 58.5 + - + +
312A TRP* 3.3 25.1 - - + +
313A ALA* 2.9 26.2 + - - +
331A LEU* 4.3 15.9 - - + -
334A CYS* 5.4 0.2 - - - -
335A TRP* 3.1 46.0 - - - +
338A VAL* 3.7 22.7 - - + -
339A LEU* 3.5 27.1 - - + -
494A MET* 4.9 2.7 - - - -
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Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 3.0 23.3 + - + +
307A VAL* 3.8 11.4 - - + +
308A HIS 3.2 0.2 - - - -
309A MET* 1.3 75.7 - - + +
311A SER* 1.3 62.4 + - - +
313A ALA* 3.4 6.0 + - - +
314A LYS* 3.0 48.4 + - + +
331A LEU* 4.7 16.6 - - + -
490A LEU* 4.7 12.3 - - + -
494A MET* 5.6 3.8 - - + -
323B SER* 6.2 2.9 - - - -
324B LEU* 5.1 12.1 - - + +
325B PHE* 3.6 35.2 - - + -
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Residues in contact with SER 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A PRO* 5.9 2.5 - - - -
307A VAL* 3.3 14.8 + - - +
308A HIS* 3.3 11.0 + - - -
310A ILE* 1.3 77.6 - - - +
312A TRP* 1.3 63.5 + - - +
314A LYS* 3.3 10.2 + - - +
315A LYS* 3.1 47.9 + - - +
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Residues in contact with TRP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LEU* 5.1 4.4 + - - +
275A ALA* 3.5 40.6 - - + +
276A GLU* 4.3 5.3 + - - -
277A PRO* 4.1 15.9 - - + +
308A HIS 3.0 14.8 + - - +
309A MET* 3.3 34.5 - - + +
310A ILE 3.2 0.2 - - - -
311A SER* 1.3 76.9 - - - +
313A ALA* 1.3 68.4 + - + +
315A LYS* 3.0 15.5 + - - +
316A ILE* 3.4 29.6 + - + +
338A VAL* 4.0 16.6 - - + -
398A LEU 5.9 0.4 + - - -
401A LYS* 3.4 62.3 - - + +
402A ALA* 4.0 3.3 - - + +
405A LEU* 3.7 34.5 - - + -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A MET 2.9 16.5 + - - +
310A ILE 3.4 3.6 + - - +
312A TRP* 1.3 81.2 - - + +
314A LYS* 1.3 61.8 + - - +
316A ILE* 3.1 20.2 + - - +
319A PHE* 3.2 37.9 - - + +
331A LEU* 3.9 14.1 - - + -
405A LEU* 3.8 21.8 - - + -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 3.0 34.9 + - + +
311A SER* 3.7 9.0 - - - +
312A TRP 3.2 0.4 - - - -
313A ALA* 1.3 76.0 - - - +
315A LYS* 1.3 60.8 + - + +
316A ILE 3.3 4.3 + - - +
319A PHE* 4.2 11.0 - - + -
320A VAL* 3.3 39.0 - - + +
327A GLN* 4.9 2.5 - - - +
324B LEU* 4.5 25.4 - - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A THR* 3.2 25.1 - - - +
274A GLU* 4.3 26.6 - - - +
275A ALA* 3.7 34.3 - - + +
311A SER* 3.1 36.3 + - - +
312A TRP 3.0 9.8 + - - +
314A LYS* 1.3 78.9 - - - +
316A ILE* 1.3 61.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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