Contacts of the helix formed by residues 323 - 348 (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 SER 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 6.2 2.9 - - - -
321B GLU 3.9 0.2 + - - -
322B LEU* 1.3 77.8 - - - +
324B LEU* 1.3 65.1 + - - +
325B PHE* 3.6 10.7 + - - +
326B ASP* 2.8 34.7 + - - -
327B GLN* 3.0 21.9 + - - +
422B SER* 2.9 16.6 + - - -
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 5.1 13.8 - - + +
314A LYS* 4.5 22.8 - - + +
319A PHE* 4.6 1.8 - - + -
324A LEU* 3.6 24.7 - - + -
327A GLN* 3.4 44.0 - - + +
328A VAL* 3.9 12.3 - - + -
331A LEU* 4.2 20.6 - - + -
322B LEU 3.8 0.2 + - - -
323B SER* 1.3 72.5 - - - +
325B PHE* 1.3 71.7 + - + +
327B GLN* 3.2 16.8 + - - +
328B VAL* 3.2 24.8 + - - +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE* 3.6 34.8 - - + -
328A VAL* 3.8 22.0 - - + -
331A LEU* 4.0 26.9 - - + -
332A GLU* 3.7 27.1 - - + -
490A LEU* 4.6 11.2 - - + -
493A GLU* 3.9 30.3 - - + -
494A MET* 3.7 26.0 - - + -
323B SER* 3.3 7.8 - - - +
324B LEU* 1.3 86.7 - - + +
326B ASP* 1.3 63.0 + - - +
328B VAL* 3.3 3.0 + - - +
329B ARG* 2.9 24.6 + - - +
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Residues in contact with ASP 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.1 11.7 - - + -
323B SER* 2.8 24.6 + - - +
325B PHE* 1.3 76.0 - - - +
327B GLN* 1.3 64.6 - - - +
329B ARG* 3.1 25.0 + - - +
330B LEU* 3.0 33.1 + - + +
409B SER* 5.9 1.4 - - - -
422B SER* 2.5 41.1 + - - +
423B SER* 4.6 4.8 + - - -
426B LEU* 6.1 5.3 - - + +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.7 27.7 - - + +
314B LYS* 4.9 6.2 - - - +
319B PHE* 3.6 50.0 - - + +
320B VAL* 3.6 25.8 + - - +
322B LEU* 3.0 24.7 + - + +
323B SER 3.0 16.3 + - - +
324B LEU* 3.2 15.1 + - - +
326B ASP* 1.3 77.9 - - - +
328B VAL* 1.3 60.3 + - - +
330B LEU* 3.7 1.1 + - - +
331B LEU* 3.3 28.5 + - - +
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.3 34.1 - - + +
325A PHE* 3.4 24.5 - - + +
328A VAL* 3.4 39.5 - - + -
324B LEU 3.2 3.8 + - - +
325B PHE 3.9 6.1 - - - +
327B GLN* 1.3 74.7 - - - +
329B ARG* 1.3 61.2 + - - +
331B LEU* 4.6 0.4 - - - -
332B GLU* 2.8 62.2 + - - +
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLU* 4.0 24.4 + - - +
325B PHE 2.9 18.2 + - - +
326B ASP* 3.1 25.7 + - - +
328B VAL* 1.3 73.3 - - - +
330B LEU* 1.3 67.1 + - - +
332B GLU* 3.9 8.4 - - - +
333B SER* 2.8 32.8 + - - -
408B SER 5.8 0.2 - - - +
409B SER* 3.3 35.8 + - - +
410B MET 4.7 9.9 + - - +
423B SER* 5.8 0.8 + - - -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B PHE* 3.5 28.3 - - + -
322B LEU* 3.7 21.5 - - + -
326B ASP* 3.0 19.9 + - + +
327B GLN 3.7 3.4 - - - +
329B ARG* 1.3 78.4 - - - +
331B LEU* 1.3 62.7 + - - +
333B SER* 3.4 0.4 - - - -
334B CYS* 3.0 26.3 + - - -
405B LEU* 3.5 24.7 - - + +
406B LEU* 4.3 4.7 - - + +
408B SER* 3.2 22.9 + - - +
409B SER* 3.6 29.2 - - - +
426B LEU* 4.1 19.1 - - + -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU* 3.9 19.3 - - + -
325A PHE* 3.6 31.6 - - + -
309B MET* 4.1 35.0 - - + +
310B ILE* 4.8 8.1 - - + -
313B ALA* 4.2 15.3 - - + -
319B PHE* 4.3 9.4 - - + -
327B GLN 3.3 19.2 + - - +
328B VAL 3.9 1.3 - - - +
329B ARG 3.3 0.4 - - - -
330B LEU* 1.3 76.3 - - - +
332B GLU* 1.3 60.1 + - - +
334B CYS* 3.0 1.1 + - - -
335B TRP* 2.7 36.4 + - - +
405B LEU* 4.0 20.4 - - + +
494B MET* 4.2 4.5 - - + -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A PHE* 3.8 14.0 - - + +
328A VAL* 5.9 0.2 - - - +
332A GLU* 5.8 0.7 - - - +
328B VAL* 2.8 51.8 + - + +
329B ARG* 4.0 5.7 - - - +
331B LEU* 1.3 72.6 - - - +
333B SER* 1.3 59.1 + - - +
335B TRP* 3.2 19.2 + - - -
473B MET* 4.7 5.0 - - - +
493B GLU* 5.8 0.7 - - - +
494B MET* 4.0 16.6 - - - +
497B ALA* 3.5 37.1 - - + +
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG* 2.8 26.2 + - - -
330B LEU 3.4 4.3 - - - -
332B GLU* 1.3 79.7 - - - +
334B CYS* 1.3 58.3 + - - +
335B TRP* 5.2 0.4 - - - -
337B GLU* 3.7 8.7 - - - +
408B SER* 3.2 30.8 + - - -
466B ARG* 5.4 4.7 + - - -
473B MET* 5.9 2.8 - - - +
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Residues in contact with CYS 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B MET* 6.0 0.2 - - - -
330B LEU 3.0 24.4 + - - +
331B LEU* 4.2 1.1 - - - -
333B SER* 1.3 78.0 - - - +
335B TRP* 1.3 68.8 - - - +
336B MET 3.2 2.5 - - - -
337B GLU* 3.1 29.9 + - - +
338B VAL* 3.1 19.9 + - - +
404B ILE* 4.0 11.7 - - + +
405B LEU* 3.3 41.5 - - - -
408B SER* 4.0 11.0 - - - -
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Residues in contact with TRP 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA* 5.0 0.7 - - + -
306B LEU* 3.4 22.2 - - + -
309B MET* 3.2 25.0 - - - +
331B LEU 2.7 18.8 + - - +
332B GLU 3.2 25.6 - - - -
334B CYS* 1.3 71.9 - - - +
336B MET* 1.3 104.8 + - + +
338B VAL 3.4 0.5 + - - -
339B LEU* 3.2 31.0 + - + +
473B MET* 3.0 36.4 - - + +
476B LEU* 4.1 0.2 - - + -
491B LEU* 3.6 29.2 - - + -
494B MET* 3.2 49.4 + - + -
495B LEU* 3.6 21.1 - - + -
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Residues in contact with MET 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA* 6.1 0.9 - - + -
334B CYS 3.2 0.6 - - - -
335B TRP* 1.3 119.4 - - + +
337B GLU* 1.3 66.3 + - - +
339B LEU* 3.2 11.0 + - + +
340B MET* 3.0 43.8 + - + +
469B SER* 3.3 20.9 - - - +
472B GLY 4.5 15.0 - - - -
473B MET* 3.9 17.2 - - + -
476B LEU* 4.1 16.4 - - + -
501B 272 4.2 29.2 - - + +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B SER 3.7 5.5 - - - +
334B CYS* 3.1 26.1 + - - +
336B MET* 1.3 78.7 - - - +
338B VAL* 1.3 57.1 + - - +
340B MET* 3.5 1.3 + - - -
341B MET* 3.0 28.1 + - - +
404B ILE* 4.0 23.2 - - + +
462B LEU* 4.6 3.6 - - - +
465B VAL* 3.7 24.8 - - + +
466B ARG* 3.2 48.3 + - - +
469B SER* 3.5 26.2 - - - +
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B MET* 3.8 20.6 - - + -
312B TRP* 4.2 26.5 - - + -
334B CYS* 3.1 29.7 + - - +
335B TRP 3.6 8.1 - - - +
336B MET 3.1 0.2 - - - -
337B GLU* 1.3 76.0 - - - +
339B LEU* 1.3 65.6 + - - +
341B MET* 3.4 7.1 + - - +
342B GLY* 3.2 17.8 + - - -
401B LYS* 3.8 26.9 - - + +
404B ILE* 4.1 16.6 - - + -
405B LEU* 4.9 0.7 - - + +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA* 4.0 20.9 - - + -
305B GLU* 3.4 45.5 - - + +
306B LEU* 4.1 6.3 - - + -
309B MET* 3.7 14.6 - - + -
335B TRP* 3.2 44.0 + - + +
336B MET* 3.2 12.4 + - - +
338B VAL* 1.3 77.7 - - + +
340B MET* 1.3 57.4 + - - +
342B GLY* 3.1 4.4 + - - -
343B LEU* 2.9 25.8 + - - +
346B ARG* 4.3 1.7 + - - -
501B 272 3.8 22.7 - - + +
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Residues in contact with MET 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B MET* 3.0 23.5 + - - +
337B GLU* 4.1 4.0 - - - +
339B LEU* 1.3 75.5 - - - +
341B MET* 1.3 56.7 + - - +
342B GLY 3.3 0.2 - - - -
343B LEU* 3.6 8.9 - - - +
344B MET* 2.8 42.2 + - + +
376B ILE* 4.5 2.2 - - + -
380B LEU* 3.6 30.7 - - + -
465B VAL* 4.7 3.1 - - + +
468B ALA* 3.8 17.9 - - + +
469B SER* 3.5 32.1 - - - -
472B GLY* 4.3 7.6 - - - -
501B 272 3.3 45.1 - - - +
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Residues in contact with MET 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU 3.0 19.8 + - - +
338B VAL 3.6 6.3 - - - +
339B LEU 3.1 0.2 - - - -
340B MET* 1.3 75.2 - - - +
342B GLY* 1.3 60.1 + - - +
344B MET* 3.3 20.3 + - + +
345B TRP* 3.0 26.3 + - - +
387B PHE* 3.7 34.3 - - + -
392B LEU* 4.0 22.2 - - + -
397B TYR* 3.7 22.2 - - + -
400B VAL* 4.2 19.5 - - + -
401B LYS* 4.0 12.8 - - + -
404B ILE* 4.2 17.3 - - + -
462B LEU* 5.6 0.4 - - - -
465B VAL* 4.6 2.2 - - - -
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Residues in contact with GLY 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL 3.2 7.1 + - - -
339B LEU 3.1 7.1 + - - -
341B MET* 1.3 76.4 - - - +
343B LEU* 1.3 60.1 + - - +
345B TRP* 3.3 1.7 + - - +
346B ARG* 2.9 49.0 + - - +
397B TYR* 3.4 24.1 + - - -
401B LYS* 5.5 0.2 - - - -
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU 2.9 12.1 + - - +
340B MET* 3.6 7.0 - - - +
342B GLY* 1.3 76.9 - - - +
344B MET* 1.3 62.3 + - + +
346B ARG* 3.2 15.2 + - - +
347B SER* 2.9 32.5 + - - +
354B LEU* 4.3 13.0 - - + -
355B ILE 3.3 38.1 - - - +
356B PHE* 3.5 27.6 - - + +
380B LEU* 3.8 30.5 - - + -
384B THR* 5.9 0.2 - - - +
501B 272 3.6 24.2 - - + +
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Residues in contact with MET 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B MET* 2.8 34.7 + - + +
341B MET* 3.4 21.3 - - + +
343B LEU* 1.3 79.8 - - + +
345B TRP* 1.3 62.1 + - - +
347B SER 3.4 0.2 + - - -
348B ILE* 3.1 21.0 + - - +
380B LEU* 4.4 15.3 - - + +
383B THR* 3.4 34.8 - - - -
384B THR* 3.5 29.8 - - - +
387B PHE* 3.7 24.2 - - + +
465B VAL* 3.3 35.0 - - + -
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Residues in contact with TRP 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET* 3.0 19.3 + - + +
342B GLY 3.8 3.4 - - - +
343B LEU 3.3 0.4 - - - -
344B MET* 1.3 77.2 - - - +
346B ARG* 1.3 69.9 + - + +
348B ILE* 2.9 47.5 - - + +
392B LEU* 3.0 45.3 - - + -
393B GLN* 3.7 7.0 - - - -
394B HIS* 3.3 50.0 + + + -
397B TYR* 3.8 36.6 - + + -
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Residues in contact with ARG 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B HIS* 6.3 3.6 - - - -
305B GLU* 4.0 12.9 + - - -
339B LEU 4.3 1.2 + - - -
342B GLY* 2.9 36.6 + - - +
343B LEU* 3.2 26.4 - - - +
344B MET 3.4 0.2 - - - -
345B TRP* 1.3 85.5 - - + +
347B SER* 1.3 58.4 + - - +
348B ILE* 3.5 0.9 - - - -
350B HIS* 4.0 11.1 + - - -
355B ILE* 2.9 45.1 + - + +
356B PHE* 2.9 28.2 + - - +
357B ALA* 4.9 6.3 - - - +
358B PRO* 5.3 5.8 - - - -
397B TYR* 5.5 0.4 + - - -
501B 272 3.7 14.6 + - - -
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Residues in contact with SER 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 2.9 19.8 + - - +
344B MET 3.8 2.9 - - - -
345B TRP 3.1 0.8 - - - -
346B ARG* 1.3 76.3 - - - +
348B ILE* 1.3 58.6 + - - +
349B ASP 3.1 3.4 - - - -
350B HIS* 2.8 28.5 + - - +
353B LYS 3.8 17.9 - - - -
354B LEU* 3.6 6.2 - - - -
355B ILE* 2.7 34.7 + - - +
384B THR* 3.9 15.9 - - - +
388B ARG* 4.3 1.4 + - - -
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Residues in contact with ILE 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B MET 3.1 12.3 + - - +
345B TRP* 2.9 40.8 - - + +
346B ARG 3.5 0.9 - - - -
347B SER* 1.3 75.8 - - - +
349B ASP* 1.3 79.8 + - - +
350B HIS 3.5 0.2 - - - -
384B THR* 3.7 9.4 - - + +
387B PHE* 4.2 3.8 - - + +
388B ARG* 3.0 52.7 + - + +
391B LYS* 5.1 1.3 - - - -
392B LEU* 3.7 46.7 - - + +
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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