Contacts of the helix formed by residues 317 - 350 (chain B) in PDB entry 6R7Z
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 VAL 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU 3.9 0.6 + - - +
313B ARG* 3.3 18.2 + - - +
314B ILE 3.4 0.6 + - - -
316B LEU* 1.3 80.4 - - - +
318B SER* 1.3 63.6 + - - +
319B LEU 3.5 0.2 - - - -
320B PRO* 3.7 3.8 - - - +
321B PHE* 3.2 23.2 + - - +
387B TRP* 4.4 17.3 - - + -
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG 3.4 2.8 + - - -
314B ILE* 2.9 24.5 + - - -
317B VAL* 1.3 78.6 - - - +
319B LEU* 1.3 53.1 + - - +
321B PHE* 3.0 7.3 + - - +
322B VAL* 2.7 35.9 + - - +
384B LEU* 5.2 19.7 - - - -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE 3.2 8.7 + - - +
315B TYR* 4.6 10.8 - - - +
318B SER* 1.3 78.5 - - - +
320B PRO* 1.4 64.5 - - + +
322B VAL* 3.8 7.2 - - - +
323B CYS* 2.9 28.1 + - - +
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Residues in contact with PRO 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B TYR 4.5 2.0 - - - +
316B LEU* 3.3 39.0 - - - +
317B VAL* 3.7 4.7 - - - +
319B LEU* 1.4 91.8 - - + +
321B PHE* 1.3 56.8 + - - +
323B CYS* 3.7 6.6 - - + +
324B LEU* 2.8 30.7 + - - +
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Residues in contact with PHE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL 3.2 19.6 + - - +
318B SER* 3.0 7.7 + - - +
320B PRO* 1.3 73.9 - - - +
322B VAL* 1.3 60.5 + - - +
324B LEU* 3.4 6.1 + - - +
325B CYS* 3.0 28.1 + - - +
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER 2.7 18.7 + - - +
319B LEU* 3.8 9.0 - - - +
321B PHE* 1.3 72.7 - - - +
323B CYS* 1.3 58.1 + - - +
325B CYS* 3.3 6.2 + - - +
326B LEU* 2.8 29.7 + - - +
403B LYS* 6.0 6.3 - - + -
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Residues in contact with CYS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU 2.9 18.5 + - - +
320B PRO* 3.7 7.9 - - + +
322B VAL* 1.3 73.5 - - - +
324B LEU* 1.3 59.4 + - - +
326B LEU* 3.6 8.1 - - - +
327B TYR* 2.8 30.2 + - - +
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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
----------------------------------------------------------
320B PRO 2.8 20.4 + - - +
321B PHE* 3.7 7.6 - - - +
322B VAL 3.3 0.2 - - - -
323B CYS* 1.3 73.2 - - - +
325B CYS* 1.3 57.9 + - - +
327B TYR* 3.4 6.3 + - - +
328B PHE* 3.0 28.2 + - - +
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Residues in contact with CYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PHE 3.0 17.6 + - - +
322B VAL* 3.8 6.1 - - - +
324B LEU* 1.3 74.3 - - - +
326B LEU* 1.3 60.0 + - - +
328B PHE* 3.4 6.6 + - - +
329B SER* 3.0 29.0 + - - -
377B TYR* 5.8 4.7 - - + -
407B PHE* 4.2 19.1 - - + -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B VAL 2.8 17.2 + - - +
323B CYS* 3.6 9.2 - - - +
325B CYS* 1.3 75.0 - - - +
327B TYR* 1.3 59.5 + - - +
329B SER* 3.3 6.6 + - - -
330B LEU* 2.9 29.5 + - - +
407B PHE* 5.2 5.3 - - + -
410B LEU* 5.9 7.4 - - + -
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B CYS 2.8 18.2 + - - +
324B LEU* 3.7 8.1 - - - +
325B CYS 3.3 0.2 - - - -
326B LEU* 1.3 78.6 - - - +
328B PHE* 1.3 56.0 + - - +
330B LEU* 3.3 6.7 + - - +
331B TYR* 2.8 29.2 + - - +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU 3.0 16.9 + - - +
325B CYS* 3.9 6.3 - - - +
327B TYR* 1.3 74.8 - - - +
329B SER* 1.3 59.9 + - - +
331B TYR* 3.6 7.0 - - - +
332B VAL* 2.8 30.1 + - - +
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B CYS 3.0 18.1 + - - -
326B LEU* 3.6 7.4 - - - -
327B TYR 3.3 0.2 - - - -
328B PHE* 1.3 74.5 - - - +
330B LEU* 1.3 60.1 + - - +
332B VAL* 3.4 6.1 + - - +
333B MET* 2.9 27.4 + - - +
373B MET* 6.4 0.2 - - - -
407B PHE* 4.1 20.6 - - - -
410B LEU* 5.9 4.9 - - - -
411B ASN* 5.5 11.2 - - - -
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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
----------------------------------------------------------
326B LEU 2.9 17.5 + - - +
327B TYR* 3.7 7.0 - - - +
329B SER* 1.3 76.4 - - - +
331B TYR* 1.3 57.3 + - - +
333B MET* 3.3 8.0 + - - +
334B MET* 2.9 28.6 + - - +
414B ALA* 6.3 1.3 - - - -
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B TYR 2.8 18.1 + - - +
328B PHE* 3.6 8.7 - - - +
329B SER 3.2 0.2 - - - -
330B LEU* 1.3 75.2 - - - +
332B VAL* 1.3 59.5 + - - +
334B MET* 3.3 6.3 + - - +
335B ILE* 2.8 28.8 + - - +
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE 2.8 17.0 + - - +
329B SER* 3.8 7.0 - - - +
331B TYR* 1.3 74.0 - - - +
333B MET* 1.3 59.4 + - - +
335B ILE* 3.6 8.5 - - - +
336B TYR* 2.9 29.1 + - - +
369B VAL* 6.5 0.9 - - + -
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Residues in contact with MET 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER 2.9 19.1 + - - +
330B LEU* 3.4 9.4 - - - +
331B TYR 3.2 0.2 - - - -
332B VAL* 1.3 76.8 - - - +
334B MET* 1.3 57.6 + - - +
336B TYR* 3.2 10.6 + - + +
337B PHE* 3.0 42.8 + - + -
414B ALA* 4.9 16.8 - - + -
415B SER* 5.9 2.0 - - - +
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Residues in contact with MET 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU 2.9 16.7 + - - +
331B TYR* 3.7 6.7 - - - +
333B MET* 1.3 71.9 - - - +
335B ILE* 1.3 61.5 + - - +
337B PHE* 3.3 10.3 + - - +
338B ASP* 3.0 27.2 + - - +
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR 2.8 17.9 + - - +
332B VAL* 3.6 9.9 - - - +
333B MET 3.3 0.2 - - - -
334B MET* 1.3 77.2 - - - +
336B TYR* 1.3 55.7 + - - +
338B ASP* 3.4 7.0 + - - +
339B MET* 3.0 27.9 + - - +
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Residues in contact with TYR 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL 2.9 18.9 + - - +
333B MET* 3.2 11.9 + - + +
335B ILE* 1.3 77.3 - - - +
337B PHE* 1.3 81.9 + + - +
339B MET* 3.3 6.7 + - + +
340B GLU* 2.7 33.7 + - + +
362B PRO* 3.4 45.6 - - + +
363B SER* 3.4 22.6 + - - -
366B TYR* 3.7 19.1 - - + -
415B SER* 4.6 16.4 - - - -
432B SER* 5.2 9.0 - - - -
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Residues in contact with PHE 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MET* 3.0 34.7 + - + -
334B MET* 3.8 10.1 - - - +
335B ILE 3.3 0.4 - - - -
336B TYR* 1.3 90.0 - + - +
338B ASP* 1.3 60.9 + - - +
340B GLU* 3.5 9.5 - - + +
341B VAL* 2.9 30.0 + - - +
414B ALA 5.1 0.7 - - - -
415B SER* 4.1 26.7 - - - -
418B TYR* 3.6 33.9 - - + -
419B ILE* 5.3 6.5 - - + -
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Residues in contact with ASP 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B MET 3.0 16.8 + - - +
335B ILE* 3.7 7.6 - - - +
337B PHE* 1.3 76.5 - - - +
339B MET* 1.3 56.7 + - - +
341B VAL* 3.5 5.6 + - - +
342B TRP* 3.0 29.1 + - - +
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE 3.0 14.3 + - - +
336B TYR* 3.5 11.7 - - + +
338B ASP* 1.3 75.8 - - - +
340B GLU* 1.3 59.2 + - - +
342B TRP* 3.7 13.4 - - + +
343B ALA* 2.8 30.3 + - - +
362B PRO* 5.1 13.1 - - + +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B TYR* 2.7 35.0 + - + +
337B PHE* 3.3 15.7 + - + +
339B MET* 1.3 72.4 - - - +
341B VAL* 1.3 54.4 + - - +
343B ALA* 3.3 5.9 + - - +
344B LEU* 2.7 35.2 + - - +
362B PRO* 5.0 7.4 - - + +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE 2.9 17.3 + - - +
338B ASP* 4.0 6.3 - - - +
340B GLU* 1.3 73.0 - - - +
342B TRP* 1.3 60.4 + - - +
344B LEU* 3.6 7.8 - - - +
345B GLY* 2.8 25.3 + - - -
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Residues in contact with TRP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASP 3.0 18.5 + - - +
339B MET* 3.7 14.4 - - + +
341B VAL* 1.3 77.9 - - - +
343B ALA* 1.3 72.3 + - + +
345B GLY* 3.3 2.8 + - - +
346B LEU* 2.7 44.3 + - + +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B MET 2.8 18.3 + - - +
340B GLU* 3.7 7.2 - - - +
342B TRP* 1.3 88.8 - - + +
344B LEU* 1.3 56.8 + - - +
346B LEU* 3.5 6.2 - - + +
347B HIS* 2.7 34.0 + - - +
358B LEU* 5.1 9.0 - - + +
359B LEU* 5.5 6.6 - - + +
362B PRO* 4.8 15.0 - - + -
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Residues in contact with LEU 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU 2.7 21.0 + - - +
341B VAL* 3.6 9.4 - - - +
343B ALA* 1.3 73.7 - - - +
345B GLY* 1.3 57.4 + - - +
347B HIS* 3.2 8.4 + - - +
348B GLU* 2.7 27.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL 2.8 15.2 + - - -
342B TRP* 3.6 4.0 - - - -
344B LEU* 1.3 76.4 - - - +
346B LEU* 1.3 56.3 + - - +
348B GLU* 3.2 10.5 + - - +
349B ASN* 2.8 28.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 2.7 36.7 + - + +
343B ALA* 3.2 11.4 + - - +
345B GLY* 1.3 72.5 - - - +
347B HIS* 1.3 61.6 + - - +
349B ASN* 3.7 7.1 - - - +
350B SER* 3.1 27.0 + - - -
355B THR* 4.9 1.4 - - - -
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Residues in contact with HIS 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ALA 2.7 19.5 + - - +
344B LEU* 3.5 9.4 - - - +
346B LEU* 1.3 73.6 - - - +
348B GLU* 1.3 62.4 + - - +
349B ASN 3.4 0.3 + - - -
351B GLY 3.0 25.3 + - - +
355B THR* 3.6 32.8 - - - +
359B LEU* 5.8 5.8 - - + -
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU 2.7 16.7 + - - +
345B GLY* 3.4 11.4 - - - +
347B HIS* 1.3 77.9 - - - +
349B ASN* 1.3 60.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLY 2.8 15.6 + - - +
346B LEU* 3.7 8.7 - - - +
347B HIS 3.2 0.4 - - - -
348B GLU* 1.3 81.3 - - - +
350B SER* 1.3 69.2 + - - +
----------------------------------------------------------
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B LEU 3.1 12.5 + - - -
348B GLU 3.8 0.2 - - - -
349B ASN* 1.3 82.2 - - - +
351B GLY* 1.3 60.7 + - - +
355B THR* 5.1 6.1 - - - -
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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