Contacts of the helix formed by residues 314 - 345 (chain B) in PDB entry 6D6U
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 GLN 314 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE 3.3 13.2 - - - +
311B THR* 3.9 6.5 - - - +
313B SER* 1.3 84.2 + - - +
315B PRO* 1.3 74.0 - - + +
316B ALA* 3.5 24.0 + - + +
317B ARG* 3.2 50.5 + - - +
318B ALA 4.0 0.5 + - - -
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 6.2 3.1 - - + +
311B THR* 4.2 17.7 - - - +
312B LYS 5.6 0.7 - - - +
313B SER 4.6 1.6 - - - +
314B GLN* 1.3 89.1 - - + +
316B ALA* 1.3 62.8 + - + +
317B ARG 3.2 0.2 - - - -
318B ALA* 3.3 4.8 + - - +
319B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLN* 3.3 23.9 - - + +
315B PRO* 1.3 83.6 - - + +
317B ARG* 1.3 56.6 + - - +
319B ALA* 3.4 7.1 + - - +
320B LYS* 2.9 31.0 + - - +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 4.8 27.4 - - + -
313B SER* 3.6 22.3 + - - -
314B GLN* 3.2 40.5 + - + +
315B PRO 3.2 0.8 - - - -
316B ALA* 1.3 77.2 - - - +
318B ALA* 1.3 56.7 + - - +
320B LYS* 3.3 6.7 + - - +
321B ILE* 2.9 38.4 + - + +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 5.0 10.3 - - + +
307B VAL* 3.7 26.4 - - + +
310B PHE* 5.1 1.3 + - + +
311B THR* 3.9 27.3 - - - +
314B GLN 4.0 1.0 + - - -
315B PRO 3.3 8.7 + - - +
317B ARG* 1.3 79.3 - - - +
319B ALA* 1.3 62.3 + - - +
321B ILE* 3.2 12.0 + - - +
322B ASP* 3.0 29.8 + - - +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ARG* 5.3 14.9 - - - +
315B PRO 2.9 18.1 + - - +
316B ALA* 3.6 8.5 - - - +
318B ALA* 1.3 77.8 - - - +
320B LYS* 1.3 57.0 + - - +
322B ASP* 3.4 6.3 + - - +
323B ARG* 2.9 28.9 + - - +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ALA 2.9 18.0 + - - +
317B ARG* 3.7 5.8 - - - +
319B ALA* 1.3 73.6 - - - +
321B ILE* 1.3 66.1 + - + +
323B ARG* 3.2 9.4 + - + +
324B LEU* 2.9 53.8 + - + +
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Residues in contact with ILE 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 3.1 32.1 - - + +
306B THR* 5.3 5.4 - - + -
307B VAL* 3.7 18.8 - - + -
310B PHE* 4.1 26.7 - - + -
317B ARG* 2.9 27.9 + - + +
318B ALA* 3.2 6.5 + - - +
320B LYS* 1.3 77.0 - - + +
322B ASP* 1.3 57.3 + - - +
324B LEU* 3.3 9.6 + - + +
325B SER* 2.9 36.2 + - - +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 4.2 24.0 - - - +
247B LEU 5.2 2.1 - - - +
249B ARG* 4.5 22.0 + - - +
255B ARG* 5.0 6.8 + - - -
303B GLU* 3.4 17.2 - - - +
307B VAL* 4.7 8.0 - - - +
318B ALA 3.0 21.5 + - - +
319B ALA* 3.8 6.5 - - - +
321B ILE* 1.3 75.8 - - - +
323B ARG* 1.3 62.2 + - - +
325B SER* 4.6 3.1 - - - -
326B ARG* 3.0 52.5 + - + +
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA 2.9 17.9 + - - +
320B LYS* 3.2 11.9 + - - +
322B ASP* 1.3 75.8 - - - +
324B LEU* 1.3 73.9 + - - +
326B ARG* 4.3 11.2 + - - +
327B ILE* 3.3 33.1 + - - +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LYS* 2.9 45.2 + - + +
321B ILE* 3.8 7.6 - - + +
323B ARG* 1.3 91.8 - - - +
325B SER* 1.3 60.2 + - - +
327B ILE* 3.3 5.6 + - - +
328B ALA* 2.9 29.4 + - + +
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.9 29.3 - - - -
303B GLU* 3.9 17.4 - - - +
321B ILE* 2.9 21.8 + - - +
322B ASP* 3.2 1.5 + - - -
324B LEU* 1.3 76.8 - - - +
326B ARG* 1.3 63.2 + - - +
328B ALA* 4.1 8.1 - - - -
329B PHE* 3.0 41.3 + - - +
330B PRO* 3.9 0.3 - - - +
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Residues in contact with ARG 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.1 45.5 + - + -
246B TRP* 3.3 74.3 + - + +
247B LEU 4.5 3.2 + - - -
249B ARG* 5.2 9.1 - - - +
322B ASP* 3.0 36.1 + - - +
323B ARG* 4.6 8.3 - - - +
324B LEU 3.3 0.2 - - - -
325B SER* 1.3 76.4 - - - +
327B ILE* 1.3 62.4 + - + +
330B PRO* 3.2 23.4 - - - +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG* 3.3 33.8 + - - +
324B LEU 3.3 7.1 + - - +
326B ARG* 1.3 81.1 - - + +
328B ALA* 1.3 66.6 + - - +
329B PHE 3.5 0.4 - - - -
330B PRO* 4.0 1.2 - - - +
331B LEU* 3.5 30.5 + - + +
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Residues in contact with ALA 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 2.9 19.1 + - + +
325B SER* 3.0 8.0 + - - +
327B ILE* 1.3 78.4 - - - +
329B PHE* 1.3 73.1 + - + +
331B LEU* 4.1 2.5 - - - +
332B LEU* 3.2 34.2 + - + +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLN* 6.1 2.5 - - + -
245B PHE* 3.4 42.6 - + + -
296B PHE* 4.9 15.7 - + + -
299B SER* 4.0 27.1 - - - -
300B ALA* 4.2 14.8 - - + -
303B GLU* 4.8 5.4 - - + -
325B SER* 3.0 23.3 + - - +
328B ALA* 1.3 88.3 - - + +
330B PRO* 1.3 69.5 - - + +
332B LEU* 3.1 16.3 + - + +
333B PHE* 3.0 22.2 + - - +
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Residues in contact with PRO 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLN* 3.3 41.5 - - + +
325B SER 3.9 1.3 - - - +
326B ARG* 3.2 26.9 - - - +
327B ILE 4.0 1.8 - - - +
328B ALA 3.9 0.9 - - - -
329B PHE* 1.3 94.3 - - + +
331B LEU* 1.3 56.7 + - - +
333B PHE* 3.3 7.7 + - + +
334B GLY* 2.9 26.0 + - - -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ILE* 3.5 25.7 + - + +
328B ALA* 3.7 2.2 + - - +
329B PHE 3.3 0.8 - - - -
330B PRO* 1.3 79.2 - - - +
332B LEU* 1.3 59.6 + - + +
334B GLY* 3.3 1.7 + - - -
335B ILE* 2.9 54.8 + - + +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PHE* 4.3 19.3 - - + -
328B ALA* 3.2 25.0 + - + +
329B PHE* 3.1 16.4 + - + +
331B LEU* 1.3 80.8 - - + +
333B PHE* 1.3 57.6 + - - +
335B ILE* 3.3 16.8 + - + +
336B PHE* 2.9 28.6 + - - +
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Residues in contact with PHE 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 3.9 44.0 - - + -
238B VAL* 4.0 28.7 - - + -
239B ILE* 4.6 12.3 - - + -
242B GLN* 6.2 1.3 - - - +
289B PHE* 4.8 8.1 - + - -
292B VAL* 4.8 10.5 - - + -
293B CYS* 5.1 4.9 - - - -
296B PHE* 3.5 34.5 - + + -
329B PHE 3.0 12.8 + - - +
330B PRO* 3.8 9.9 - - + +
332B LEU* 1.3 75.9 - - - +
334B GLY* 1.3 59.5 + - - +
336B PHE* 3.2 6.7 + + - +
337B ASN* 2.9 61.8 + - - +
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Residues in contact with GLY 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B PRO 2.9 14.8 + - - -
331B LEU* 3.8 3.4 - - - -
333B PHE* 1.3 79.4 - - - +
335B ILE* 1.3 60.6 + - - +
337B ASN* 3.3 10.2 + - - +
338B LEU* 2.9 22.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 2.9 47.6 + - + +
332B LEU* 3.7 17.3 - - + +
334B GLY* 1.3 75.8 - - - +
336B PHE* 1.3 57.7 + - - +
338B LEU* 3.2 16.5 + - + +
339B VAL* 2.9 38.6 + - + +
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Residues in contact with PHE 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 4.6 8.5 - - + -
289B PHE* 4.3 21.5 - + - -
292B VAL* 3.3 50.5 - - + -
296B PHE* 5.0 3.6 - - + -
332B LEU 2.9 16.7 + - - +
333B PHE* 3.6 12.3 - + - +
334B GLY 3.2 0.4 - - - -
335B ILE* 1.3 77.1 - - - +
337B ASN* 1.3 67.5 + - - +
339B VAL* 3.2 11.2 + - + -
340B TYR* 2.9 50.2 + + + +
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Residues in contact with ASN 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 4.0 12.2 - - - +
289B PHE* 3.9 20.4 - - - -
333B PHE* 2.9 50.2 + - - +
334B GLY* 3.6 9.3 - - - +
336B PHE* 1.3 76.8 - - - +
338B LEU* 1.3 62.1 - - - +
340B TYR* 4.4 2.2 - - - +
341B TRP* 3.0 54.8 + - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLY 2.9 13.8 + - - +
335B ILE* 3.3 21.3 - - + +
336B PHE 3.2 0.2 - - - -
337B ASN* 1.3 79.5 - - - +
339B VAL* 1.3 64.4 + - + +
342B ALA* 3.4 28.0 + - + +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ILE* 2.9 32.6 + - + +
336B PHE* 3.8 12.6 - - + +
338B LEU* 1.3 80.6 - - + +
340B TYR* 1.3 65.0 + - - +
342B ALA* 4.0 3.8 + - - +
343B THR* 3.5 17.2 + - - +
----------------------------------------------------------
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Residues in contact with TYR 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE 5.0 0.5 + - - -
147B PRO* 5.3 1.0 - - - +
148B MET* 6.1 0.2 - - - -
231B TYR* 3.8 14.4 + + - -
285B ALA* 2.4 33.4 + - - +
288B TRP* 5.1 6.3 - - + -
289B PHE* 4.4 24.6 - + + +
336B PHE* 2.9 42.8 + + + +
337B ASN* 3.8 5.6 - - - +
339B VAL* 1.3 79.1 - - - +
341B TRP* 1.3 103.8 + + - +
342B ALA 3.0 1.4 + - - -
343B THR* 3.3 12.3 + - - -
344B TYR* 3.6 43.1 + + - -
----------------------------------------------------------
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Residues in contact with TRP 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 4.7 13.2 - - + -
223B ILE* 4.4 19.3 - - + -
227B VAL* 4.7 14.8 - - + -
231B TYR* 3.3 46.9 - + + -
235B ILE* 4.7 7.9 - - + +
289B PHE* 4.7 6.4 - + - -
337B ASN* 3.0 48.4 + - + +
340B TYR* 1.3 100.5 - + - +
342B ALA* 1.3 62.2 + - - +
343B THR 3.4 0.6 + - - -
344B TYR* 4.2 4.0 + + + +
345B LEU* 4.1 34.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LEU* 3.4 22.7 + - + +
339B VAL* 4.4 3.4 - - - +
340B TYR 3.0 1.4 + - - -
341B TRP* 1.3 79.8 - - - +
343B THR* 1.3 66.7 + - - +
345B LEU* 4.2 10.8 + - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B VAL* 3.5 14.2 + - - +
340B TYR 3.3 7.4 + - - -
342B ALA* 1.3 80.2 - - - +
344B TYR* 1.3 83.3 + - + +
345B LEU 3.5 4.3 + - - -
----------------------------------------------------------
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Residues in contact with TYR 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLU 4.9 1.9 + - - -
145B ASP* 5.0 16.4 - - + -
146B PHE 5.6 1.3 - - - -
147B PRO* 6.3 1.1 - - + -
148B MET* 3.4 38.8 - - + +
285B ALA* 3.2 37.5 - - + +
288B TRP* 5.3 4.9 - - - +
340B TYR* 3.6 45.0 + + - +
341B TRP* 4.2 3.8 + + + +
342B ALA 3.6 0.2 - - - -
343B THR* 1.3 92.4 - - + +
345B LEU* 1.3 66.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 3.5 22.2 - - + -
223B ILE* 6.0 2.5 - - + -
341B TRP* 4.1 27.4 + - + +
342B ALA 4.2 7.4 + - - +
343B THR 3.4 7.7 - - - -
344B TYR* 1.3 85.2 - - - +
----------------------------------------------------------
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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