Contacts of the helix formed by residues 309 - 336 (chain B) in PDB entry 6DWN
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 ASN 309 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER* 4.1 8.6 + - - -
119B GLN* 3.0 33.6 + - - +
120B SER* 5.5 0.9 - - - -
121B MET 5.3 0.4 + - - -
134B ARG* 3.2 8.7 + - - +
259B TYR* 3.7 25.6 + - + +
262B MET* 3.8 22.4 - - + -
305B GLU 3.3 15.4 + - - +
306B LYS* 3.0 20.1 - - - +
308B ILE* 1.3 75.5 - - - +
310B ILE* 1.3 63.4 + - - +
311B VAL 3.3 1.1 - - - -
312B LEU* 3.0 21.8 + - + +
313B ASP* 3.7 7.6 + - - +
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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
----------------------------------------------------------
121B MET* 4.0 14.1 - - + -
134B ARG* 3.6 44.0 - - + +
137B LEU* 4.3 13.7 - - + -
138B ALA* 3.8 29.8 - - + -
281B ILE* 6.2 0.4 - - + -
285B LEU* 4.1 9.6 - - + -
306B LYS 3.5 17.3 - - - +
307B ILE* 3.6 19.5 - - - +
308B ILE 3.0 1.6 + - - -
309B ASN* 1.3 74.3 - - - +
311B VAL* 1.3 66.6 + - - +
312B LEU 3.0 3.1 + - - -
313B ASP* 3.1 17.7 + - - +
314B LEU* 3.1 16.5 + - + +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B CYS* 4.2 6.8 - - + +
203B PHE* 4.2 23.0 - - + -
262B MET* 5.0 12.8 - - + -
266B VAL* 5.6 1.3 - - + -
281B ILE* 3.6 23.3 - - + -
282B THR* 3.9 24.2 - - + +
285B LEU* 3.5 20.4 - - + -
308B ILE* 3.2 19.9 + - + +
309B ASN* 4.6 0.9 - - - -
310B ILE* 1.3 77.2 - - - +
312B LEU* 1.3 60.0 + - + +
313B ASP 3.4 0.2 - - - -
314B LEU* 3.8 8.7 - - - +
315B PHE* 2.9 31.5 + - - +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER* 3.6 23.1 - - - +
203B PHE* 5.6 7.0 - - + -
255B ASN 5.8 0.2 - - - +
258B PHE* 3.4 51.9 - - + +
259B TYR* 3.8 27.8 - - + -
261B PHE* 6.1 2.2 - - + -
262B MET* 4.7 17.5 - - + -
309B ASN* 3.0 16.3 + - - +
310B ILE 3.0 0.8 - - - -
311B VAL* 1.3 79.2 - - + +
313B ASP* 1.3 59.6 + - - +
315B PHE* 3.5 5.8 + - + +
316B GLY* 2.9 26.3 + - - -
602B AQ4 4.1 10.8 + - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B SER* 3.6 15.9 + - - -
120B SER* 3.3 13.7 + - - -
121B MET* 3.2 39.4 + - + +
122B SER* 3.2 26.2 + - - +
309B ASN* 3.7 8.4 + - - +
310B ILE* 3.1 7.9 + - - +
312B LEU* 1.3 74.9 - - - +
314B LEU* 1.3 67.5 + - + +
317B ALA* 3.0 27.9 + - - +
601B HEM 4.6 2.4 - - + +
602B AQ4 3.8 19.0 - - + -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B MET* 4.4 1.8 - - + -
138B ALA* 3.9 32.5 - - + +
142B LEU* 3.9 34.3 - - + -
198B ILE* 3.9 2.4 - - - +
202B CYS* 4.3 9.4 - - - -
281B ILE* 4.1 24.7 - - + -
310B ILE* 3.1 19.3 + - + +
311B VAL* 3.8 8.7 - - - +
313B ASP* 1.3 77.8 - - - +
315B PHE* 1.3 56.8 + - - +
318B GLY* 3.0 26.9 + - - -
458B ILE* 4.1 2.9 - - + -
601B HEM 3.6 35.9 - - + +
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Residues in contact with PHE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B THR* 3.7 31.9 - - + -
198B ILE* 3.9 27.4 - - + -
199B CYS* 4.1 17.5 - - + -
202B CYS* 4.3 4.0 - - - -
203B PHE* 4.0 31.0 - + + -
214B LEU* 5.5 4.0 - - + -
217B LEU* 5.0 9.6 - - + -
218B VAL* 4.5 7.0 - - + -
258B PHE* 3.7 36.8 - + - -
261B PHE* 6.0 2.2 - + - -
311B VAL 2.9 19.2 + - - +
312B LEU* 4.0 5.2 - - + +
314B LEU* 1.3 76.7 - - - +
316B GLY* 1.3 63.7 + - - +
319B PHE* 3.1 40.5 + + - -
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 5.2 0.4 - - - -
312B LEU 2.9 14.9 + - - -
314B LEU 3.3 0.2 - - - -
315B PHE* 1.3 82.1 - - - +
317B ALA* 1.3 60.1 + - - +
319B PHE* 3.7 11.7 - - - -
320B ASP* 3.4 23.7 + - - +
602B AQ4 3.4 35.5 + - - -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP 3.0 16.2 + - - +
316B GLY* 1.3 76.5 - - - +
318B GLY* 1.3 57.1 + - - +
320B ASP* 4.9 0.2 - - - -
321B THR* 2.5 39.1 + - + +
601B HEM 3.6 31.2 - - + +
602B AQ4 3.3 37.8 + - + -
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 4.1 2.1 - - - +
198B ILE* 4.2 12.6 - - - -
314B LEU 3.0 19.2 + - - -
315B PHE 3.3 0.9 + - - -
316B GLY 3.2 0.6 - - - -
317B ALA* 1.3 79.9 - - - +
319B PHE* 1.3 62.0 + - - +
322B VAL* 3.5 27.0 + - - +
601B HEM 3.8 21.7 - - - -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 5.8 2.5 - - - -
191B VAL* 4.3 9.4 - - + -
194B VAL* 4.0 9.0 - - - -
195B THR* 3.5 27.4 - - + +
198B ILE* 4.0 15.4 - - + +
218B VAL* 3.7 35.0 - - + -
222B ASN* 4.3 2.2 - - - -
258B PHE* 4.5 5.6 - + - -
315B PHE* 3.1 47.1 + + - -
316B GLY* 3.7 19.3 - - - -
318B GLY* 1.3 75.3 - - - +
320B ASP* 1.3 61.6 + - - +
323B THR* 2.3 35.9 + - - +
602B AQ4 3.5 39.3 - + - -
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Residues in contact with ASP 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 4.5 3.9 + - - -
224B PHE* 5.5 3.5 - - - -
225B GLY* 5.7 1.6 - - - -
316B GLY 3.4 17.4 + - - +
317B ALA* 4.4 0.9 - - - +
318B GLY 3.3 1.0 - - - -
319B PHE* 1.3 84.3 - - - +
321B THR* 1.3 65.8 + - + +
323B THR* 3.9 1.1 - - - -
324B THR* 2.9 30.5 + - - -
496B LEU* 5.5 2.3 - - - +
497B THR* 2.6 33.7 + - - +
499B LYS* 2.8 22.0 + - - -
602B AQ4 2.5 42.0 + - + +
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Residues in contact with THR 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ALA* 2.5 27.1 + - - +
318B GLY 3.8 1.4 + - - -
320B ASP* 1.3 76.7 - - - +
322B VAL* 1.3 68.6 + - - +
324B THR* 3.3 1.1 + - - -
325B ALA* 3.0 22.0 + - - +
381B PHE* 3.6 14.0 - - - -
382B VAL* 5.1 0.2 - - + -
497B THR* 3.9 22.4 - - + -
601B HEM 2.9 50.6 - - + +
602B AQ4 4.1 17.3 - - + -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 3.9 15.5 - - + -
318B GLY 3.5 17.3 + - - +
321B THR* 1.3 83.2 + - - +
323B THR* 1.3 63.2 + - - +
325B ALA* 3.1 7.5 + - - +
326B ILE* 2.9 34.5 + - + +
463B ALA* 4.1 21.1 - - + -
466B GLU* 3.9 22.9 - - + +
467B VAL* 3.9 17.3 - - + -
601B HEM 3.8 23.8 - - + -
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Residues in contact with THR 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 3.6 29.4 - - + -
190B VAL* 4.2 7.0 - - + +
191B VAL* 3.6 34.7 - - + +
194B VAL* 3.2 26.1 - - - +
319B PHE* 2.3 28.2 + - - -
320B ASP 3.9 1.8 - - - -
321B THR 3.3 0.8 - - - -
322B VAL* 1.3 77.9 - - - +
324B THR* 1.3 57.3 + - - +
326B ILE* 3.4 3.5 + - - +
327B SER* 2.9 28.1 + - - -
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B TYR* 4.7 3.8 + - - -
320B ASP 2.9 18.6 + - - -
321B THR* 3.7 5.6 - - - -
323B THR* 1.3 76.7 - - - +
325B ALA* 1.3 63.1 + - - +
327B SER* 3.3 6.0 + - - -
328B TRP* 2.9 42.0 + - + +
381B PHE* 3.8 17.7 - - + -
497B THR* 4.1 3.9 + - - -
498B MET 3.2 28.5 - - - +
499B LYS* 3.4 29.4 + - + +
500B HIS* 6.3 0.2 - - + -
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR 3.0 14.4 + - - +
322B VAL 3.1 8.7 + - - +
324B THR* 1.3 77.3 - - - +
326B ILE* 1.3 62.9 + - - +
328B TRP* 3.3 3.1 + - - +
329B SER* 3.0 26.6 + - - -
375B THR* 4.2 2.8 - - - +
376B PHE* 3.9 17.0 - - + -
381B PHE* 3.8 26.2 - - + -
467B VAL* 4.1 16.4 - - + -
601B HEM 4.2 2.5 - - + -
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B VAL* 3.6 20.4 - - + -
194B VAL* 3.7 28.0 - - + -
322B VAL* 2.9 25.7 + - + +
323B THR 3.9 3.1 - - - +
325B ALA* 1.3 75.1 - - - +
327B SER* 1.3 63.9 + - - +
329B SER* 3.2 7.7 + - - -
330B LEU* 3.1 35.9 + - + +
467B VAL* 4.5 17.7 - - + +
470B PHE* 3.7 35.0 - - + -
471B LEU* 4.6 12.6 - - + -
474B LEU* 6.0 4.9 - - + -
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Residues in contact with SER 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 5.4 4.3 - - - +
187B TYR* 3.7 27.8 + - - +
190B VAL* 5.0 3.5 - - - +
323B THR* 2.9 18.5 + - - -
324B THR* 3.6 7.0 - - - -
326B ILE* 1.3 78.6 - - - +
328B TRP* 1.3 62.2 + - - +
330B LEU* 3.4 10.8 + - - +
331B MET* 3.2 25.6 + - - +
500B HIS* 2.4 36.2 + - - -
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B THR* 2.9 39.2 + - + +
325B ALA* 3.7 4.5 - - - +
327B SER* 1.3 73.0 - - - +
329B SER* 1.3 67.0 + - - +
331B MET* 3.1 9.6 + - + +
332B TYR* 2.9 59.2 + + + -
375B THR* 4.2 13.0 - - + -
379B SER* 4.0 15.0 - - - +
381B PHE* 3.8 14.0 - + + +
490B MET* 3.4 39.0 - - + -
492B PRO* 4.0 22.7 - - + -
498B MET* 3.0 20.9 + - + -
499B LYS* 3.7 21.4 - - - +
500B HIS* 3.9 29.3 - + + -
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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 ALA* 3.0 16.3 + - - +
326B ILE* 3.5 9.5 - - - -
328B TRP* 1.3 76.5 - - - +
330B LEU* 1.3 57.7 + - - +
332B TYR* 3.2 2.2 + - - +
333B LEU* 2.9 34.5 + - - +
371B PHE* 3.6 23.6 - - - -
372B ILE* 5.4 1.2 - - - +
375B THR* 3.7 18.9 + - - +
467B VAL* 4.8 4.2 - - - +
471B LEU* 3.8 27.2 - - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.7 28.7 - - + -
190B VAL* 4.1 19.1 - - + -
326B ILE* 3.1 21.4 + - + +
327B SER* 3.7 7.6 - - - +
328B TRP 3.3 0.2 - - - -
329B SER* 1.3 75.4 - - - +
331B MET* 1.3 63.2 + - - +
333B LEU* 3.3 13.0 + - + +
334B VAL* 3.0 28.8 + - - +
471B LEU* 4.7 11.2 - - + -
474B LEU* 5.1 6.5 - - + -
475B LEU* 5.8 0.2 - - + -
480B PHE* 3.7 42.6 - - + +
506B PHE* 4.0 15.9 - - + -
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Residues in contact with MET 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 5.7 0.9 - - + -
327B SER 3.2 15.9 + - - +
328B TRP* 3.1 11.7 + - + +
330B LEU* 1.3 75.8 - - - +
332B TYR* 1.3 60.1 + - - +
334B VAL* 3.4 2.3 + - - +
335B MET* 3.1 29.1 + - - +
488B VAL* 3.7 26.9 - - + -
489B ASP 4.0 11.9 - - - +
490B MET* 3.7 23.1 - - + -
500B HIS* 3.6 45.1 - - + +
501B ALA 4.5 4.5 - - - +
503B CYS* 4.6 3.1 - - + -
506B PHE* 3.4 36.1 - - + -
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B TRP* 2.9 55.9 + + + -
329B SER 3.2 4.7 + - - +
331B MET* 1.3 74.1 - - - +
333B LEU* 1.3 60.5 + - - +
336B ASN* 2.9 42.8 + - - +
371B PHE* 4.2 4.9 - - + -
375B THR* 4.0 15.5 - - + -
378B HIS* 2.7 41.9 + + + -
379B SER* 3.4 26.4 + - - -
427B PHE* 3.6 45.1 - + + -
490B MET* 3.6 20.6 - - + -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER 2.9 28.1 + - - +
330B LEU* 3.7 19.3 - - + +
332B TYR* 1.3 78.1 - - - +
334B VAL* 1.3 62.8 + - + +
336B ASN 3.2 21.1 - - - +
337B PRO* 3.5 2.3 - - - +
339B VAL* 4.2 2.9 - - + -
340B GLN* 3.6 40.1 + - + +
343B ILE* 3.8 21.1 - - + -
371B PHE* 3.5 28.3 - - + -
471B LEU* 4.8 5.4 - - + -
475B LEU* 4.0 30.3 - - + -
480B PHE* 4.9 3.8 - - + -
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Residues in contact with VAL 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU 3.0 12.7 + - - +
331B MET* 3.9 3.1 - - - +
333B LEU* 1.3 77.5 - - - +
335B MET* 1.3 68.8 + - + +
336B ASN 3.6 0.3 + - - -
337B PRO* 3.8 14.1 - - - +
340B GLN* 5.0 0.2 - - - +
480B PHE* 3.9 12.8 - - + -
481B SER* 3.7 27.6 - - - +
482B VAL* 3.1 42.2 + - + +
488B VAL* 5.8 2.2 - - + -
506B PHE* 3.4 34.3 - - + -
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Residues in contact with MET 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B MET 3.1 19.6 + - - +
334B VAL* 1.3 79.3 - - + +
336B ASN* 1.3 72.5 + - - +
337B PRO* 3.5 6.9 - - - +
482B VAL* 3.8 21.5 - - + -
486B VAL 5.6 0.9 - - - +
488B VAL* 3.5 41.3 - - + +
490B MET* 3.9 29.2 - - + -
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Residues in contact with ASN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B TYR* 2.9 33.4 + - - +
333B LEU 3.2 9.3 - - - +
335B MET* 1.3 92.3 + - - +
337B PRO* 1.3 66.8 - - - +
338B ARG* 3.1 6.0 + - + +
339B VAL* 3.1 35.4 + - + +
340B GLN 3.4 1.2 + - - -
427B PHE* 3.9 31.4 - - + +
490B MET* 5.5 0.2 - - - +
----------------------------------------------------------
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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).
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