Contacts of the helix formed by residues 386 - 421 (chain B) in PDB entry 4CZ8
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 386 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ALA* 4.5 3.9 - - - +
382B SER 5.0 0.4 - - - -
383B PRO 4.0 13.2 - - - +
385B LEU* 1.3 78.5 - - - +
387B VAL* 1.3 58.9 + - - +
388B HIS* 3.8 8.3 + - - +
389B TRP* 3.1 53.9 + - + +
390B GLY* 2.9 24.1 + - - -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.8 12.7 - - + +
377B ALA* 4.3 22.1 - - + +
378B LEU* 3.7 34.1 - - + -
385B LEU 4.1 0.4 + - - -
386B THR* 1.3 72.6 - - - +
388B HIS* 1.3 58.7 + - - +
390B GLY* 3.0 2.8 + - - -
391B GLU* 2.9 35.3 + - + +
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Residues in contact with HIS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B VAL* 5.4 12.5 - - + +
321B ASN* 5.8 2.0 + - - -
386B THR* 3.2 8.2 + - - +
387B VAL* 1.3 79.5 - - - +
389B TRP* 1.3 64.2 + + - +
391B GLU* 3.1 14.8 + - - +
392B ILE* 2.9 48.6 + - + +
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Residues in contact with TRP 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 6.0 0.2 - + - -
112B PHE* 4.8 10.0 + - + +
113B ASN 5.3 2.9 - - - -
114B SER* 4.7 19.7 - - - -
115B SER* 5.7 2.7 - - - -
118B LEU* 3.5 37.6 - - + +
383B PRO 5.6 0.2 - - - -
384B LEU 3.9 17.5 - - - -
385B LEU* 5.6 1.6 - - + -
386B THR* 3.1 48.4 + - + +
388B HIS* 1.3 83.1 - + - +
390B GLY* 1.3 59.8 + - - +
392B ILE* 3.4 21.2 - - + +
393B ILE* 2.9 33.9 + - - +
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PRO* 4.8 8.1 - - - +
374B LEU* 4.3 27.2 - - - +
377B ALA* 5.6 0.2 - - - -
386B THR 2.9 13.9 + - - -
387B VAL* 3.0 6.0 + - - -
389B TRP* 1.3 74.3 - - - +
391B GLU* 1.3 58.6 + - - +
393B ILE* 3.3 7.9 + - - +
394B MSE 2.9 30.5 + - - +
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Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 2.6 37.3 + - - -
314B ASN* 4.2 11.2 + - - +
317B VAL* 3.8 28.4 - - + +
374B LEU* 3.3 18.0 - - + +
387B VAL* 2.9 27.8 + - + +
388B HIS* 3.1 13.9 + - - +
390B GLY* 1.3 75.0 - - - +
392B ILE* 1.3 57.9 + - - +
394B MSE 3.5 8.0 + - - +
395B ALA* 2.9 31.7 + - - +
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.6 24.9 - - + -
112B PHE* 3.7 29.2 - - + -
317B VAL* 4.5 5.2 - - + -
321B ASN* 3.6 36.1 - - + +
388B HIS* 2.9 36.3 + - + +
389B TRP* 3.4 24.2 - - + +
390B GLY 3.2 0.2 - - - -
391B GLU* 1.3 74.0 - - - +
393B ILE* 1.3 67.1 + - - +
395B ALA* 3.6 3.7 - - - +
396B THR* 2.9 28.1 + - - +
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.5 23.3 - - + -
118B LEU* 3.6 23.8 - - + +
121B LEU* 5.1 4.5 - - + -
122B PHE* 3.6 25.6 - - + +
125B ILE* 3.7 19.5 - - + -
370B ALA 4.3 1.1 - - - +
373B PRO* 3.6 28.0 - - + -
389B TRP 2.9 19.3 + - - +
390B GLY* 3.5 9.6 - - - +
392B ILE* 1.3 74.8 - - - +
394B MSE 1.3 62.9 + - - +
396B THR* 2.4 22.6 + - - -
397B VAL* 2.9 19.7 + - + +
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Residues in contact with MSE 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 4.4 10.5 - - - -
309B LEU* 3.9 14.4 - - + +
312B GLU* 3.3 16.6 - - + +
313B MSE 3.4 34.5 - - + +
314B ASN 5.4 0.7 - - - -
370B ALA* 3.8 23.5 - - + +
371B SER* 3.3 27.1 - - - +
374B LEU* 4.1 24.5 - - + -
390B GLY 2.9 17.2 + - - +
391B GLU* 3.8 7.6 - - - +
393B ILE* 1.3 78.2 - - - +
395B ALA* 1.3 64.2 + - - +
397B VAL* 3.3 3.6 + - - +
398B VAL* 2.9 32.7 + - + +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B MSE 6.3 0.2 - - - -
317B VAL* 4.4 9.0 - - + +
318B ILE* 3.6 38.8 - - + -
321B ASN* 5.7 5.2 - - + -
391B GLU 2.9 19.2 + - - +
392B ILE* 3.6 4.5 - - - +
394B MSE 1.3 76.9 - - - +
396B THR* 1.3 64.1 + - + +
398B VAL* 3.2 8.2 + - - +
399B ILE* 2.9 28.4 + - + +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B PHE* 3.6 20.9 - - + -
112B PHE* 3.8 25.8 - - + -
122B PHE* 3.2 23.1 - - - -
321B ASN* 6.2 0.4 - - + -
325B GLY* 4.2 13.6 - - - +
328B VAL* 5.1 2.7 - - + -
392B ILE 2.9 17.5 + - - +
393B ILE* 2.4 31.2 + - - -
395B ALA* 1.3 75.0 - - + +
397B VAL* 1.3 62.0 + - - +
399B ILE* 3.0 9.8 + - - +
400B THR* 2.9 26.8 + - - +
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Residues in contact with VAL 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 3.6 21.1 - - + -
125B ILE* 3.8 18.2 - - + -
126B ILE* 4.6 3.4 - - + -
309B LEU* 6.0 0.4 - - + -
366B PRO* 3.6 39.0 - - + +
367B SER* 4.5 0.9 - - - +
370B ALA* 3.6 13.5 - - + -
393B ILE* 2.9 25.4 + - + +
394B MSE 3.6 4.3 - - - +
396B THR* 1.3 80.7 + - - +
398B VAL* 1.3 63.5 + - - +
400B THR* 3.2 7.8 - - - +
401B VAL* 2.9 34.3 + - + +
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 5.2 1.1 - - + -
309B LEU* 4.1 31.6 - - + -
313B MSE 3.6 43.3 - - + -
318B ILE* 5.8 3.4 - - + -
370B ALA* 5.3 0.7 - - + -
394B MSE 2.9 26.3 + - + +
395B ALA* 3.4 10.5 - - - +
397B VAL* 1.3 75.2 - - - +
399B ILE* 1.3 70.4 + - + +
401B VAL* 3.2 6.6 + - - +
402B LEU* 2.9 39.8 + - + +
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Residues in contact with ILE 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.9 25.8 - - + +
321B ASN 5.6 1.8 - - - +
322B LEU* 4.9 14.1 - - + +
325B GLY* 3.7 25.8 - - - +
326B LEU* 3.7 20.2 - - + +
329B ALA* 4.2 1.3 - - + -
395B ALA* 2.9 23.4 + - + +
396B THR* 3.0 8.5 + - - +
398B VAL* 1.3 84.7 - - + +
400B THR* 1.3 53.3 + - - +
402B LEU* 3.4 6.5 + - + +
403B THR* 2.7 51.0 + - + +
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Residues in contact with THR 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE* 4.0 10.8 - - + -
126B ILE* 3.5 30.1 - - + +
325B GLY 5.4 0.2 - - - -
328B VAL* 6.1 0.2 - - - -
329B ALA* 3.5 20.7 + - - +
332B VAL* 3.9 17.4 - - - +
333B MSE 5.0 0.9 - - - +
362B ARG* 4.3 5.0 - - - +
396B THR 2.9 19.7 + - - +
397B VAL* 3.2 14.6 - - - +
399B ILE* 1.3 74.3 - - - +
401B VAL* 1.3 56.5 + - - +
403B THR* 3.2 7.8 + - - -
404B SER* 2.9 32.9 + - - -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 4.2 21.3 - - + -
36B ILE* 5.8 1.8 - - + -
126B ILE* 4.6 1.3 - - + -
306B PHE* 4.5 2.2 - - + -
309B LEU* 5.6 4.3 - - + -
362B ARG* 3.7 28.2 - - + +
363B GLY 4.0 9.2 - - - +
366B PRO* 4.5 4.9 - - + -
367B SER* 3.7 25.6 - - - +
397B VAL* 2.9 36.2 + - + +
398B VAL* 3.5 6.5 - - - +
400B THR* 1.3 77.2 - - - +
402B LEU* 1.3 67.0 + - + +
405B VAL* 2.9 29.8 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B VAL* 4.3 6.1 - - + -
33B PRO* 3.7 39.2 - - + +
36B ILE* 4.0 32.8 - - + -
313B MSE 5.6 0.9 - - + -
398B VAL* 2.9 30.2 + - + +
399B ILE* 3.9 7.0 - - + +
401B VAL* 1.3 76.8 - - + +
403B THR* 1.3 60.6 + - + +
405B VAL* 3.7 4.0 - - + +
406B ILE* 2.9 34.6 + - - +
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Residues in contact with THR 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.7 28.7 - - + -
329B ALA* 3.4 10.4 - - - +
330B LEU* 4.7 5.8 - - + -
333B MSE 4.0 9.1 - - - -
399B ILE* 2.7 31.4 + - + +
400B THR* 3.2 11.8 + - - -
402B LEU* 1.3 71.9 - - + +
404B SER* 1.3 67.7 + - - +
406B ILE* 3.9 8.1 - - + -
407B VAL* 2.9 33.6 + - - +
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Residues in contact with SER 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MSE 3.6 30.0 - - - +
360B GLY 4.2 2.6 + - - -
361B PRO* 3.1 22.4 - - - +
362B ARG* 3.5 18.3 + - - +
400B THR* 2.9 24.6 + - - -
401B VAL 3.9 0.4 - - - -
403B THR* 1.3 76.0 + - - +
405B VAL* 1.3 65.0 + - - +
407B VAL* 4.0 0.2 - - - +
408B GLU* 2.9 34.2 + - - +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 3.8 25.6 - - - +
32B VAL* 4.1 33.7 - - + -
33B PRO* 4.5 5.6 - - + -
130B ASP 5.9 0.4 - - - +
133B THR* 4.6 12.3 - - + +
134B LEU* 5.4 0.2 - - - +
361B PRO* 4.1 10.1 - - + +
362B ARG 3.1 24.7 - - - +
363B GLY* 4.8 1.3 - - - -
401B VAL* 2.9 17.2 + - + +
402B LEU* 3.7 4.0 - - + +
404B SER* 1.3 77.0 - - - +
406B ILE* 1.3 57.9 + - - +
408B GLU* 3.9 0.7 - - - +
409B THR* 2.5 43.2 + - - +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 5.9 5.6 - - + -
30B SER* 5.9 4.0 - - - -
33B PRO* 5.2 18.2 - - + -
402B LEU 2.9 25.6 + - - +
403B THR* 3.4 12.8 - - + +
405B VAL* 1.3 76.9 - - + +
407B VAL* 1.3 65.9 + - + +
409B THR* 3.8 6.2 - - + -
410B LEU* 2.9 56.5 + - + +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 5.9 4.3 - - + -
333B MSE 3.6 26.2 - - + -
403B THR* 2.9 27.8 + - - +
406B ILE* 1.3 78.3 - - + +
408B GLU* 1.3 61.8 + - - +
410B LEU* 3.9 3.0 - - - +
411B TRP* 2.9 60.7 + - + +
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Residues in contact with GLU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.0 7.6 - - + -
333B MSE 4.0 17.7 - - - +
358B LEU 2.8 27.5 - - - +
359B GLU* 3.0 34.7 - - - +
360B GLY 4.4 2.0 - - - +
361B PRO* 3.6 13.9 - - + -
404B SER* 2.9 28.7 + - - +
405B VAL 3.9 2.7 - - - +
407B VAL* 1.3 75.8 - - - +
409B THR* 1.3 62.3 + - - +
411B TRP* 2.4 41.6 + - - -
412B ILE* 3.0 29.3 + - - +
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Residues in contact with THR 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 4.6 19.1 - - - +
133B THR* 4.6 14.5 + - - +
134B LEU* 4.5 12.4 - - - +
137B LEU* 4.8 17.3 - - + +
405B VAL* 2.5 34.5 + - - +
406B ILE* 3.8 8.7 - - + -
408B GLU* 1.3 75.9 - - - +
410B LEU* 1.3 66.9 + - + +
412B ILE* 3.2 18.5 - - - +
413B PRO* 4.3 3.1 - - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ILE* 2.9 44.9 + - + +
407B VAL* 4.1 3.4 - - - +
409B THR* 1.3 86.9 - - + +
411B TRP* 1.3 59.3 + - - +
412B ILE 3.4 0.9 - - - -
413B PRO* 3.2 16.0 - - - +
414B ILE* 5.0 2.3 - - - +
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Residues in contact with TRP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MSE 5.3 5.2 - - + -
334B ILE* 4.4 24.7 - - + -
358B LEU* 3.5 35.0 - - + -
359B GLU* 3.3 11.3 + - - -
407B VAL* 2.9 34.1 + - + +
408B GLU* 2.4 60.7 + - - -
410B LEU* 1.3 75.6 - - - +
412B ILE* 1.3 66.4 + - - +
413B PRO* 3.4 2.2 - - - -
414B ILE* 3.3 18.3 - - + +
415B LEU* 3.3 36.2 + - + +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.7 4.5 - - + +
137B LEU* 3.6 31.9 - - + +
138B PHE* 3.5 38.8 - - + -
141B TYR* 4.9 4.7 - - + -
143B VAL* 5.3 3.6 - - + -
355B PHE* 4.7 9.4 - - + -
359B GLU* 3.9 16.6 - - - +
408B GLU 3.0 19.5 + - - +
409B THR* 3.2 22.0 - - - +
411B TRP* 1.3 78.9 - - - +
413B PRO* 1.4 73.0 - - + +
415B LEU* 3.3 5.5 + - - +
416B LYS* 3.2 19.3 + - + +
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Residues in contact with PRO 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 5.3 2.0 - - + -
141B TYR* 3.5 42.2 - - + +
409B THR 4.3 2.0 - - - +
410B LEU 3.2 20.0 - - - +
411B TRP 3.4 1.6 - - - -
412B ILE* 1.4 103.2 - - + +
414B ILE* 1.3 66.1 + - + +
416B LYS* 3.1 21.8 + - + +
417B ASP* 3.5 5.5 + - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU 5.0 1.6 - - - +
411B TRP* 3.3 28.7 - - + +
413B PRO* 1.3 81.5 - - + +
415B LEU* 1.3 87.5 + - + +
417B ASP* 3.2 19.5 + - + +
418B LYS* 3.3 12.8 + - - +
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 4.2 19.1 - - + -
358B LEU* 4.4 27.4 - - + -
359B GLU* 4.3 7.0 - - - +
411B TRP* 3.3 44.0 - - + +
412B ILE* 3.3 6.9 + - - +
413B PRO 3.1 0.8 - - - -
414B ILE* 1.3 88.9 - - + +
416B LYS* 1.3 63.8 + - - +
418B LYS* 3.6 12.4 + - + -
419B LEU* 3.3 39.1 + - + +
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B TYR* 3.8 42.6 - - + +
142B ARG 5.6 0.2 - - - +
143B VAL* 4.9 15.0 - - + -
355B PHE* 4.6 9.6 - - + -
412B ILE* 3.2 10.9 + - + +
413B PRO* 3.1 13.9 + - + +
415B LEU* 1.3 75.8 - - - +
417B ASP* 1.3 73.7 + - - +
419B LEU* 3.0 2.8 + - - +
420B ASP* 2.6 67.9 + - - +
421B VAL* 5.6 3.2 - - - +
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B PRO 3.5 5.1 + - - +
414B ILE* 3.2 16.7 + - + +
416B LYS* 1.3 91.5 + - - +
418B LYS* 1.3 60.1 + - - +
421B VAL* 3.3 39.2 + - - +
422B GLY 4.0 1.4 + - - -
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ILE 3.3 11.2 + - - +
415B LEU* 3.6 14.3 + - + +
416B LYS 3.1 0.4 - - - -
417B ASP* 1.3 80.5 - - - +
419B LEU* 1.3 67.8 + - + +
422B GLY* 3.9 24.4 - - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 5.3 6.8 + - - -
350B PHE* 6.4 0.4 - - + -
351B ARG* 3.4 48.4 - - + +
354B LEU* 5.2 13.5 - - + -
355B PHE* 3.5 48.2 - - + +
358B LEU* 5.9 0.9 - - + -
415B LEU* 3.3 25.5 + - + +
416B LYS* 3.0 3.2 + - - +
418B LYS* 1.3 89.2 - - + +
420B ASP* 1.3 67.5 + - - +
422B GLY* 4.6 2.4 - - - -
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Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG 5.0 6.6 - - - +
143B VAL* 5.0 10.6 - - - +
144B LYS* 4.8 18.2 - - - +
416B LYS* 2.6 50.7 + - + +
419B LEU* 1.3 81.6 - - - +
421B VAL* 1.3 69.2 + - + +
422B GLY* 3.4 0.4 - - - -
----------------------------------------------------------
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Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LYS* 5.6 3.1 - - - +
417B ASP* 3.3 34.6 + - - +
420B ASP* 1.3 81.7 - - + +
422B GLY* 1.3 63.3 + - - +
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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