Contacts of the helix formed by residues 388 - 418 (chain B) in PDB entry 5A86
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 PHE 388 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B HIS 3.4 1.0 + - - -
387B ARG* 1.3 116.5 - - + +
389B LEU* 1.3 59.1 + - - +
390B PHE 3.3 2.7 - - - -
391B LEU* 3.2 28.2 + - + +
392B LYS* 2.9 38.6 + - + +
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.2 26.7 - - + +
335B LEU* 4.0 21.1 - - + -
339B GLU* 4.0 11.0 - - - +
377B ILE* 4.0 21.2 - - + +
381B ARG* 3.9 33.0 - - - +
386B HIS* 3.2 31.2 + - + +
387B ARG 3.2 3.9 - - - -
388B PHE* 1.3 76.1 - - - +
390B PHE* 1.3 63.6 + - - +
392B LYS* 3.1 10.1 + - + +
393B ILE* 2.9 33.9 + - + +
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ALA* 3.3 34.5 - - + -
373B LEU* 3.9 15.5 - - + -
374B LYS* 3.7 49.1 - - + -
377B ILE* 3.7 22.4 - - + +
388B PHE 3.3 0.8 - - - -
389B LEU* 1.3 76.0 - - - +
391B LEU* 1.3 75.7 + - + +
393B ILE* 3.2 5.8 + - - +
394B MET* 3.0 62.0 + - + +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B PHE* 3.2 31.8 + - + +
390B PHE* 1.3 92.7 - - + +
392B LYS* 1.3 60.8 + - - +
394B MET* 3.4 8.2 + - + +
395B ALA* 3.0 29.6 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU* 4.2 32.1 - - + +
385B ALA 4.6 11.5 + - - -
386B HIS* 5.4 1.0 - - - +
387B ARG 3.6 22.3 + - - -
388B PHE* 2.9 26.5 + - + +
389B LEU* 3.5 11.3 - - - +
391B LEU* 1.3 75.2 - - + +
393B ILE* 1.3 57.5 + - - +
395B ALA* 3.3 7.2 + - - +
396B MET* 2.9 35.9 + - + +
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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
----------------------------------------------------------
333B LEU* 4.4 5.8 - - + -
335B LEU* 3.8 34.3 - - + -
339B GLU* 4.7 4.3 - - + -
343B MET* 3.4 33.5 - - + +
373B LEU* 3.8 23.8 - - + -
377B ILE* 4.0 22.7 - - + -
389B LEU* 2.9 26.0 + - + +
390B PHE* 3.5 7.0 - - - +
392B LYS* 1.3 74.6 - - - +
394B MET* 1.3 62.8 + - - +
396B MET* 3.1 10.3 + - - +
397B LEU* 3.0 26.8 + - + +
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Residues in contact with MET 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 4.0 31.2 - - + -
366B GLN* 6.1 2.2 - - + -
370B ALA* 4.2 19.3 - - + -
373B LEU* 4.7 3.4 - - - -
390B PHE* 3.0 52.2 + - + +
391B LEU* 3.8 9.9 - - + +
393B ILE* 1.3 74.7 - - - +
395B ALA* 1.3 62.0 + - - +
397B LEU* 3.3 15.7 + - + +
398B THR* 3.2 24.4 + - - -
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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
----------------------------------------------------------
391B LEU 3.0 18.1 + - - +
392B LYS* 3.5 7.6 - - - +
394B MET* 1.3 75.2 - - - +
396B MET* 1.3 63.1 + - + +
398B THR* 3.2 9.5 + - - -
399B GLU* 3.1 21.3 + - - +
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Residues in contact with MET 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B PHE* 3.3 54.2 - - + +
329B MET* 3.9 38.6 - - + -
330B LEU* 4.1 23.8 - - + -
333B LEU* 4.3 13.5 - - + -
343B MET* 4.9 6.3 - - + -
392B LYS* 2.9 23.0 + - + +
393B ILE* 3.1 10.0 + - - +
395B ALA* 1.3 77.3 - - + +
397B LEU* 1.3 56.8 + - - +
399B GLU* 3.2 8.4 + - + +
400B LEU 2.8 25.1 + - - -
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 4.9 3.3 - - - +
286B LEU* 4.4 10.5 - - + -
343B MET* 3.7 48.2 - - + +
346B ILE* 3.8 37.0 - - + -
347B SER* 4.5 10.5 - - - -
393B ILE* 3.0 18.2 + - + +
394B MET* 3.6 21.8 - - + +
395B ALA 3.3 0.2 - - - -
396B MET* 1.3 72.7 - - - +
398B THR* 1.3 64.2 + - - +
400B LEU* 3.4 13.1 + - + +
401B ARG* 3.1 22.2 + - - +
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Residues in contact with THR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B MET 3.2 12.9 + - - -
395B ALA* 3.2 12.3 + - - -
397B LEU* 1.3 75.6 - - - +
399B GLU* 1.3 62.9 + - - +
401B ARG* 3.2 16.9 + - + +
402B SER* 3.3 12.0 + - - -
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 4.3 9.9 - - - +
326B PHE* 4.6 7.6 - - + -
395B ALA 3.1 13.2 + - - +
396B MET* 3.5 14.6 - - + +
398B THR* 1.3 74.5 - - - +
400B LEU* 1.3 59.2 + - - +
402B SER* 2.9 17.1 + - - -
403B ILE* 2.9 56.4 + - + +
406B GLN* 5.6 0.9 - - - +
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Residues in contact with LEU 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 4.4 7.9 - - + -
282B GLU* 3.7 40.4 - - + +
285B GLN* 4.4 8.1 - - + -
286B LEU* 4.0 17.7 - - + -
323B MET* 4.2 22.4 - - + -
326B PHE* 3.8 34.9 - - + -
396B MET 2.8 19.8 + - - +
397B LEU* 3.6 14.4 - - + +
398B THR 3.3 0.2 - - - -
399B GLU* 1.3 72.8 - - - +
401B ARG* 1.3 56.3 + - - +
403B ILE* 3.3 5.1 + - + -
404B ASN* 2.9 28.8 + - - +
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Residues in contact with ARG 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU* 3.5 21.0 + - - +
350B SER* 5.2 2.9 - - - -
352B ASP* 2.7 66.6 + - - +
353B ARG* 3.3 31.5 - - - +
354B PRO* 4.9 2.8 - - - +
397B LEU 3.1 13.2 + - - +
398B THR* 3.5 12.3 - - + +
399B GLU 3.2 0.4 - - - -
400B LEU* 1.3 75.3 - - - +
402B SER* 1.4 60.9 + - - +
404B ASN* 3.4 3.9 + - + +
405B ALA* 3.3 20.1 + - - +
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Residues in contact with SER 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B THR 3.3 10.0 + - - -
399B GLU* 2.9 23.6 + - - -
401B ARG* 1.4 72.6 - - - +
403B ILE* 1.3 65.9 + - - +
405B ALA* 3.4 8.3 + - - +
406B GLN* 3.2 30.1 + - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 4.2 6.5 - - + -
322B PRO* 3.7 33.2 - - + +
323B MET* 3.5 35.9 - - + +
326B PHE* 4.0 21.3 - - + -
399B GLU* 2.9 43.1 + - + +
400B LEU* 3.7 7.9 - - - +
402B SER* 1.3 74.8 - - - +
404B ASN* 1.3 54.3 + - - +
406B GLN* 3.2 11.6 + - + +
407B HIS* 2.8 35.2 + - + +
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Residues in contact with ASN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LYS 5.3 1.0 + - - -
278B GLY* 3.0 28.1 + - - -
281B PHE* 3.3 40.6 - - + +
282B GLU* 3.0 19.3 + - + +
353B ARG* 4.3 1.4 - - - +
400B LEU 2.9 17.7 + - - +
401B ARG* 3.4 7.4 - - - +
402B SER 3.3 0.2 - - - -
403B ILE* 1.3 75.7 - - - +
405B ALA* 1.3 56.8 + - - +
407B HIS* 3.3 1.2 + - - +
408B THR* 2.8 45.0 + - - -
429B PHE* 4.9 2.3 - - - -
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B ARG 3.3 9.3 + - - +
402B SER* 3.6 11.0 - - - +
403B ILE 3.3 0.2 - - - -
404B ASN* 1.3 79.1 - - - +
406B GLN* 1.3 61.1 + - - +
408B THR* 3.4 7.1 + - - -
409B GLN* 3.2 28.2 + - - +
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B PRO* 4.5 24.5 - - - +
399B GLU* 5.6 0.5 - - - +
402B SER* 3.2 21.6 + - - +
403B ILE* 3.4 16.3 - - + +
405B ALA* 1.3 76.2 - - - +
407B HIS* 1.3 64.5 + - - +
409B GLN* 3.3 9.3 + - - +
410B ARG* 3.2 40.5 + - - +
413B ARG* 5.2 0.7 + - - -
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Residues in contact with HIS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B MET* 5.1 12.5 - - + +
281B PHE* 3.3 38.7 - + + -
403B ILE* 2.8 20.9 + - + +
404B ASN 3.9 1.8 - - - +
406B GLN* 1.3 70.6 - - - +
408B THR* 1.3 64.5 + - - +
410B ARG* 3.1 21.4 + - + +
411B LEU* 2.9 39.0 + - + +
429B PHE* 5.7 5.7 - + - -
1432B D7E 3.5 39.2 - - + +
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Residues in contact with THR 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B ASN* 2.8 34.6 + - - -
405B ALA* 3.7 8.5 - - - -
406B GLN 3.3 0.2 - - - -
407B HIS* 1.3 79.9 - - - +
409B GLN* 1.4 60.0 + - - +
411B LEU* 3.2 8.5 + - - +
412B LEU* 3.1 37.7 + - + +
429B PHE* 4.0 40.5 - - + +
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Residues in contact with GLN 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ALA 3.2 19.1 + - - +
406B GLN* 3.6 10.5 - - - +
407B HIS 3.3 0.4 - - - -
408B THR* 1.4 76.3 - - - +
410B ARG* 1.4 62.7 + - - +
412B LEU* 3.7 20.5 + - - +
413B ARG* 3.2 47.4 + - - +
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LYS 4.6 1.1 + - - -
205B ASP* 3.1 58.4 + - + +
207B CYS 4.4 2.8 + - - -
208B SER 5.0 0.4 - - - +
209B LEU* 5.9 2.0 - - - +
321B GLU* 2.7 41.0 + - - -
322B PRO* 4.8 3.2 - - - +
406B GLN* 3.2 32.9 + - - +
407B HIS* 3.1 23.3 + - + +
409B GLN* 1.4 72.4 - - - +
411B LEU* 1.4 61.3 + - - +
413B ARG* 3.3 15.6 + - - +
414B ILE* 2.9 39.5 + - + +
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B MET* 5.3 3.8 - - + -
407B HIS* 2.9 26.1 + - + +
408B THR* 3.2 11.0 + - - +
410B ARG* 1.4 76.3 - - - +
412B LEU* 1.3 53.8 + - + +
414B ILE* 3.3 7.6 + - - +
415B GLN* 2.8 36.4 + - + +
420B PHE* 3.6 29.4 - - + -
421B ALA* 4.8 2.0 - - + -
425B MET* 4.1 15.5 - - + -
429B PHE* 3.4 50.0 - - + -
431B ILE* 4.1 18.4 - - + -
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B THR* 3.1 20.7 + - + +
409B GLN* 4.0 25.6 - - - +
410B ARG 3.4 0.2 - - - -
411B LEU* 1.3 76.0 - - + +
413B ARG* 1.3 54.9 + - + +
415B GLN* 3.3 4.6 + - + +
416B ASP* 2.8 35.7 + - - +
429B PHE* 3.9 17.5 - - + +
430B GLY 4.6 5.6 - - - +
431B ILE* 3.5 33.7 - - + -
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 5.7 2.0 - - - +
201B GLN* 3.4 27.3 + - - +
202B VAL* 3.8 14.8 - - + +
205B ASP* 2.9 44.8 + - - +
406B GLN 5.2 0.2 + - - -
409B GLN* 3.2 40.5 + - - +
410B ARG* 3.3 20.6 + - - +
412B LEU* 1.3 78.6 - - + +
414B ILE* 1.3 61.6 + - - +
416B ASP* 3.3 19.7 - - - +
417B ILE* 3.4 6.9 + - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 4.0 19.3 - - + -
205B ASP* 4.8 6.5 - - + +
206B LEU* 3.5 28.9 - - + -
209B LEU* 5.7 0.9 - - + -
237B PHE* 4.1 13.9 - - + -
240B LEU* 3.6 32.8 - - + -
410B ARG* 2.9 32.6 + - + +
411B LEU* 3.8 6.3 - - - +
413B ARG* 1.3 71.7 - - + +
415B GLN* 1.3 55.2 + - - +
417B ILE* 3.1 3.4 + - - +
418B HIS 2.6 35.6 + - - +
420B PHE* 3.7 15.9 - - + -
----------------------------------------------------------
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 2.8 22.2 + - + +
412B LEU* 3.5 9.2 - - + +
414B ILE* 1.3 71.5 - - - +
416B ASP* 1.3 63.3 + - - +
418B HIS 3.8 4.7 - - - -
419B PRO* 3.2 49.2 - - - +
420B PHE* 3.0 14.4 + - + +
421B ALA* 3.0 40.8 + - - +
426B GLN* 5.0 5.1 - - - +
431B ILE* 3.8 36.1 - - + +
----------------------------------------------------------
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Residues in contact with ASP 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 2.8 39.8 + - - +
412B LEU 2.8 14.3 + - - +
413B ARG* 3.3 14.8 - - - +
414B ILE 3.2 0.2 - - - -
415B GLN* 1.3 76.5 - - - +
417B ILE* 1.3 60.0 + - + +
419B PRO* 4.8 3.1 - - - +
----------------------------------------------------------
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 3.8 22.0 - - - +
198B LYS* 4.1 24.5 - - + +
199B TRP* 3.7 43.6 - - + +
202B VAL* 3.7 38.8 - - + -
237B PHE* 3.9 9.4 - - + -
413B ARG 3.4 6.2 + - - +
414B ILE* 3.1 10.6 + - - +
416B ASP* 1.3 84.3 - - - +
418B HIS* 1.3 64.0 + - + +
419B PRO* 3.8 6.6 - - - +
----------------------------------------------------------
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Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LYS* 3.5 34.4 + - + +
237B PHE* 3.4 57.3 + + + +
240B LEU* 4.2 9.8 - - + +
241B PRO* 5.8 4.6 - - - +
414B ILE* 2.6 21.5 + - + +
417B ILE* 1.3 74.5 + - - +
419B PRO* 1.4 78.8 + - + +
420B PHE* 3.3 18.9 - - + +
----------------------------------------------------------
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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