Contacts of the helix formed by residues 392 - 413 (chain B) in PDB entry 1IAS
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 HIS 392 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B ASN* 3.2 21.0 + - - +
390B MET 4.8 1.3 - - - -
391B LYS* 1.3 113.6 + - - +
393B PHE* 1.3 66.5 + - - +
394B GLU* 3.0 8.7 - - + +
395B SER* 2.8 35.2 + - - +
396B PHE* 4.3 3.5 + - - -
398B ARG* 6.4 0.4 - - - +
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Residues in contact with PHE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ALA* 3.4 41.3 - - + -
329B ILE 3.8 1.3 - - - -
330B ALA* 3.7 21.8 - - + -
356B VAL* 3.6 32.5 - - + -
357B ARG 4.2 0.2 - - - -
358B HIS* 3.4 50.5 - + + +
365B ILE* 3.9 14.6 - - + +
391B LYS 3.8 4.2 + - - -
392B HIS* 1.3 70.5 - - - +
394B GLU* 1.3 65.3 + - + +
396B PHE* 3.0 34.2 + + - +
397B LYS* 3.5 26.7 + - + -
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Residues in contact with GLU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B HIS* 3.0 8.4 + - + +
393B PHE* 1.3 80.7 - - - +
395B SER* 1.3 63.0 + - - +
397B LYS* 3.0 46.1 + - - +
398B ARG* 3.0 61.5 + - - +
484B THR* 6.0 2.4 - - - +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 4.2 4.0 - - - +
388B ILE* 3.6 27.6 - - - +
389B ASN* 2.6 31.8 + - - +
392B HIS* 2.8 17.3 + - - +
394B GLU* 1.3 77.9 - - - +
396B PHE* 1.3 58.6 + - - +
398B ARG* 3.4 15.6 + - - +
399B ALA* 3.1 26.0 + - - +
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 3.4 21.5 - - + -
332B ARG* 3.7 30.4 - - + +
356B VAL* 4.2 12.8 - - + -
365B ILE* 3.9 25.1 - - + -
367B ILE* 5.8 7.2 - - + -
388B ILE* 4.6 8.5 - - + -
390B MET* 3.5 57.9 - - + -
392B HIS 4.3 3.4 - - - -
393B PHE* 3.0 33.3 + + - +
395B SER* 1.3 72.1 - - - +
397B LYS* 1.3 65.6 + - - +
398B ARG 3.1 1.6 - - - -
399B ALA* 3.2 8.8 + - + +
400B ASP* 3.1 25.3 + - - +
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Residues in contact with LYS 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B HIS* 3.4 68.8 + - + +
318B MET* 5.5 0.4 - - - +
319B GLU* 6.3 0.4 - - - +
328B ALA* 4.3 2.5 - - - +
330B ALA* 4.3 0.9 - - + +
393B PHE* 3.5 34.7 + - + +
394B GLU* 3.0 39.4 + - - +
396B PHE* 1.3 77.5 - - - +
398B ARG* 1.3 62.6 - - + +
400B ASP* 3.1 17.7 + - - +
401B ILE* 3.2 10.4 + - + +
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Residues in contact with ARG 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B GLU* 4.6 1.6 - - - +
392B HIS* 6.4 0.2 - - - +
394B GLU* 3.0 46.8 + - - +
395B SER* 3.5 15.2 + - - +
397B LYS* 1.3 74.4 - - + +
399B ALA* 1.3 64.9 + - - +
401B ILE* 3.1 19.7 + - + +
402B TYR 3.2 9.4 + - - -
479B GLY* 3.5 24.0 - - - +
480B ALA* 3.4 35.9 + - - +
482B ARG* 3.2 24.3 + - + +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 6.5 1.1 - - - -
378B TYR 5.2 0.5 - - - +
380B ALA* 3.9 28.8 + - + +
382B GLU* 4.2 2.7 + - - +
383B VAL* 4.2 15.9 - - + -
388B ILE* 5.1 2.2 - - + -
395B SER 3.1 13.7 + - - +
396B PHE* 3.2 11.4 + - + +
398B ARG* 1.3 76.0 - - - +
400B ASP* 1.3 63.3 + - - +
402B TYR* 3.4 4.9 + - - +
403B ALA* 3.3 20.8 + - - +
482B ARG* 3.9 2.0 - - - +
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.1 9.2 - - + -
317B HIS* 2.8 26.8 + - + +
330B ALA* 3.4 4.9 - - - +
331B HIS* 2.8 33.8 + - - +
332B ARG* 2.9 26.4 + - - -
333B ASP 4.4 1.6 + - - -
334B LEU* 3.9 9.8 + - + +
396B PHE 3.1 13.2 + - - +
397B LYS 3.2 11.0 - - - +
399B ALA* 1.3 78.6 - - - +
401B ILE* 1.3 57.8 + - - +
403B ALA* 3.3 7.4 + - - +
404B MET* 2.9 27.5 + - - +
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 3.8 20.9 - - + -
317B HIS* 4.3 3.1 - - + +
397B LYS* 3.4 15.9 - - + +
398B ARG* 3.1 10.4 + - - +
400B ASP* 1.3 72.5 - - - +
402B TYR* 1.3 67.7 + - - +
404B MET* 2.9 6.8 + - - +
405B GLY* 2.8 21.0 + - - -
474B CYS* 3.4 32.7 - - + -
482B ARG* 4.4 6.7 - - + -
483B LEU 3.5 23.6 - - - +
484B THR* 4.2 1.3 - - - -
485B ALA* 3.6 31.2 - - + +
488B ILE* 4.3 7.9 - - + -
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Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B TYR 3.3 13.9 - - - -
379B MET 3.3 23.8 + - - -
380B ALA* 3.4 18.2 - - + -
381B PRO* 3.9 22.0 - - + -
398B ARG 3.2 3.0 + - - -
399B ALA 3.6 7.0 - - - +
400B ASP 3.4 0.2 - - - -
401B ILE* 1.3 78.5 - - - +
403B ALA* 1.3 65.6 + - - +
405B GLY* 3.2 9.9 + - - -
406B LEU* 3.2 26.9 + - + +
428B TYR* 2.6 39.7 + - - -
445B VAL* 3.9 6.6 - - + +
451B ARG* 4.4 9.6 - - - -
474B CYS 3.5 19.4 + - - +
475B TRP* 3.7 25.8 + + - -
482B ARG* 4.0 18.4 - - - +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 3.9 29.6 - - + +
378B TYR* 3.9 21.3 - - + +
399B ALA 3.3 7.4 + - - +
400B ASP* 3.3 8.9 + - - +
401B ILE 3.2 0.6 - - - -
402B TYR* 1.3 79.2 - - - +
404B MET* 1.3 68.2 + - - +
405B GLY 2.9 2.0 - - - -
406B LEU* 2.9 20.6 + - - +
407B VAL* 3.0 15.4 + - - +
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Residues in contact with MET 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.1 48.7 - - + +
310B ALA* 3.3 16.2 - - - +
313B LEU* 3.4 33.2 - - + -
334B LEU* 4.2 8.5 - - + +
400B ASP 2.9 15.3 + - - +
401B ILE* 2.9 11.2 + - + +
403B ALA* 1.3 76.4 - - - +
405B GLY* 1.3 58.1 + - - +
407B VAL* 3.3 9.7 + - + +
408B PHE* 3.0 51.0 + - + -
474B CYS* 5.3 1.1 - - - -
485B ALA* 5.7 2.0 - - - -
488B ILE* 4.6 15.5 - - + -
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ILE 2.8 12.8 + - - -
402B TYR 3.6 4.9 - - - -
403B ALA 2.9 0.6 - - - -
404B MET* 1.3 75.5 - - - +
406B LEU* 1.3 64.6 + - - +
408B PHE* 3.1 10.7 + - - +
409B TRP* 3.0 21.1 + - - +
471B MET* 4.2 5.3 - - - +
474B CYS* 4.1 17.9 - - - -
475B TRP* 3.5 16.8 - - - -
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ARG 4.0 6.1 - - - +
378B TYR* 3.8 32.3 - - + +
402B TYR* 3.2 38.2 + - + +
403B ALA* 2.9 7.2 + - - +
405B GLY* 1.3 75.7 - - - +
407B VAL* 1.3 62.4 + - - +
409B TRP* 3.2 9.2 - - - +
410B GLU* 3.1 26.3 + - - +
427B PRO* 3.7 19.8 - - + +
428B TYR* 4.1 9.0 - - + +
452B PRO* 3.8 22.9 - - + -
475B TRP* 3.3 28.0 - - + +
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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
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288B LEU* 3.7 30.7 - - + -
309B THR* 5.2 3.6 - - + -
334B LEU* 5.0 1.6 - - + -
335B LYS* 3.9 15.0 - - - +
336B SER* 3.9 22.9 - - - +
339B ILE* 4.1 13.2 - - + -
378B TYR* 4.0 1.8 - - + -
403B ALA 3.0 18.8 + - - +
404B MET* 3.5 14.6 - - + +
406B LEU* 1.3 73.5 - - - +
408B PHE* 1.3 69.1 + - + +
409B TRP 3.0 1.3 - - - -
410B GLU* 3.0 24.2 + - + +
411B ILE* 3.0 17.9 + - + +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ALA* 3.3 40.4 - - + -
309B THR* 4.4 8.7 - - + -
310B ALA* 4.3 0.4 - - + -
404B MET* 3.0 44.7 + - + -
405B GLY* 3.1 10.7 + - - +
407B VAL* 1.3 78.5 - - + +
409B TRP* 1.3 58.5 + - - +
411B ILE* 3.2 10.9 + - + +
412B ALA* 2.9 31.5 + - - +
467B MET* 3.6 27.5 - - + +
470B ILE* 4.2 17.9 - - + -
471B MET* 4.2 11.0 - - + -
474B CYS* 5.9 0.4 - - - -
488B ILE* 3.8 25.4 - - + -
492B LEU* 3.8 13.0 - - + -
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Residues in contact with TRP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLY 3.0 9.0 + - - +
406B LEU* 3.2 10.1 - - - +
407B VAL 3.0 0.2 - - - -
408B PHE* 1.3 75.4 - - - +
410B GLU* 1.3 84.8 + - + +
412B ALA 3.5 0.2 + - - -
413B ARG* 3.1 58.4 + - - +
425B GLN 3.2 23.3 - - - -
426B LEU 3.5 9.9 - - - -
427B PRO* 3.7 15.9 - - + -
428B TYR 5.0 0.9 - - - -
429B TYR* 3.6 27.6 - + - -
452B PRO* 3.5 24.4 - - + +
453B ASN* 3.1 29.5 + - + -
454B ILE* 5.1 0.2 - - + -
455B PRO* 4.5 0.6 - - + +
458B TRP* 3.6 18.6 - + - -
471B MET* 3.1 36.3 - - + +
475B TRP* 3.8 6.7 - + + -
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LEU* 3.7 15.0 - - + +
336B SER* 2.9 22.6 + - - -
378B TYR* 2.6 37.1 + - - -
406B LEU 3.3 8.7 - - - +
407B VAL* 3.0 17.4 + - - +
409B TRP* 1.3 85.7 - - + +
411B ILE* 1.3 62.4 + - - +
413B ARG* 3.6 13.0 - - - +
414B ARG* 3.8 8.8 - - - +
424B TYR* 2.6 37.5 + - + -
425B GLN 4.0 7.0 - - - +
427B PRO* 3.6 18.5 - - + +
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Residues in contact with ILE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.1 19.7 - - + -
292B LEU* 4.0 18.6 - - + +
297B VAL* 4.5 4.5 - - + +
302B MET* 3.7 34.1 - - + +
305B LEU* 4.0 31.4 - - + +
306B ALA* 4.2 15.3 - - + +
309B THR* 5.2 1.6 - - - +
407B VAL* 3.0 19.6 + - + +
408B PHE* 3.4 14.8 - - + +
410B GLU* 1.3 74.2 - - - +
412B ALA* 1.3 62.1 + - - +
413B ARG 3.0 1.3 - - - -
414B ARG* 2.8 26.7 + - - +
415B CYS* 3.6 3.6 + - - +
467B MET* 4.8 1.3 - - + -
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET* 3.7 25.5 - - - -
408B PHE 2.9 18.4 + - - +
411B ILE* 1.3 73.9 - - - +
413B ARG* 1.3 62.8 + - - +
415B CYS* 2.9 20.5 + - - +
457B ARG* 4.1 0.3 + - - -
458B TRP* 3.7 37.7 + - + -
464B LEU* 4.2 7.1 - - + +
467B MET* 4.4 11.4 - - + -
471B MET* 5.0 1.1 - - - -
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TRP* 3.1 59.2 + - - +
410B GLU* 3.6 8.5 - - - +
411B ILE 3.0 0.4 + - - -
412B ALA* 1.3 77.5 - - - +
414B ARG* 1.3 61.2 + - + +
415B CYS 3.4 0.9 + - - -
421B HIS* 4.1 1.0 - - - +
422B GLU* 3.0 68.6 + - + +
423B ASP* 2.4 36.3 + - - +
425B GLN* 3.7 18.9 - - - +
429B TYR* 2.9 30.7 + - - -
455B PRO* 5.6 4.4 - - + +
457B ARG* 4.1 0.3 + - - -
458B TRP* 3.5 12.0 - - + -
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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