Contacts of the helix formed by residues 338 - 366 (chain B) in PDB entry 1IW1
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 GLY 338 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 4.0 5.2 - - - +
337B LEU* 1.3 81.0 - - - +
339B VAL* 1.3 66.1 + - - -
340B ALA 3.1 3.6 + - - -
341B GLU* 3.0 18.4 + - - +
342B PHE* 3.3 9.7 + - - +
451B TYR* 3.5 19.7 - - - -
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLY* 1.3 71.0 - - - -
340B ALA* 1.3 61.7 + - - +
342B PHE* 3.2 7.8 + - + +
343B THR* 2.8 39.4 + - - +
390B LEU* 4.1 22.7 - - + +
451B TYR* 3.8 32.6 - - + +
453B VAL* 4.0 15.0 - - + -
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLY* 3.1 1.4 - - - -
339B VAL* 1.3 78.6 - - - +
341B GLU* 1.3 70.5 + - - +
343B THR* 3.3 6.8 + - - -
344B ARG* 3.0 46.9 + - - +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 4.0 18.1 - - + -
332B LEU* 4.2 2.9 - - + -
337B LEU* 3.7 36.9 - - + -
338B GLY* 3.0 30.1 + - - +
340B ALA* 1.3 82.2 - - - +
342B PHE* 1.3 64.5 + - - +
344B ARG* 3.3 27.6 + - - +
345B LEU* 3.0 22.0 + - - +
511B LEU* 6.0 0.9 - - - +
912B SO4 5.6 0.9 + - - -
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 4.0 14.1 - - + +
338B GLY 3.3 9.2 + - - +
339B VAL* 3.2 10.8 + - + +
341B GLU* 1.3 75.9 - - - +
343B THR* 1.3 64.0 + - - +
345B LEU* 3.1 12.3 + - + +
346B GLN* 3.0 52.8 + - + +
390B LEU* 4.0 28.5 - - + -
443B ILE* 5.0 1.3 - - + -
447B MET* 3.6 35.7 - - + -
451B TYR* 5.4 1.1 - - + -
453B VAL* 4.7 11.4 - - + -
457B ALA 4.3 2.5 - - - -
458B LEU* 3.5 32.8 - - + -
461B TYR* 3.8 20.0 - + - -
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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* 2.8 32.1 + - - +
340B ALA* 3.5 7.4 - - - -
342B PHE* 1.3 73.2 - - - +
344B ARG* 1.3 58.6 + - + +
346B GLN* 3.1 4.1 + - - +
347B GLU* 2.9 40.9 + - - +
387B LEU* 4.0 3.8 - - + +
390B LEU* 3.7 34.7 + - + +
391B ASN* 3.7 29.8 - - - +
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Residues in contact with ARG 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ALA* 3.0 30.0 + - - +
341B GLU* 3.6 31.4 + - - +
342B PHE 3.2 0.2 - - - -
343B THR* 1.3 73.7 - - - +
345B LEU* 1.3 65.4 + - - +
347B GLU* 3.3 18.5 + - - +
348B GLN* 3.1 27.0 + - - +
511B LEU* 3.9 19.1 - - + -
514B GLY* 5.9 6.4 + - - -
515B LEU* 5.8 3.1 - - - -
912B SO4 2.7 44.2 + - - -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 4.7 2.9 - - + -
329B MET* 3.9 27.8 - - + -
332B LEU* 4.3 13.5 - - + -
341B GLU 3.0 12.3 + - - +
342B PHE* 3.1 15.2 + - + +
344B ARG* 1.3 77.7 - - - +
346B GLN* 1.3 73.7 + - - +
348B GLN* 3.2 3.1 + - - +
349B ALA* 2.9 26.0 + - + +
352B PHE* 5.8 4.3 - - + -
443B ILE* 6.0 0.7 - - + -
461B TYR* 4.9 5.8 - - - +
507B VAL* 4.4 9.9 - - + -
508B PHE* 3.9 17.5 - - + -
511B LEU* 3.6 29.5 - - + +
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Residues in contact with GLN 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B PHE* 3.0 51.9 + - + +
343B THR* 3.1 6.9 + - - +
345B LEU* 1.3 92.2 + - - +
347B GLU* 1.3 57.8 + - - +
349B ALA* 3.6 12.5 - - - +
350B TRP* 2.9 28.4 + - - +
383B LEU* 3.7 25.2 - - + +
386B ASP* 4.8 3.7 - - + +
387B LEU* 3.9 18.0 - - + +
390B LEU* 4.6 4.7 - - + -
457B ALA 6.0 0.2 - - - +
460B PHE* 3.8 13.2 - - - +
461B TYR* 3.7 22.6 + - - -
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 2.9 25.3 + - - +
344B ARG* 3.6 23.1 - - - +
345B LEU 3.2 0.4 - - - -
346B GLN* 1.3 73.7 - - - +
348B GLN* 1.3 71.5 + - - +
350B TRP* 3.2 11.6 + - - +
351B LEU* 3.3 17.2 + - - +
387B LEU* 3.7 22.4 - - + -
391B ASN* 3.2 17.8 + - - +
396B TRP* 4.0 1.9 - - + +
399B ARG* 3.0 25.1 + - - -
400B ILE* 3.5 36.2 - - + +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ARG* 3.1 14.5 + - + +
345B LEU* 3.6 7.9 - - - +
347B GLU* 1.3 79.3 + - - +
349B ALA* 1.3 63.7 + - - +
351B LEU* 3.0 18.1 + - - +
352B PHE* 3.1 18.4 + - + -
400B ILE* 5.4 1.2 - - - +
401B THR 3.0 26.0 + - - +
402B ALA* 3.6 2.8 - - - -
403B SER* 2.9 32.1 + - - +
406B VAL* 3.0 27.8 - - + +
507B VAL* 4.5 12.8 - - + -
511B LEU* 4.5 15.7 - - + -
515B LEU 5.3 4.2 + - - -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 2.9 18.1 + - + +
346B GLN* 3.6 18.6 - - - +
347B GLU 3.2 0.2 - - - -
348B GLN* 1.3 78.4 - - - +
350B TRP* 1.3 56.9 + - - +
352B PHE* 3.6 23.5 - - + -
353B TYR* 2.7 47.5 + - + +
383B LEU* 3.8 8.7 - - + -
432B ARG* 5.7 1.1 - - - +
460B PHE* 5.3 2.2 - - + -
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Residues in contact with TRP 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLN 2.9 14.4 + - - +
347B GLU 3.2 6.7 + - - +
349B ALA* 1.3 76.0 - - - +
351B LEU* 1.3 82.6 + - + +
353B TYR* 4.3 0.2 - - - +
354B THR* 2.8 43.1 + - - -
380B ALA* 3.3 29.5 + - - +
381B GLU* 5.7 2.0 + - - -
383B LEU* 3.7 12.7 - - + +
384B ALA* 3.8 19.6 - - + +
387B LEU* 3.9 12.3 - - + -
396B TRP* 3.5 32.3 - + - -
397B ARG* 4.9 3.6 - - + -
400B ILE* 3.6 20.0 - - + -
650C TRP* 3.9 26.2 - + - -
697C ARG* 3.5 36.3 - - + -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU 3.3 13.0 + - - +
348B GLN* 3.0 17.1 + - - +
350B TRP* 1.3 95.1 - - + +
352B PHE* 1.3 60.9 + - - +
354B THR* 3.7 4.5 - - - -
355B ALA* 3.4 20.1 + - - +
400B ILE* 4.2 10.8 - - + -
401B THR* 3.8 6.5 - - - +
402B ALA* 3.6 37.0 - - + +
406B VAL* 4.2 8.3 - - + -
410B VAL* 3.9 7.8 - - + +
694C SER* 4.8 3.1 + - - -
695C GLU* 6.5 0.4 - - - -
697C ARG* 3.8 31.8 - - + +
698C SER* 3.7 12.1 - - - +
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Residues in contact with PHE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 5.4 4.5 - - + -
348B GLN* 3.1 24.4 + - + -
349B ALA* 3.6 22.4 - - + -
351B LEU* 1.3 73.9 - - - +
353B TYR* 1.3 90.7 + + - +
355B ALA 3.3 0.5 + - - -
356B LEU* 2.8 31.2 + - + +
406B VAL* 4.3 10.5 - - + -
409B TYR* 3.6 42.4 - + + -
410B VAL* 4.0 16.4 - - + -
413B LEU* 3.5 7.1 - - + +
432B ARG* 3.9 20.6 - - + -
504B ASN* 3.9 12.8 - - - -
507B VAL* 4.2 22.0 - - + -
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ALA* 2.7 31.7 + - + +
350B TRP 4.3 1.1 - - - +
352B PHE* 1.3 84.6 - + - +
354B THR* 1.3 64.3 + - - +
356B LEU* 4.1 7.9 - - + -
357B GLU* 2.9 49.3 + - - +
379B ARG* 3.8 8.5 - - + -
380B ALA* 4.4 9.6 - - - +
383B LEU* 3.9 20.9 - - + -
432B ARG* 2.7 42.7 + - + +
433B TYR* 3.7 26.7 - + - -
436B ASP* 2.5 29.5 + - - -
460B PHE* 3.6 16.4 - + - -
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Residues in contact with THR 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TRP* 2.8 41.4 + - - -
351B LEU 3.7 5.4 - - - -
352B PHE 3.3 0.2 - - - -
353B TYR* 1.3 76.7 - - - +
355B ALA* 1.3 63.0 + - - +
357B GLU* 3.4 2.8 + - - +
358B GLN* 3.1 39.3 + - + +
380B ALA* 3.9 14.0 - - + +
694C SER* 4.4 4.0 - - - -
697C ARG* 3.4 41.3 + - - +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU 3.4 9.9 + - - +
352B PHE 3.3 7.3 + - - +
353B TYR 3.2 0.4 - - - -
354B THR* 1.3 78.6 - - - +
356B LEU* 1.3 64.2 + - - +
358B GLN* 3.2 9.7 + - - +
359B ALA* 3.1 22.0 + - - +
410B VAL* 3.9 26.5 - - + -
413B LEU* 4.1 19.9 - - + +
414B GLU* 4.6 7.1 - - + +
417B ARG* 5.6 0.3 - - - +
694C SER* 3.9 10.1 + - - +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 2.8 21.7 + - + +
353B TYR* 3.3 14.3 + - + +
355B ALA* 1.3 72.2 - - - +
357B GLU* 1.3 58.1 + - - +
359B ALA* 3.1 3.5 + - - +
360B VAL* 2.8 34.8 + - + +
409B TYR* 5.5 1.1 - - + +
413B LEU* 3.7 19.4 - - + +
425B LEU* 3.9 15.7 - - + -
428B HIS* 3.9 31.2 - - + +
429B HIS* 4.4 1.8 - - - +
432B ARG* 4.0 29.2 - - + -
433B TYR* 3.9 32.1 - - + +
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Residues in contact with GLU 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 2.9 28.8 + - - +
354B THR* 4.1 3.6 - - - +
356B LEU* 1.3 74.9 - - + +
358B GLN* 1.3 61.6 + - + +
360B VAL* 3.7 6.8 - - + +
361B ASP* 3.0 38.8 + - - +
378B ASN* 3.4 24.4 - - - +
379B ARG 2.7 25.4 + - - -
380B ALA* 3.0 29.7 + - + +
381B GLU 4.9 0.2 + - - -
433B TYR* 2.7 29.6 + - - +
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Residues in contact with GLN 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B THR* 3.1 30.2 + - + +
355B ALA* 3.2 8.1 + - - +
357B GLU* 1.3 78.9 - - - +
359B ALA* 1.3 61.0 + - - +
361B ASP* 3.4 9.2 + - - +
362B ALA* 3.1 22.5 + - - +
414B GLU* 4.8 0.6 + - - +
417B ARG* 2.9 40.2 - - - +
688C ASP* 2.8 35.7 + - - +
694C SER* 3.9 15.3 - - - -
697C ARG* 4.1 1.0 + - - -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ALA 3.1 10.2 + - - +
356B LEU* 3.5 9.2 - - - +
358B GLN* 1.3 74.5 - - - +
360B VAL* 1.3 65.3 + - - +
362B ALA* 3.2 1.9 + - - +
363B VAL* 2.9 27.2 + - - +
413B LEU* 3.7 26.5 - - + +
416B ILE* 4.3 5.2 - - + -
417B ARG* 3.9 19.4 - - + +
425B LEU* 3.7 16.6 - - + -
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B LEU* 2.8 30.3 + - + +
357B GLU* 3.7 11.9 - - + +
358B GLN 3.4 0.2 - - - -
359B ALA* 1.3 77.2 - - - +
361B ASP* 1.3 56.2 + - - +
363B VAL* 3.3 0.5 + - - -
364B ARG* 2.8 54.8 + - - +
373B LEU* 3.9 21.5 - - + +
378B ASN* 5.4 3.8 - - - +
425B LEU* 3.7 19.7 - - + +
429B HIS* 3.9 24.2 - - + +
433B TYR* 4.6 5.4 - - - +
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Residues in contact with ASP 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B GLU* 3.0 25.1 + - - +
358B GLN* 3.7 9.0 - - - +
360B VAL* 1.3 75.5 - - - +
362B ALA* 1.3 63.3 + - - +
364B ARG* 2.8 30.9 + - - +
365B ALA* 3.0 25.3 + - - +
378B ASN* 5.0 9.2 + - - +
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Residues in contact with ALA 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B GLN 3.1 16.7 + - - +
359B ALA 3.7 3.8 - - - +
361B ASP* 1.3 77.2 - - - +
363B VAL* 1.3 62.9 + - + +
365B ALA* 3.3 8.8 + - - +
366B SER* 3.3 18.9 + - - -
417B ARG* 3.9 29.2 - - + +
420B VAL* 4.0 11.2 - - + +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B ALA 2.9 20.0 + - - +
360B VAL 3.9 1.8 - - - +
362B ALA* 1.3 75.1 - - + +
364B ARG* 1.3 65.0 + - - +
366B SER* 2.7 25.6 + - - +
367B GLY 3.5 3.1 + - - -
368B PHE* 3.5 26.9 + - + +
369B ALA* 5.4 0.2 - - + -
373B LEU* 3.8 8.3 - - + -
416B ILE* 5.0 4.0 - - + +
420B VAL* 4.3 12.3 - - + -
421B ASP 4.2 7.2 - - - +
422B GLY* 3.9 29.2 - - - +
425B LEU* 3.7 28.5 - - + -
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Residues in contact with ARG 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B VAL* 2.8 38.4 + - - +
361B ASP* 2.8 39.2 + - - +
363B VAL* 1.3 72.2 - - - +
365B ALA* 1.3 58.8 + - - +
367B GLY* 3.0 20.4 + - - -
368B PHE 4.3 4.7 - - - -
370B GLU* 3.7 28.0 - - + +
373B LEU* 2.9 45.7 + - + +
374B ASP 4.3 0.4 - - - -
375B PRO* 3.9 27.9 - - - +
378B ASN* 4.8 4.6 + - - +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASP 3.0 18.8 + - - +
362B ALA* 3.6 7.9 - - - +
363B VAL 3.2 0.4 - - - -
364B ARG* 1.3 77.1 - - - +
366B SER* 1.3 58.0 + - - +
367B GLY 3.2 1.5 + - - -
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Residues in contact with SER 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ALA 3.3 3.9 + - - -
363B VAL* 2.7 22.0 + - - +
365B ALA* 1.3 77.5 - - - +
367B GLY* 1.3 58.6 + - - +
368B PHE* 3.7 12.8 + - - +
420B VAL* 3.7 28.3 - - - +
----------------------------------------------------------
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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