Contacts of the helix formed by residues 365 - 398 (chain A) in PDB entry 6W4E
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 LYS 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A SER* 2.7 28.7 + - - +
364A ALA* 1.3 81.3 - - + +
366A PRO* 1.4 63.9 - - + +
367A ALA 3.5 0.2 - - - -
369A GLU* 2.8 39.5 + - - +
372A ARG* 4.6 3.0 + - - +
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A SER 3.1 16.2 - - - +
362A GLU* 3.2 32.8 - - + +
365A LYS* 1.4 90.1 - - + +
367A ALA* 1.3 56.5 + - - +
369A GLU* 3.3 9.9 + - + +
370A ASP* 2.8 30.6 + - - +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU 2.8 23.0 + - - +
363A LYS* 3.4 15.9 - - + +
366A PRO* 1.3 73.0 - - - +
368A LEU* 1.3 57.0 + - - +
370A ASP* 3.2 8.1 + - - +
371A LEU* 2.8 40.5 + - + +
407D SER* 5.4 9.6 - - - +
411D THR* 4.2 17.5 - - + -
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Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS 3.2 14.3 + - - +
364A ALA* 3.1 38.4 - - + +
365A LYS 3.5 0.4 + - - -
366A PRO 3.3 0.6 - - - -
367A ALA* 1.3 77.6 - - - +
369A GLU* 1.3 57.8 + - - +
371A LEU* 3.2 15.6 + - + +
372A ARG* 2.8 61.2 + - + +
416A 17F 3.8 32.1 - - + -
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LYS 2.8 24.4 + - - +
366A PRO* 3.5 9.0 - - - +
368A LEU* 1.3 71.5 - - - +
370A ASP* 1.3 57.8 + - - +
372A ARG* 3.2 19.8 + - + +
373A GLN* 2.9 54.7 + - + +
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Residues in contact with ASP 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A PRO 2.8 18.0 + - - +
367A ALA* 3.3 9.2 - - - +
369A GLU* 1.3 77.6 + - - +
371A LEU* 1.3 57.9 + - - +
373A GLN* 3.3 17.2 + - - +
374A GLY* 2.9 24.4 + - - -
403D ASP 4.2 6.1 - - - +
404D ASN* 5.1 1.0 + - - -
407D SER* 2.6 31.2 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS 5.6 0.9 - - - +
367A ALA* 2.8 30.4 + - + +
368A LEU* 3.2 24.2 + - + +
370A ASP* 1.3 75.8 - - - +
372A ARG* 1.3 54.2 + - + +
374A GLY* 3.1 2.2 + - - -
375A LEU* 2.8 49.0 + - + +
416A 17F 4.6 26.5 - - + -
404D ASN* 3.6 26.5 - - - +
407D SER* 5.1 12.3 - - - +
408D VAL* 6.1 2.9 - - + -
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Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ALA 3.9 5.9 + - - -
365A LYS* 4.6 3.0 + - - +
368A LEU* 2.8 61.3 + - + +
369A GLU* 3.2 26.4 + - - +
371A LEU* 1.3 72.2 - - - +
373A GLN* 1.3 58.7 + - + +
375A LEU* 3.1 10.4 + - + +
376A LEU* 2.9 39.7 + - + +
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Residues in contact with GLN 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A GLU* 2.9 43.1 + - + +
370A ASP* 3.5 20.5 - - - +
372A ARG* 1.3 76.6 - - + +
374A GLY* 1.3 58.0 + - - +
376A LEU* 3.6 18.4 + - + +
377A PRO* 2.9 23.9 - - - +
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP 2.9 14.5 + - - -
371A LEU* 3.1 4.7 + - - -
373A GLN* 1.3 77.2 - - - +
375A LEU* 1.3 60.0 + - - +
376A LEU 3.3 0.2 - - - -
377A PRO* 3.4 12.6 - - - +
378A VAL* 3.1 22.9 - - - +
400D LYS* 5.1 6.3 - - - -
404D ASN* 6.3 0.9 - - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU* 2.8 27.7 + - + +
372A ARG* 3.1 10.1 + - + +
374A GLY* 1.3 76.2 - - - +
376A LEU* 1.3 61.5 + - - +
377A PRO 3.5 0.2 - - - -
378A VAL* 3.2 22.3 + - + +
379A LEU* 2.8 43.8 + - + +
416A 17F 4.4 26.9 - - + -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ARG* 2.9 28.0 + - + +
373A GLN* 3.7 19.5 - - + +
375A LEU* 1.3 77.3 - - - +
377A PRO* 1.4 68.9 - - + +
379A LEU* 3.2 12.7 + - + +
380A GLU* 3.0 24.5 + - - +
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Residues in contact with PRO 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLN 2.9 28.5 - - - +
374A GLY* 3.4 15.0 - - - +
376A LEU* 1.4 81.6 - - + +
378A VAL* 1.3 51.5 + - - -
380A GLU* 3.2 12.1 + - + +
381A SER* 2.8 37.4 + - - -
400D LYS* 4.4 25.7 + - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLY 3.1 22.2 - - - +
375A LEU* 3.2 27.1 + - + +
376A LEU 3.1 0.4 - - - -
377A PRO* 1.3 79.5 - - + +
379A LEU* 1.3 62.6 + - + +
381A SER* 2.9 8.5 + - - -
382A PHE* 2.8 54.1 + - + +
400D LYS* 5.2 10.3 - - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 2.8 28.5 + - + +
376A LEU* 3.6 12.1 - - + +
378A VAL* 1.3 80.9 - - + +
380A GLU* 1.3 53.6 + - - +
382A PHE* 3.7 8.8 - - + +
383A LYS* 2.8 58.6 + - + +
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU 3.0 16.4 + - - +
377A PRO* 3.2 15.3 - - + +
379A LEU* 1.3 79.4 - - - +
381A SER* 1.3 61.9 + - - +
383A LYS* 3.4 20.9 + - - +
384A VAL* 3.3 23.9 + - - +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PRO 2.8 18.3 + - - -
378A VAL* 2.9 14.6 + - - -
380A GLU* 1.3 72.6 - - - +
382A PHE* 1.3 61.3 + - - +
384A VAL* 3.1 11.3 + - - +
385A SER* 2.9 31.6 + - - -
400D LYS* 5.6 2.1 + - - -
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 2.8 44.6 + - + +
379A LEU* 3.7 12.6 - - + +
381A SER* 1.3 79.1 + - - +
383A LYS* 1.3 53.0 + - - +
385A SER* 3.2 9.6 + - - -
386A PHE* 2.7 75.3 + + + -
415A 17F 4.9 10.3 - - + -
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 2.8 45.5 + - + +
380A GLU* 3.5 20.1 + - + +
382A PHE* 1.3 76.7 - - - +
384A VAL* 1.3 57.6 + - + +
386A PHE* 3.7 8.0 - - + +
387A LEU* 2.9 43.2 + - + +
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU 3.3 17.3 - - - +
381A SER* 3.1 10.0 + - - +
383A LYS* 1.3 75.5 - - + +
385A SER* 1.3 53.1 + - - +
387A LEU* 3.3 10.9 + - + +
388A SER* 2.7 41.7 + - - +
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A SER* 2.9 15.7 + - - -
382A PHE* 3.5 15.5 - - - -
384A VAL* 1.3 77.4 - - - +
386A PHE* 1.3 58.8 + - - +
388A SER* 3.0 7.7 + - - -
389A ALA* 2.9 30.8 + - - +
594D LYS* 5.4 4.2 + - - -
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Residues in contact with PHE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE* 2.7 59.3 + + + +
383A LYS* 3.7 7.9 - - + +
385A SER* 1.3 75.6 - - - +
387A LEU* 1.3 57.9 + - + +
389A ALA* 3.3 7.7 + - + +
390A LEU* 2.9 41.8 + - + +
415A 17F 4.0 26.0 - - + -
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LYS* 2.9 33.4 + - + +
384A VAL* 3.7 8.3 - - + +
385A SER 3.3 0.2 - - - -
386A PHE* 1.3 77.2 - - + +
388A SER* 1.3 63.1 + - - +
390A LEU* 3.3 18.5 + - + +
391A GLU* 3.1 30.5 + - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A VAL* 2.7 27.8 + - - +
385A SER* 3.0 15.8 + - - -
387A LEU* 1.3 75.5 - - - +
389A ALA* 1.3 50.5 + - - +
391A GLU* 3.3 14.4 + - - +
392A GLU* 2.7 40.3 + - - +
594D LYS* 3.8 36.0 - - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER 2.9 19.6 + - - +
386A PHE* 3.5 10.1 - - + +
388A SER* 1.3 74.2 - - - +
390A LEU* 1.3 60.8 + - + +
392A GLU* 3.2 7.3 + - - +
393A TYR* 2.9 47.5 + - + -
591D TYR* 5.6 1.6 - - + -
594D LYS* 5.4 1.1 - - - +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PHE* 2.9 32.0 + - + +
387A LEU* 3.3 20.4 + - + +
389A ALA* 1.3 76.1 - - + +
391A GLU* 1.3 59.9 + - + +
393A TYR* 3.6 4.8 + - - +
394A THR* 2.7 33.9 + - - +
414A PCW 5.7 10.3 - - + -
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.1 17.3 + - - +
388A SER* 3.6 13.1 - - - +
390A LEU* 1.3 75.7 - - + +
392A GLU* 1.3 55.2 + - - +
394A THR* 3.1 5.3 + - - -
395A LYS* 2.7 55.0 + - + +
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Residues in contact with GLU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER 2.7 28.8 + - - +
389A ALA* 3.5 7.2 - - - +
391A GLU* 1.3 74.1 - - - +
393A TYR* 1.3 61.8 + - - +
395A LYS* 2.7 19.3 + - - +
396A LYS* 2.6 61.0 + - - +
587D ALA 4.9 0.5 - - - +
590D GLU* 3.2 13.4 - - - +
591D TYR* 3.5 33.1 + - + -
594D LYS* 2.6 39.1 + - + -
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Residues in contact with TYR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA* 2.9 35.6 + - + +
390A LEU* 3.9 5.6 - - - +
392A GLU* 1.3 76.5 - - - +
394A THR* 1.3 58.8 + - - +
396A LYS* 5.4 0.2 - - - -
397A LEU* 2.8 62.4 + - + +
414A PCW 5.9 12.2 - - + +
421A PCW 5.0 16.9 - - + +
591D TYR* 3.4 31.3 - + - -
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Residues in contact with THR 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU 2.7 22.8 + - - -
391A GLU* 3.1 5.6 + - - -
393A TYR* 1.3 78.6 - - - +
395A LYS* 1.3 62.4 + - - +
397A LEU* 5.2 0.4 - - - -
398A ASN* 3.0 49.5 + - + +
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 2.7 36.7 + - + +
392A GLU* 2.7 42.3 + - - +
394A THR* 1.3 75.1 - - + +
396A LYS* 1.3 67.8 + - + +
398A ASN 4.2 6.9 - - - +
590D GLU* 2.8 25.1 + - - +
594D LYS* 4.1 2.8 - - - +
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Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 2.6 44.5 + - - +
393A TYR* 4.6 0.7 - - - +
395A LYS* 1.3 87.4 - - + +
397A LEU* 1.3 70.7 + - + +
398A ASN 3.4 4.4 + - - +
583D SER* 3.6 34.6 - - - +
586D SER* 2.9 39.4 + - - +
587D ALA* 3.7 14.5 - - + +
590D GLU* 2.6 24.8 + - - +
591D TYR* 5.3 4.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A TYR* 2.8 54.1 + - + +
394A THR* 5.2 0.2 - - - -
396A LYS* 1.3 80.6 - - + +
398A ASN* 1.3 61.0 + - - +
591D TYR* 6.0 0.7 - - - +
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A THR* 3.0 39.9 + - + +
395A LYS 4.2 7.1 - - - +
396A LYS 4.2 5.2 - - - +
397A LEU* 1.3 82.9 - - - +
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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