Contacts of the helix formed by residues 368 - 402 (chain A) in PDB entry 3NYL
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 GLU 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 2.3 32.9 + - - -
364A GLY 5.2 0.5 + - - -
365A ASP* 3.6 26.0 + - - +
366A GLU 3.2 3.5 - - - +
367A ASN* 1.3 72.6 - - - +
369A HIS* 1.3 57.5 + - + +
371A HIS* 2.5 44.8 + - - +
372A PHE* 3.0 8.8 + - - +
438A HIS* 2.8 26.9 + - + +
441A ARG* 3.7 32.3 + - + +
442A VAL* 5.3 4.7 - - + -
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Residues in contact with HIS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN 2.6 7.3 + - - +
368A GLU* 1.3 80.0 - - - +
370A ALA* 1.3 63.1 + - - +
372A PHE* 3.4 13.5 + + - +
373A GLN* 2.9 43.7 + - + +
438A HIS* 5.0 10.8 + - + -
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASN* 2.8 25.5 + - + +
368A GLU 2.7 3.4 + - - -
369A HIS* 1.3 75.4 - - - +
371A HIS* 1.3 55.7 + - + +
373A GLN* 3.0 6.5 + - - +
374A LYS* 2.6 39.2 + - + +
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Residues in contact with HIS 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 3.8 22.1 - - + -
362A THR* 4.3 27.4 + - + +
365A ASP* 3.0 36.8 - - + +
367A ASN* 3.9 12.6 - - + +
368A GLU* 2.5 32.0 + - - +
370A ALA* 1.3 73.9 - - + +
372A PHE* 1.3 52.7 + - - +
374A LYS* 3.5 6.6 - - - +
375A ALA* 2.6 38.1 + - - +
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 3.6 15.2 - + + -
368A GLU 3.0 8.7 + - - +
369A HIS* 3.6 15.5 - + - +
371A HIS* 1.3 76.9 - - - +
373A GLN* 1.3 62.9 + - + +
375A ALA* 3.2 3.9 - - + +
376A LYS* 2.9 82.7 + - + +
434A LEU* 3.9 4.7 - - + -
435A VAL* 3.9 33.7 - - + -
438A HIS* 3.5 59.5 - + + +
439A MET* 6.2 0.7 - - + -
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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 HIS* 2.9 41.4 + - + +
370A ALA* 3.7 3.8 - - - +
372A PHE* 1.3 74.5 - - + +
374A LYS* 1.3 68.2 + - - +
375A ALA 3.0 1.3 - - - -
376A LYS* 3.1 31.3 + - - +
377A GLU* 2.8 31.3 + - + +
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA 2.6 22.5 + - - +
371A HIS* 3.6 7.4 - - - +
373A GLN* 1.3 71.9 - - - +
375A ALA* 1.3 56.2 + - - +
377A GLU* 3.9 5.6 - - - +
378A ARG* 2.9 36.7 + - + +
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Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA* 4.2 9.1 - - - +
359A TYR* 4.0 22.2 - - + -
371A HIS 2.6 22.1 + - - +
372A PHE* 3.2 7.6 - - + +
374A LYS* 1.3 72.7 - - - +
376A LYS* 1.3 61.4 + - + +
378A ARG* 3.9 2.9 - - - +
379A LEU* 3.0 31.2 + - - +
434A LEU* 4.0 21.5 - - + +
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 2.9 70.6 + - + +
373A GLN* 3.5 21.1 + - - +
375A ALA* 1.3 73.0 - - - +
377A GLU* 1.3 57.4 + - - +
379A LEU* 4.0 2.2 - - - +
380A GLU* 3.0 33.1 + - - +
431A ARG* 2.9 45.9 - - + +
434A LEU* 4.1 16.4 - - + -
435A VAL* 5.6 0.4 - - + +
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Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLN* 2.8 19.8 + - + +
374A LYS* 3.9 4.9 - - - +
376A LYS* 1.3 78.6 - - - +
378A ARG* 1.3 56.3 + - + +
380A GLU* 4.1 5.2 - - - +
381A ALA* 3.2 25.5 + - - +
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA* 4.0 18.5 - - + +
374A LYS* 2.9 23.7 + - + +
375A ALA* 4.0 3.6 - - - +
377A GLU* 1.3 78.6 - - + +
379A LEU* 1.3 64.3 + - - +
381A ALA* 3.6 6.0 - - - +
382A LYS* 3.3 21.9 + - + +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASP* 4.8 4.5 - - - +
355A ALA* 3.9 13.5 - - + -
356A VAL* 3.5 26.9 - - + -
375A ALA 3.0 18.4 + - - +
376A LYS* 4.0 3.4 - - - +
378A ARG* 1.3 74.7 - - - +
380A GLU* 1.3 64.1 + - - +
382A LYS* 3.3 7.5 + - + +
383A HIS* 2.9 29.3 + - + +
427A ALA* 4.7 3.8 - - + +
430A GLU* 3.9 16.4 - - + +
431A ARG* 3.7 30.3 - - + +
434A LEU* 3.7 21.3 - - + -
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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 LYS 3.0 20.1 + - - +
377A GLU* 4.1 5.8 - - - +
379A LEU* 1.3 76.8 - - - +
381A ALA* 1.3 69.9 + - - +
383A HIS* 3.2 12.7 + - - +
384A ARG* 3.0 52.9 + - + +
431A ARG* 5.8 2.5 + - - +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU 3.2 17.9 + - - +
378A ARG* 3.6 8.5 - - - +
380A GLU* 1.3 81.2 - - - +
382A LYS* 1.3 65.0 + - - +
384A ARG* 2.9 20.4 + - - +
385A GLU* 3.2 12.9 + - - +
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG 3.3 9.5 + - - +
379A LEU* 3.3 10.2 + - + +
381A ALA* 1.3 79.6 - - - +
383A HIS* 1.3 62.4 + - - +
385A GLU* 3.0 27.5 - - + +
386A ARG* 3.1 9.8 + - + +
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Residues in contact with HIS 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 2.9 16.5 + - + +
380A GLU* 3.3 17.3 - - - +
381A ALA 3.0 0.2 + - - -
382A LYS* 1.3 76.3 - - - +
384A ARG* 1.3 79.1 + - - +
385A GLU 3.0 0.3 + - - -
386A ARG* 3.2 6.4 + - - +
387A MET* 2.8 61.7 + - + +
423A LEU* 4.5 2.1 + - - +
424A GLU* 2.8 31.0 + - - -
427A ALA* 3.5 32.0 - - + +
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Residues in contact with ARG 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLU* 3.0 36.4 + - + +
381A ALA* 2.9 11.7 + - - +
383A HIS* 1.3 95.2 + - - +
385A GLU* 1.3 64.2 + - - +
387A MET* 3.8 21.7 - - - +
388A SER* 3.0 26.6 + - - -
424A GLU* 5.2 5.9 + - - -
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Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.2 9.8 + - - +
382A LYS* 3.0 19.9 + - + +
384A ARG* 1.3 75.1 - - - +
386A ARG* 1.3 68.5 + - - +
388A SER* 2.9 17.5 + - - -
389A GLN* 2.9 22.3 + - + +
392A ARG* 4.9 6.2 + - - -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LYS* 3.1 9.6 + - + +
383A HIS* 3.9 7.0 - - - +
385A GLU* 1.3 78.2 - - - +
387A MET* 1.3 65.9 + - + +
389A GLN* 3.2 14.8 + - - +
390A VAL* 2.9 23.4 + - + +
423A LEU* 3.6 35.7 - - + +
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Residues in contact with MET 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 2.8 49.0 + - + +
384A ARG* 3.8 21.5 - - - +
386A ARG* 1.3 74.8 - - + +
388A SER* 1.3 62.5 + - - +
390A VAL* 3.2 6.7 + - + +
391A MET* 3.0 34.1 + - + +
420A VAL* 4.9 10.3 - - - +
423A LEU* 3.2 47.8 - - + -
424A GLU* 3.1 33.4 - - + +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ARG* 3.0 17.3 + - - -
385A GLU* 2.9 7.5 + - - -
387A MET* 1.3 75.7 - - - +
389A GLN* 1.3 57.5 + - - +
391A MET* 3.7 7.8 - - - +
392A ARG* 2.9 49.8 + - - +
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Residues in contact with GLN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 2.9 27.6 + - + +
386A ARG* 3.2 20.4 + - - +
388A SER* 1.3 74.5 - - - +
390A VAL* 1.3 57.9 + - - +
392A ARG* 3.6 25.2 - - - +
393A GLU* 3.0 32.3 + - - +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 2.9 16.1 + - - +
387A MET* 3.6 7.2 - - + +
389A GLN* 1.3 77.3 - - - +
391A MET* 1.3 53.3 + - + +
393A GLU* 3.3 14.4 - - - +
394A TRP* 2.8 34.6 + - - +
416A PHE* 3.8 5.3 - - + -
419A LYS* 4.7 13.0 - - + -
420A VAL* 5.0 14.4 - - + -
423A LEU* 4.5 17.0 - - + -
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Residues in contact with MET 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 3.0 25.5 + - + +
388A SER* 3.2 7.4 + - - +
390A VAL* 1.3 75.0 - - - +
392A ARG* 1.3 65.8 + - - +
394A TRP* 3.5 31.7 + - + +
395A GLU* 3.4 16.5 + - - +
420A VAL* 4.5 17.9 - - + -
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 4.9 6.5 + - - -
388A SER* 2.9 29.5 + - - +
389A GLN* 3.6 34.7 - - - +
391A MET* 1.3 72.0 - - + +
393A GLU* 1.3 65.6 + - - +
395A GLU* 2.9 19.1 + - - +
396A GLU* 3.2 10.7 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLN 3.0 21.0 + - - +
390A VAL* 3.3 10.2 - - - +
392A ARG* 1.3 80.4 - - - +
394A TRP* 1.3 62.0 + - - +
395A GLU 3.2 0.3 + - - -
396A GLU* 3.3 9.6 + - + +
397A ALA* 3.1 20.8 + - - +
416A PHE* 3.8 15.2 - - + -
419A LYS* 3.1 32.0 + - - -
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Residues in contact with TRP 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL 2.8 18.2 + - - +
391A MET* 3.5 34.3 - - + +
392A ARG 3.2 0.2 - - - -
393A GLU* 1.3 71.9 - - - +
395A GLU* 1.3 63.1 + - - +
397A ALA* 3.3 4.3 + - + +
398A GLU* 3.0 23.3 + - + +
412A VAL* 5.3 2.6 - - + +
413A ILE* 3.8 39.3 - - + +
416A PHE* 3.5 43.3 - + + +
417A GLN* 4.4 18.4 - - + -
420A VAL* 4.2 19.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A MET 3.4 7.4 + - - +
392A ARG* 2.9 11.9 + - - +
394A TRP* 1.3 74.7 - - - +
396A GLU* 1.3 60.3 + - - +
397A ALA 2.9 1.3 - - - -
398A GLU* 2.6 37.0 + - - +
399A ARG* 2.8 33.0 + - + +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG 3.2 6.8 + - - +
393A GLU* 3.5 12.3 - - + +
395A GLU* 1.3 77.7 - - - +
397A ALA* 1.3 61.9 + - - +
399A ARG* 3.7 13.2 + - - +
400A GLN* 3.1 33.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLU 3.1 9.1 + - - +
394A TRP 3.3 10.5 - - - +
395A GLU 2.9 0.6 - - - -
396A GLU* 1.3 79.0 - - - +
398A GLU* 1.3 57.5 + - - +
400A GLN* 3.8 3.9 - - - +
401A ALA* 3.1 31.7 + - - +
412A VAL* 3.8 12.3 - - + +
416A PHE* 3.7 29.8 - - + -
----------------------------------------------------------
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Residues in contact with GLU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TRP* 3.0 18.3 + - + +
395A GLU* 2.6 27.0 + - - +
397A ALA* 1.3 68.5 - - - +
399A ARG* 1.3 66.4 + - - +
400A GLN 3.0 1.3 + - - -
401A ALA* 3.4 2.4 + - - -
402A LYS* 2.8 27.2 + - - +
409A LYS* 6.1 4.3 - - + +
412A VAL* 4.9 3.8 - - + +
413A ILE* 6.4 2.5 - - + -
----------------------------------------------------------
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Residues in contact with ARG 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLU* 2.8 33.1 + - - +
396A GLU* 4.2 10.9 - - - +
398A GLU* 1.3 72.8 - - - +
400A GLN* 1.3 77.4 + - - +
402A LYS* 3.2 17.8 - - - +
403A ASN 4.7 0.2 + - - -
----------------------------------------------------------
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Residues in contact with GLN 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU* 3.1 23.3 + - + +
397A ALA* 3.8 5.4 - - - +
398A GLU 3.1 0.2 - - - -
399A ARG* 1.3 90.5 + - - +
401A ALA* 1.3 61.8 + - - +
402A LYS 2.8 10.3 + - - -
403A ASN* 3.7 9.2 + - - +
404A LEU* 4.5 3.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA 3.1 16.3 + - - +
398A GLU* 3.6 2.0 - - - +
400A GLN* 1.3 78.9 - - - +
402A LYS* 1.3 57.6 + - - +
403A ASN 3.4 1.1 - - - -
404A LEU* 2.8 52.7 + - + +
409A LYS* 4.5 14.5 - - + +
412A VAL* 4.0 23.8 - - + -
----------------------------------------------------------
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Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU 2.8 12.9 + - - +
399A ARG* 3.2 21.5 - - - +
400A GLN 2.8 6.1 + - - -
401A ALA* 1.3 69.5 - - - +
403A ASN* 1.3 56.6 + - - +
404A LEU 2.8 17.9 + - - +
409A LYS* 5.5 12.3 - - - +
----------------------------------------------------------
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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