Contacts of the helix formed by residues 366 - 396 (chain A) in PDB entry 2DDH
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 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A SER* 1.3 83.9 - - - +
367A LEU* 1.3 61.6 + - + +
368A PRO 3.5 1.3 - - - -
369A GLU* 3.4 17.7 - - + +
370A LEU* 3.0 26.6 + - - +
450A GLY* 5.4 7.4 - - - -
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A SER 3.3 9.6 - - - +
366A GLU* 1.3 85.3 - - + +
368A PRO* 1.3 73.7 - - + +
369A GLU 3.1 1.3 - - - -
370A LEU* 2.9 20.7 + - + -
371A HIS* 2.7 53.4 + - + -
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Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A SER* 3.6 19.1 - - - +
367A LEU* 1.3 94.6 - - + +
369A GLU* 1.3 55.9 + - - +
371A HIS* 3.3 6.7 + - + +
372A ALA* 2.9 31.4 + - - +
434A PHE* 4.1 17.7 - - + -
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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 SER 5.4 0.7 - - - +
366A GLU* 3.4 23.3 - - + +
368A PRO* 1.3 80.2 - - - +
370A LEU* 1.3 58.1 + - - +
372A ALA* 3.7 0.3 - - - +
373A LEU* 3.0 38.3 + - + +
434A PHE* 3.4 36.9 - - + -
449A GLY 4.4 1.7 - - - +
450A GLY* 3.4 11.3 - - - -
451A MET* 3.1 37.2 + - - +
452A VAL* 4.2 7.8 + - - +
530A HIS* 5.1 2.6 + - - -
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Residues in contact with LEU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.9 28.3 - - + -
348A MET* 5.3 3.1 - - - +
351A THR* 4.0 28.5 - - + +
352A TYR* 4.5 22.7 - - + +
366A GLU 3.0 14.3 + - - +
367A LEU* 2.9 30.1 + - + +
369A GLU* 1.3 76.0 - - - +
371A HIS* 1.3 66.8 + - - +
373A LEU* 4.1 5.0 - - + +
374A THR* 2.9 31.5 + - - +
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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
----------------------------------------------------------
278A MET* 6.3 2.8 - - - +
279A VAL* 4.4 19.1 - - + +
282A ARG* 3.2 11.6 + - - +
367A LEU* 2.7 58.7 + - + +
368A PRO* 3.8 6.3 - - + +
370A LEU* 1.3 72.9 - - - +
372A ALA* 1.3 62.1 + - - +
374A THR* 2.9 25.3 - - - +
375A ALA* 3.0 9.0 + - - +
430A GLN* 4.1 11.9 - - - +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PRO 2.9 18.2 + - - +
369A GLU 3.7 2.0 - - - +
371A HIS* 1.3 77.1 - - - +
373A LEU* 1.3 62.0 + - - +
375A ALA* 3.3 2.3 + - - +
376A GLY 3.1 4.9 + - - -
430A GLN* 4.5 8.3 - - - +
431A THR* 2.8 37.2 + - + +
434A PHE* 3.4 43.7 - - + -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A TYR* 4.3 22.2 - - + +
369A GLU* 3.0 27.8 + - + +
370A LEU* 4.1 5.6 - - + +
372A ALA* 1.3 76.6 - - - +
374A THR* 1.3 59.2 + - - +
376A GLY* 3.2 1.8 + - - -
377A LEU* 2.8 55.7 + - + +
431A THR* 5.0 2.9 - - - -
451A MET* 4.4 15.9 - - + -
530A HIS* 3.8 29.2 - - + +
531A CYS* 4.7 4.9 - - - -
534A VAL* 3.9 18.6 - - + -
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.7 20.2 + - + -
282A ARG* 3.0 42.8 - - - +
283A SER* 4.7 0.5 + - - -
348A MET* 3.3 22.9 - - - +
370A LEU* 2.9 23.3 + - - +
371A HIS* 2.9 29.2 - - - +
373A LEU* 1.3 75.5 - - - +
375A ALA* 1.3 64.1 + - - +
377A LEU* 4.9 0.2 - - - -
378A LYS* 3.1 25.3 + - - +
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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
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282A ARG* 3.8 18.2 - - - +
371A HIS 3.0 19.0 + - - +
372A ALA 3.6 4.7 - - - +
373A LEU 3.2 0.2 - - - -
374A THR* 1.3 78.4 - - - +
376A GLY* 1.3 63.1 + - - +
378A LYS* 3.5 3.0 + - - +
379A ALA 3.4 14.6 + - - -
427A MET* 3.4 37.2 - - - +
430A GLN* 3.8 22.0 - - + +
431A THR* 3.9 0.7 - - - +
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ALA 3.1 3.4 + - - -
373A LEU 3.6 2.5 - - - -
375A ALA* 1.3 74.7 - - - +
377A LEU* 1.3 59.7 + - - +
379A ALA* 3.3 3.8 + - - +
380A PHE* 2.8 29.3 + - - +
427A MET 4.6 0.7 - - - -
428A MET* 3.8 12.2 - - - +
431A THR* 2.9 24.4 + - - -
531A CYS* 3.4 17.8 - - - -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A VAL* 4.1 2.2 - - + -
344A VAL* 4.2 13.0 - - + -
347A TYR* 5.2 2.7 - - + -
348A MET* 4.0 39.7 - - + -
373A LEU* 2.8 49.1 + - + +
374A THR* 4.9 0.2 - - - -
376A GLY* 1.3 69.0 - - - +
378A LYS* 1.3 61.0 + - - +
380A PHE* 4.1 4.9 - - + -
381A THR* 2.8 36.4 + - + +
531A CYS* 3.7 20.6 - - + +
534A VAL* 4.5 11.2 - - + -
535A VAL* 3.9 26.7 - - + -
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ARG* 4.2 21.5 - - + +
285A LEU* 3.6 38.4 - - + -
286A VAL* 3.9 11.3 - - - +
374A THR 3.1 19.2 + - - +
375A ALA* 3.6 6.1 - - - +
376A GLY 3.2 0.2 - - - -
377A LEU* 1.3 76.9 - - - +
379A ALA* 1.3 55.2 + - - +
381A THR* 3.5 0.2 + - - -
382A THR* 2.7 42.1 + - - +
417A ALA 2.6 29.4 + - - -
418A CYS 4.1 2.0 - - - -
420A PHE 3.1 8.9 + - - -
421A GLU 3.8 8.7 - - - +
422A GLY 2.9 20.2 + - - +
424A ASN* 2.9 18.3 + - - +
427A MET* 4.7 4.9 - - + -
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A ALA 3.4 9.3 + - - +
376A GLY 3.3 7.5 + - - +
377A LEU 3.2 0.2 - - - -
378A LYS* 1.3 79.0 - - - +
380A PHE* 1.3 65.4 + - - +
383A TRP* 3.1 27.2 + - + +
424A ASN* 3.3 53.6 + - + +
427A MET* 4.1 2.7 - - + -
428A MET* 3.9 13.9 - - + -
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Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A PHE* 4.2 8.7 - + - -
376A GLY 2.8 18.8 + - - +
377A LEU* 3.8 4.0 - - + +
379A ALA* 1.3 77.5 - - - +
381A THR* 1.3 68.8 + - + +
383A TRP* 3.9 4.1 - + - +
384A THR* 3.1 41.1 + - + +
428A MET* 4.2 8.7 - - + +
528A GLU* 3.7 46.9 - - + -
531A CYS* 4.0 13.9 - - + -
532A HIS* 3.5 35.7 - + + -
535A VAL* 4.0 23.6 - - + -
562A TYR* 3.5 19.3 - - - -
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Residues in contact with THR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A VAL* 3.6 34.5 - - + +
289A ALA* 4.0 8.2 - - - +
341A PHE* 3.5 38.5 - - + -
344A VAL* 4.7 8.3 - - + -
377A LEU* 2.8 31.9 + - - +
378A LYS 3.5 3.8 + - - -
380A PHE* 1.3 76.0 - - + +
382A THR* 1.3 61.3 + - - +
384A THR* 2.8 21.8 + - - -
385A ALA* 2.8 19.1 + - - +
535A VAL* 5.1 1.6 - - + -
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Residues in contact with THR 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LEU* 4.1 20.4 - - + +
289A ALA* 4.0 1.1 - - + -
378A LYS* 2.7 27.8 + - + +
381A THR* 1.3 82.8 + - - +
383A TRP* 1.3 55.4 + - - +
386A ASN* 2.9 30.3 + - - +
414A PHE* 3.4 28.4 - - + -
417A ALA* 3.9 22.2 + - + +
418A CYS* 3.4 9.8 - - - -
424A ASN* 2.9 28.8 + - - -
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Residues in contact with TRP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ALA 3.1 21.9 + - - +
380A PHE* 3.9 4.5 - - - +
382A THR* 1.3 78.9 + - - +
384A THR* 1.3 64.2 + - + +
386A ASN* 3.3 6.2 + - + +
387A ALA* 3.2 22.9 + - - +
418A CYS* 3.8 15.6 + - - +
423A GLU* 4.4 3.3 + - - -
424A ASN* 3.3 35.2 - - + +
425A THR* 3.7 35.2 - - - -
428A MET* 3.8 29.6 - - + -
524A VAL* 4.8 9.6 - - + -
528A GLU* 6.0 4.0 - - - -
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Residues in contact with THR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 5.0 2.6 - - - +
334A LEU* 5.2 2.9 - - - +
337A THR* 4.7 6.6 - - - +
341A PHE* 2.6 43.3 - - + -
380A PHE* 3.1 31.8 + - + +
381A THR 2.8 8.3 + - - -
383A TRP* 1.3 75.3 - - + +
385A ALA* 1.3 57.8 + - - -
387A ALA* 3.6 3.9 + - - +
388A GLY* 2.9 26.3 + - - -
562A TYR* 5.9 0.2 - - - +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA* 3.4 34.5 - - + +
293A LEU* 3.9 20.3 - - + +
341A PHE* 4.7 2.0 - - + -
381A THR 2.8 18.4 + - - +
384A THR* 1.3 77.9 + - - +
386A ASN* 1.3 58.2 + - - +
388A GLY* 3.6 0.2 - - - -
389A ILE* 2.8 40.5 + - + +
414A PHE* 4.0 8.7 - - + -
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Residues in contact with ASN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A THR 2.9 20.8 + - - +
383A TRP* 3.3 9.0 + - + +
385A ALA* 1.3 78.1 - - - +
387A ALA* 1.3 66.2 + - - +
389A ILE* 3.3 6.9 + - - +
390A GLU 3.6 2.3 + - - -
411A TYR* 3.3 44.2 + - - -
414A PHE* 3.8 8.6 - - + -
415A THR* 2.9 39.4 + - - -
418A CYS* 3.9 14.4 - - - -
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TRP 3.2 11.1 + - - +
384A THR* 4.1 4.0 - - - +
386A ASN* 1.3 82.7 - - - +
388A GLY* 1.3 64.5 + - - +
390A GLU* 3.1 9.8 + - - +
391A GLU* 3.1 27.1 + - + +
411A TYR* 5.5 0.2 - - - -
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Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.7 9.6 - - - -
334A LEU* 3.4 32.4 - - - +
384A THR 2.9 19.4 + - - -
385A ALA 3.6 1.3 - - - -
387A ALA* 1.3 78.2 - - - +
389A ILE* 1.3 61.2 + - - +
391A GLU* 3.2 6.1 + - - +
392A CYS* 3.1 20.4 + - - -
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Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A SER* 3.8 23.1 - - - +
293A LEU* 4.0 17.9 - - - +
296A ALA* 4.0 15.0 - - + -
385A ALA* 2.8 25.1 + - + +
386A ASN* 3.7 5.4 - - - +
387A ALA 3.2 0.2 - - - -
388A GLY* 1.3 72.3 - - - +
390A GLU* 1.3 58.1 + - - +
392A CYS* 3.2 6.2 + - - +
393A ARG 3.1 21.0 + - - -
407A ILE* 3.6 17.8 - - + +
410A ILE* 4.2 5.6 - - + -
411A TYR* 3.7 32.3 - - + +
414A PHE* 3.8 31.2 - - + -
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASN 3.6 2.3 + - - +
387A ALA* 3.1 11.0 + - - +
389A ILE* 1.3 76.2 - - - +
391A GLU* 1.3 64.7 + - - +
393A ARG* 2.8 48.8 + - - +
394A MET* 3.1 38.8 + - + +
407A ILE* 5.0 0.5 - - - +
408A PRO* 5.5 1.6 - - - +
411A TYR* 3.5 52.5 - - + +
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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
----------------------------------------------------------
330A LYS* 4.9 21.2 - - + +
331A LEU* 4.8 0.8 - - - +
334A LEU* 3.7 18.4 - - + -
387A ALA* 3.1 21.5 + - + +
388A GLY* 3.4 10.8 - - - +
390A GLU* 1.3 76.3 - - - +
392A CYS* 1.3 64.2 + - - +
394A MET* 3.4 24.5 + - - +
395A ALA* 3.0 24.8 + - - +
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Residues in contact with CYS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 4.8 2.0 - - - -
296A ALA* 3.6 43.3 - - + +
297A CYS* 3.7 14.1 - - - -
300A ALA* 3.6 9.5 - - + +
331A LEU* 4.2 14.6 - - - -
334A LEU* 4.1 15.7 - - - -
388A GLY 3.1 17.5 + - - -
389A ILE 3.2 8.5 + - - +
391A GLU* 1.3 77.5 - - - +
393A ARG* 1.3 63.6 + - - +
395A ALA* 3.3 8.3 + - - +
396A CYS* 3.5 17.5 + - - -
407A ILE* 3.9 3.8 - - + -
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE 3.1 5.4 + - - +
390A GLU* 2.8 43.9 + - - +
391A GLU 3.3 0.2 - - - -
392A CYS* 1.3 76.2 - - - +
394A MET* 1.3 88.8 + - - +
396A CYS* 3.1 19.8 + - - +
397A GLY 4.1 3.5 + - - +
400A GLY* 3.3 41.0 - - - +
401A TYR* 4.0 30.5 - - - +
407A ILE* 3.5 35.8 - - + +
408A PRO* 4.2 10.8 - - + +
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Residues in contact with MET 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LYS* 5.2 3.1 + - - -
390A GLU* 3.1 31.6 + - + +
391A GLU* 3.6 26.5 - - - +
393A ARG* 1.3 101.0 - - - +
395A ALA* 1.3 57.3 + - - +
396A CYS 3.0 5.6 - - - -
397A GLY* 3.0 22.2 + - - +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 4.9 0.9 - - + -
321A ILE* 4.2 5.7 - - - +
327A GLN* 2.8 38.5 + - - +
330A LYS* 4.1 24.7 - - + +
331A LEU* 3.8 20.2 - - + -
391A GLU 3.0 18.0 + - - +
392A CYS 3.6 7.0 - - - +
393A ARG 3.3 0.4 - - - -
394A MET* 1.3 76.7 - - - +
396A CYS* 1.3 58.6 + - - +
397A GLY 3.2 1.9 + - - -
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Residues in contact with CYS 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ILE* 4.7 2.2 - - - -
300A ALA* 3.8 23.8 - - - -
303A TYR* 3.4 46.9 + - + -
304A SER* 5.9 0.4 - - - -
321A ILE* 5.8 1.1 - - - -
392A CYS 3.5 15.0 - - - -
393A ARG 3.1 10.7 + - - +
394A MET 3.0 1.0 - - - -
395A ALA* 1.3 77.6 - - - +
397A GLY* 1.3 63.0 + - - +
398A GLY 3.7 0.5 + - - -
399A HIS* 3.9 3.3 + - - -
400A GLY* 3.7 17.8 + - - +
407A ILE* 4.3 11.7 - - - -
621A LEU* 4.4 8.1 - - + -
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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