Contacts of the helix formed by residues 408 - 433 (chain N) in PDB entry 3HOU
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 LEU 408 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N GLN* 3.6 52.0 - - + +
47N GLN* 3.8 14.4 - - - +
50N SER* 3.5 16.6 - - - +
213N ILE 6.3 0.4 - - - -
214N ALA* 4.2 13.5 - - + +
406N LEU* 3.0 23.4 + - + +
407N ASP* 1.3 75.3 - - - +
409N ALA* 1.3 72.1 + - + +
410N GLY 3.2 2.4 + - - -
411N PRO* 3.2 9.3 - - - +
412N LEU* 3.2 23.6 + - - +
539N LEU* 5.9 0.2 - - + -
545N ILE* 3.3 31.6 - - + -
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Residues in contact with ALA 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N GLN* 3.8 20.8 + - - +
50N SER* 4.6 0.2 - - - +
51N PHE* 4.8 1.8 - - + -
173N MET* 3.3 35.0 - - + -
203N PHE* 4.4 3.8 - - + -
212N LEU* 3.5 24.2 - - + +
408N LEU* 1.3 78.6 - - - +
410N GLY* 1.3 62.3 + - - +
412N LEU* 3.4 2.6 + - - +
413N LEU* 2.9 29.3 + - + +
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Residues in contact with GLY 410 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N SER* 2.9 28.8 + - - -
51N PHE* 4.5 0.6 - - - +
54N PHE* 3.9 17.5 - - - -
409N ALA* 1.3 75.0 - - - +
411N PRO* 1.3 60.3 - - - +
412N LEU 2.9 0.9 + - - -
413N LEU* 2.9 5.4 + - - +
414N ALA* 2.6 37.5 + - - +
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Residues in contact with PRO 411 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50N SER* 3.0 19.3 - - - +
406N LEU 5.4 0.4 - - - +
407N ASP* 4.0 23.3 - - + +
408N LEU 3.2 19.3 - - - +
410N GLY* 1.3 83.1 - - - +
412N LEU* 1.3 55.6 + - - +
414N ALA* 3.2 8.9 - - + +
415N GLN* 2.8 28.6 + - - +
547N VAL 6.0 1.8 - - - +
630N ALA* 5.9 7.4 - - + -
631N GLY* 6.5 0.7 - - - -
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Residues in contact with LEU 412 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212N LEU* 4.3 15.7 - - + -
213N ILE 4.1 7.0 - - - +
215N GLN* 4.3 12.3 - - + -
407N ASP* 3.6 21.8 - - + +
408N LEU 3.2 21.5 + - - +
409N ALA 3.5 3.8 - - - +
410N GLY 2.9 1.6 + - - -
411N PRO* 1.3 73.8 - - - +
413N LEU* 1.3 66.3 + - - +
414N ALA 3.1 0.9 - - - -
415N GLN* 3.1 4.7 + - - +
416N LEU* 3.0 16.8 + - - +
466N TRP* 3.0 39.8 + - + +
476N ARG* 3.8 24.2 - - - +
479N VAL* 3.8 22.7 - - + -
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Residues in contact with LEU 413 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N PHE* 3.3 42.4 - - + -
54N PHE* 3.9 21.1 - - + -
170N LEU* 4.9 7.9 - - + -
171N PRO* 5.5 0.9 - - + +
203N PHE* 4.0 11.7 - - + -
212N LEU* 4.5 6.3 - - + -
409N ALA 2.9 21.3 + - - +
410N GLY* 2.9 8.4 + - - +
412N LEU* 1.3 71.9 - - - +
414N ALA* 1.3 57.2 - - - +
416N LEU* 2.9 7.7 + - + +
417N PHE* 2.7 36.0 + - - +
457N LEU* 4.8 14.7 - - + +
461N LEU* 4.3 33.4 - - + -
466N TRP* 4.3 2.0 - - + -
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Residues in contact with ALA 414 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N PHE* 3.4 23.0 - - + -
58N THR* 4.0 15.5 - - + -
62N ILE* 3.7 7.0 - - + +
249N ARG* 5.7 7.0 - - - +
410N GLY 2.6 16.6 + - - +
411N PRO* 3.2 16.2 - - + +
413N LEU* 1.3 75.7 - - - +
415N GLN* 1.3 64.0 + - - +
418N LYS* 3.1 25.4 + - - +
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Residues in contact with GLN 415 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411N PRO 2.8 18.0 + - - +
412N LEU* 3.1 8.4 + - - +
414N ALA* 1.3 74.8 - - - +
416N LEU* 1.3 52.5 + - - +
418N LYS* 3.8 6.4 - - - +
419N THR* 2.8 37.1 + - + +
466N TRP* 3.9 22.7 + - - +
467N GLY* 5.1 6.7 - - - +
476N ARG* 2.6 34.3 + - - +
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Residues in contact with LEU 416 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412N LEU 3.0 9.6 + - - +
413N LEU* 2.9 11.6 + - - +
415N GLN* 1.3 76.2 - - - +
417N PHE* 1.3 66.0 + - - +
418N LYS 3.1 1.6 - - - -
419N THR* 3.0 18.7 + - - +
420N LEU* 3.0 35.7 + - + +
456N GLY 4.8 5.8 - - - +
457N LEU* 4.6 9.2 - - + -
460N ALA* 3.3 32.1 - - + -
461N LEU* 4.6 4.5 - - + -
466N TRP* 3.6 46.7 - - + +
467N GLY* 6.0 0.4 - - - -
468N GLU* 5.0 8.1 - - + +
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Residues in contact with PHE 417 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N PHE* 4.1 13.0 - + + -
59N LEU* 3.1 34.3 - - + -
62N ILE* 3.8 20.0 - - + -
63N ILE* 4.1 20.4 - - + -
95N ILE* 5.1 2.5 - - + -
128N LEU* 3.8 20.4 - - + -
167N ILE 5.6 0.4 - - - -
170N LEU* 6.0 0.7 - - + -
413N LEU 2.7 19.3 + - - +
414N ALA 4.0 2.2 - - - +
416N LEU* 1.3 71.8 - - - +
418N LYS* 1.3 53.2 + - - +
420N LEU* 3.0 5.7 + - - +
421N PHE* 2.6 52.3 + - + +
453N ILE* 3.3 41.1 - - + -
457N LEU* 4.6 18.2 - - + +
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Residues in contact with LYS 418 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N ILE* 3.5 28.9 - - + -
65N GLU* 2.8 23.7 + - - +
247N GLY 3.6 2.2 - - - +
248N SER* 3.1 24.7 - - - +
249N ARG* 2.8 40.7 - - - +
414N ALA 3.1 17.9 + - - +
415N GLN* 3.8 7.2 - - - +
416N LEU 3.1 0.2 - - - -
417N PHE* 1.3 81.6 - - - +
419N THR* 1.3 65.0 + - + +
420N LEU 3.0 1.2 + - - -
421N PHE* 3.3 1.1 + - - +
422N LYS* 3.0 56.0 + - - +
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Residues in contact with THR 419 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415N GLN* 2.8 24.0 + - + +
416N LEU* 3.0 13.7 + - - +
418N LYS* 1.3 77.3 - - - +
420N LEU* 1.3 61.1 + - - +
422N LYS* 4.1 8.8 + - + +
423N LYS* 3.7 16.1 + - - +
468N GLU* 5.4 13.0 - - - +
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Residues in contact with LEU 420 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416N LEU* 3.0 34.5 + - + +
417N PHE* 3.0 9.0 + - - +
419N THR* 1.3 76.6 - - - +
421N PHE* 1.3 57.9 + - - +
422N LYS 3.0 1.6 - - - -
423N LYS* 2.7 27.0 + - + +
424N LEU* 3.1 10.4 + - - +
452N THR* 4.2 27.0 - - + +
453N ILE* 4.5 18.7 - - + +
456N GLY* 3.7 25.8 - - - -
457N LEU* 3.8 17.0 - - + +
468N GLU* 4.2 28.7 - - + +
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Residues in contact with PHE 421 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N ILE* 3.2 34.5 - - + -
63N ILE* 3.2 45.5 - - + -
66N ASP* 4.1 14.6 - - - -
67N SER* 4.4 10.1 - - - -
92N PHE* 4.6 16.8 - + - -
417N PHE* 2.6 36.3 + - + +
418N LYS 3.9 2.5 - - - +
420N LEU* 1.3 72.2 - - - +
422N LYS* 1.3 55.0 + - + +
424N LEU* 3.4 20.6 + - + +
425N THR* 2.7 50.5 + - - -
453N ILE* 4.2 12.2 - - + +
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Residues in contact with LYS 422 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65N GLU* 3.8 2.9 + - - -
66N ASP* 3.0 41.8 - - + +
248N SER* 4.5 13.1 - - - +
418N LYS* 3.0 57.9 + - + +
419N THR* 4.4 8.1 - - + +
420N LEU 3.0 1.0 - - - -
421N PHE* 1.3 79.8 - - + +
423N LYS* 1.3 60.5 + - - +
424N LEU 3.2 1.6 - - - -
425N THR* 3.7 9.1 - - + +
426N LYS* 2.9 36.2 + - + +
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Residues in contact with LYS 423 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419N THR 3.7 11.4 + - - +
420N LEU* 2.7 15.4 + - + +
422N LYS* 1.3 78.2 - - - +
424N LEU* 1.3 58.7 + - - +
426N LYS* 3.8 10.4 - - - +
427N ASP* 2.9 41.6 + - - +
452N THR* 4.3 23.3 - - + -
468N GLU* 3.7 13.2 - - - +
470N LYS* 3.1 40.0 - - - +
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Residues in contact with LEU 424 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92N PHE* 6.1 0.7 - - + -
167N ILE* 3.2 36.3 - - + -
420N LEU 3.1 8.6 + - - +
421N PHE* 3.5 22.7 - - + +
423N LYS* 1.3 77.7 - - - +
425N THR* 1.3 54.9 + - - +
427N ASP* 2.9 10.1 + - + +
428N ILE* 2.7 54.1 + - + +
447N ALA 5.5 0.2 - - - +
448N ILE* 4.3 8.7 - - + -
449N ASN* 4.1 36.1 - - + +
452N THR* 5.3 8.7 - - - +
453N ILE* 3.6 16.4 - - + -
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Residues in contact with THR 425 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N ASP* 3.9 20.7 + - - +
67N SER* 4.1 8.8 + - - -
69N LEU* 3.4 28.4 - - + +
92N PHE* 4.6 1.9 - - - -
421N PHE* 2.7 44.9 + - - -
422N LYS* 3.7 11.4 - - + +
424N LEU* 1.3 74.8 - - - +
426N LYS* 1.3 64.1 + - + +
427N ASP 3.2 4.3 + - - -
428N ILE* 3.3 26.1 + - - +
429N PHE* 3.4 1.9 + - - +
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Residues in contact with LYS 426 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N LEU* 6.0 0.2 - - - -
422N LYS* 2.9 27.7 + - - +
423N LYS* 3.8 7.6 - - - +
424N LEU 3.2 0.2 - - - -
425N THR* 1.3 81.8 - - + +
427N ASP* 1.3 63.2 + - - +
429N PHE* 4.2 15.0 - - + -
430N ARG* 3.6 15.7 + - - +
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Residues in contact with ASP 427 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423N LYS* 2.9 32.1 + - - +
424N LEU* 3.1 19.1 - - + +
426N LYS* 1.3 77.0 - - - +
428N ILE* 1.3 66.3 + - - +
429N PHE 3.0 1.3 - - - +
430N ARG* 3.0 43.0 + - - +
431N TYR* 3.4 5.9 + - - +
447N ALA* 5.7 2.2 - - - +
449N ASN* 5.6 6.4 - - + +
452N THR* 6.1 1.6 - - - -
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Residues in contact with ILE 428 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N LEU* 3.8 5.2 - - + -
90N ILE* 4.3 12.6 - - + -
92N PHE* 3.5 35.7 - - + -
421N PHE* 5.1 0.9 - - + -
424N LEU* 2.7 40.6 + - + +
425N THR* 3.3 26.7 - - - +
427N ASP* 1.3 79.4 - - - +
429N PHE* 1.3 61.1 + - - +
430N ARG 3.3 0.2 + - - -
431N TYR* 3.4 13.2 + - - +
432N MET* 3.3 35.7 + - + +
447N ALA* 5.9 5.6 - - - -
448N ILE* 5.4 15.9 - - + -
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Residues in contact with PHE 429 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N LEU* 3.2 40.4 - - + -
70N ILE* 3.3 39.7 - - + -
425N THR 3.4 8.3 + - - +
426N LYS* 4.2 15.5 - - + -
428N ILE* 1.3 79.8 - - - +
430N ARG* 1.3 57.3 + - + +
432N MET* 3.2 23.7 + - + +
433N GLN* 2.9 66.4 + - + +
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Residues in contact with ARG 430 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426N LYS 3.6 12.6 + - - +
427N ASP* 3.0 49.7 + - - +
429N PHE* 1.3 75.5 - - + +
431N TYR* 1.3 59.5 + - - +
433N GLN* 3.2 24.4 + - - +
434N ARG* 3.0 63.3 + - - +
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Residues in contact with TYR 431 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427N ASP 3.4 4.8 + - - +
428N ILE* 3.4 10.3 + - - +
430N ARG* 1.3 77.7 - - - +
432N MET* 1.3 68.7 + - + +
434N ARG* 3.5 17.4 + - - +
435N THR* 3.2 29.3 + - - -
446N LEU* 4.0 29.7 - - + +
447N ALA* 3.0 37.5 - - + -
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Residues in contact with MET 432 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69N LEU* 3.3 31.4 - - + -
70N ILE* 4.7 16.4 - - + -
90N ILE* 3.0 36.8 - - + -
428N ILE* 3.3 10.8 - - + +
429N PHE* 3.2 42.1 + - + +
431N TYR* 1.3 78.0 - - + +
433N GLN* 1.3 53.5 + - + +
434N ARG 2.5 19.2 + - - -
435N THR* 2.9 24.8 + - - +
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Residues in contact with GLN 433 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N ILE* 5.7 3.6 - - + +
429N PHE* 2.9 61.1 + - + +
430N ARG* 3.2 15.4 + - - +
432N MET* 1.3 72.2 - - + +
434N ARG* 1.3 69.9 + - - +
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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