Contacts of the helix formed by residues 483 - 506 (chain D) in PDB entry 1JIQ
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 THR 483 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C VAL* 4.1 29.2 - - + -
48D HIS 4.5 6.5 + - - +
171D LEU* 4.0 3.1 - - - -
174D TYR* 3.5 15.9 - - + +
481D LYS* 3.0 15.3 + - + +
482D LEU* 1.3 77.1 - - - +
484D PRO* 1.3 77.5 - - - +
485D PHE* 3.8 7.7 + - - +
486D MET* 3.1 21.9 + - - +
487D LEU* 3.0 22.0 + - - +
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Residues in contact with PRO 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D LEU* 3.8 30.9 - - + -
174D TYR* 3.6 31.0 - - + -
292D ASN* 3.5 45.8 - - + +
295D GLN* 4.1 6.1 - - + -
296D LEU* 3.4 16.6 - - - +
483D THR* 1.3 89.2 - - - +
485D PHE* 1.3 62.2 + - - +
487D LEU* 3.4 0.5 + - - +
488D GLY 3.1 17.3 + - - -
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Residues in contact with PHE 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 3.4 34.5 - - + -
48D HIS* 3.3 47.6 - + + -
295D GLN* 3.3 38.9 + - + +
298D SER* 3.6 15.7 - - - -
299D GLY* 3.3 32.5 - - - -
302D TRP* 3.8 19.3 - + + -
483D THR* 3.2 6.8 + - - +
484D PRO* 1.3 79.6 - - - +
486D MET* 1.3 68.8 + - + +
488D GLY 3.2 1.9 + - - -
489D ALA* 3.0 20.6 + - + +
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Residues in contact with MET 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 4.3 6.5 - - + +
48D HIS 4.2 5.4 - - - +
49D GLY* 3.8 37.5 - - - +
50D HIS 4.0 5.2 - - - +
51D ILE* 3.6 36.1 - - + -
479D PHE* 3.8 24.7 - - + -
480D THR 4.7 1.6 - - - +
481D LYS 3.2 29.6 - - - +
482D LEU* 4.4 0.7 - - - -
483D THR* 3.1 13.6 + - - +
485D PHE* 1.3 77.9 - - + +
487D LEU* 1.3 66.7 + - - +
489D ALA* 3.2 6.0 + - - +
490D LEU* 2.9 35.0 + - + +
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D MET* 4.4 6.5 - - - -
167D VAL* 3.9 26.2 - - + -
170D ALA* 3.9 11.7 - - + -
171D LEU* 3.8 30.1 - - + -
296D LEU* 4.2 4.7 - - + -
345D LEU* 3.9 27.4 - - + -
348D PHE* 4.5 5.2 - - + -
482D LEU* 4.1 17.1 - - + +
483D THR 3.0 16.1 + - - +
484D PRO 3.7 3.8 - - - +
486D MET* 1.3 75.3 - - - +
488D GLY* 1.3 58.3 + - - +
490D LEU* 3.2 4.9 + - + +
491D VAL* 2.9 50.9 + - + +
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Residues in contact with GLY 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D TRP* 3.7 10.7 - - - -
296D LEU* 3.5 33.1 - - - +
300D ALA* 3.5 9.2 - - - -
484D PRO 3.1 7.9 + - - -
485D PHE 3.2 2.2 + - - -
487D LEU* 1.3 79.3 - - - +
489D ALA* 1.3 60.4 + - - +
491D VAL 3.5 0.2 + - - -
492D ALA* 3.0 26.0 + - - +
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Residues in contact with ALA 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D THR* 5.0 0.9 - - + -
51D ILE* 4.5 11.9 - - + -
299D GLY* 3.4 23.0 - - - +
302D TRP* 5.0 4.0 - - + -
303D MET* 3.6 24.5 - - + +
485D PHE* 3.0 18.6 + - + +
486D MET* 3.5 11.9 - - - +
488D GLY* 1.3 77.6 - - - +
490D LEU* 1.3 61.4 + - - +
493D MET* 3.0 23.9 + - - +
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Residues in contact with LEU 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 4.4 16.4 - - + -
345D LEU* 5.6 2.9 - - + -
348D PHE* 4.7 14.8 - - + -
407D LEU* 5.0 6.3 - - + -
477D ILE* 4.3 9.4 - - + -
479D PHE* 3.7 48.9 - - + -
482D LEU* 4.0 13.2 - - + -
486D MET* 2.9 27.0 + - + +
487D LEU* 3.2 5.6 + - + +
489D ALA* 1.3 77.1 - - - +
491D VAL* 1.3 62.3 + - - +
493D MET* 3.3 26.2 - - + +
494D TYR* 3.3 27.8 + - + -
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Residues in contact with VAL 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D MET* 3.9 24.2 - - + -
167D VAL* 5.5 1.3 - - + -
276D LEU* 4.7 3.6 - - + -
277D TRP* 3.5 28.5 - - + -
296D LEU* 6.0 0.4 - - + -
348D PHE* 4.0 13.7 - - + -
351D TYR* 4.0 17.9 - - + +
352D PHE* 3.8 20.7 - - + -
487D LEU* 2.9 29.2 + - + +
490D LEU* 1.3 75.5 - - - +
492D ALA* 1.3 62.5 + - - +
494D TYR* 3.2 3.5 + - - -
495D GLU* 3.0 24.0 + - - +
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Residues in contact with ALA 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ARG* 3.8 18.6 - - - +
277D TRP* 4.4 0.8 - - - -
300D ALA* 3.8 19.7 - - + +
303D MET* 3.9 13.0 - - + -
304D ASP* 4.1 2.5 - - - +
488D GLY 3.0 18.5 + - - +
489D ALA 3.8 3.1 - - - +
491D VAL* 1.3 73.6 - - - +
493D MET* 1.3 65.4 + - - +
495D GLU* 3.2 13.8 + - - +
496D HIS* 3.0 29.1 + - - -
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Residues in contact with MET 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D LEU* 5.6 0.2 - - - -
51D ILE* 5.1 3.1 - - - -
53D VAL* 4.4 9.9 - - - -
303D MET* 3.6 29.1 - - + +
316D ALA* 4.1 14.4 - - - -
317D PRO* 3.5 18.7 - - - +
320D LEU* 3.7 31.4 - - + -
477D ILE* 3.9 20.9 - - + -
489D ALA 3.0 14.0 + - - +
490D LEU* 3.3 31.9 - - + +
491D VAL 3.2 0.2 - - - -
492D ALA* 1.3 77.7 - - - +
494D TYR* 1.3 73.4 + - + +
496D HIS 3.3 0.3 + - - -
497D LYS* 3.0 24.1 + - - +
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Residues in contact with TYR 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D LEU* 4.8 6.1 - - + -
338D MET* 3.7 28.7 - - + +
348D PHE* 4.1 21.1 - + - -
352D PHE* 3.4 26.5 - + + -
356D ASP* 6.2 0.2 - - - -
405D ASP* 2.8 39.4 + - - +
407D LEU* 3.9 11.4 - - + +
477D ILE* 3.7 15.3 - - + +
490D LEU* 3.3 19.6 + - + -
491D VAL 3.2 2.8 + - - +
493D MET* 1.3 96.6 - - + +
495D GLU* 1.3 59.0 + - - +
497D LYS* 3.2 30.9 + - + +
498D ILE* 2.8 39.4 + - + +
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Residues in contact with GLU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D HIS* 3.7 5.1 - - - +
104D ARG* 2.7 39.7 + - - +
274D TYR* 3.5 39.6 + - + -
277D TRP* 2.9 28.1 + - - -
351D TYR* 4.2 11.1 + - + +
352D PHE* 4.3 6.2 - - + -
491D VAL* 3.0 20.6 + - + +
492D ALA* 3.2 9.8 + - - +
494D TYR* 1.3 75.1 - - - +
496D HIS* 1.3 64.1 + - - +
498D ILE* 3.3 11.5 + - - +
499D PHE* 3.0 25.5 + - - +
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Residues in contact with HIS 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D MET* 4.1 14.8 - - + +
85D PHE* 4.4 1.3 - + - -
100D HIS* 4.6 6.2 + - - -
101D VAL* 3.8 19.7 - - + +
104D ARG* 3.8 7.9 + - - -
303D MET* 4.4 4.5 - - + -
304D ASP* 2.6 37.1 + - - -
307D PHE* 3.3 46.6 - + + -
317D PRO* 3.7 18.8 - - + -
492D ALA 3.0 22.5 + - - +
495D GLU* 1.3 77.2 - - + +
497D LYS* 1.3 64.1 + - - +
499D PHE* 3.1 6.1 + - - +
500D VAL* 2.9 28.4 + - - +
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Residues in contact with LYS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D PRO* 3.6 17.8 - - + +
320D LEU* 3.9 25.8 + - + +
321D ALA* 3.6 19.3 - - - +
324D GLY* 5.3 3.5 - - - -
336D HIS* 3.3 42.4 + - - -
356D ASP* 4.7 7.8 + - - +
405D ASP* 4.4 2.8 + - - -
493D MET 3.0 14.4 + - - +
494D TYR* 3.2 28.8 + - + +
496D HIS* 1.3 74.4 - - - +
498D ILE* 1.3 68.1 + - + +
500D VAL 3.2 1.7 + - - -
501D GLN* 3.1 50.0 + - - +
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D TYR* 3.7 11.7 - - + +
352D PHE* 3.8 19.5 - - + -
355D GLY 3.6 8.3 - - - +
356D ASP* 3.5 44.6 - - + +
359D SER* 3.7 24.9 - - - -
360D ASN* 3.0 36.6 + - - +
494D TYR* 2.8 22.5 + - + +
495D GLU* 3.4 7.9 - - - +
497D LYS* 1.3 82.0 - - + +
499D PHE* 1.3 61.9 + - - +
501D GLN* 3.5 3.5 + - - +
502D GLY* 3.0 10.2 + - - -
509D SER* 3.9 2.0 + - - +
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Residues in contact with PHE 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 4.5 3.8 - - + -
80D ALA* 3.6 26.7 - - + -
81D ARG* 3.7 23.8 - - + -
84D MET* 3.9 21.8 - - + -
90D ILE* 4.0 16.8 - - + -
307D PHE* 3.9 20.4 - + - -
495D GLU 3.0 14.0 + - - +
496D HIS* 3.1 13.0 + - - +
498D ILE* 1.3 78.0 - - - +
500D VAL* 1.3 62.4 + - + +
502D GLY* 3.3 2.3 + - - -
503D ILE* 3.0 59.9 + - + +
509D SER* 4.6 5.9 + - - -
510D PHE* 3.6 29.4 - + + -
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Residues in contact with VAL 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ALA* 5.4 0.4 - - + -
77D VAL* 4.1 23.6 - - + -
307D PHE* 3.8 30.3 - - + -
318D VAL* 4.1 20.9 - - + +
321D ALA* 3.4 25.4 - - + -
322D LEU* 5.3 0.4 - - + -
496D HIS 2.9 20.3 + - - +
497D LYS 3.2 0.2 + - - -
499D PHE* 1.3 74.8 - - + +
501D GLN* 1.3 65.9 + - - +
503D ILE* 3.3 6.9 + - - +
504D ILE* 3.0 38.7 + - + +
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Residues in contact with GLN 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA* 3.1 31.3 - - + +
324D GLY* 3.5 20.1 - - - -
325D ILE* 4.0 12.6 - - + -
328D ILE* 4.3 2.9 - - - +
356D ASP* 4.7 10.7 + - - -
360D ASN* 4.3 6.7 - - - +
377D PRO* 4.8 5.7 - - - +
497D LYS* 3.1 41.4 + - - +
498D ILE* 3.9 5.9 - - - +
500D VAL* 1.3 77.3 - - - +
502D GLY* 1.3 57.4 + - - +
504D ILE* 3.3 2.5 + - - +
505D TRP* 2.9 65.0 + - + -
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Residues in contact with GLY 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D ASN* 3.9 3.1 - - - +
498D ILE 3.0 11.5 + - - -
499D PHE 3.7 0.7 - - - -
500D VAL 3.3 0.4 - - - -
501D GLN* 1.3 75.0 - - - +
503D ILE* 1.3 57.1 + - - +
505D TRP* 3.3 1.4 + - - -
506D ASP 2.9 23.4 + - - -
507D ILE* 3.0 32.8 + - - +
509D SER* 3.5 23.8 - - - -
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Residues in contact with ILE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 3.0 38.8 + - - +
77D VAL* 4.1 18.2 - - + -
80D ALA* 3.5 30.1 - - + -
83D ARG* 5.7 0.9 - - - +
90D ILE* 6.0 1.1 - - + -
499D PHE* 3.0 46.7 + - + +
500D VAL* 3.6 7.2 - - - +
501D GLN 3.3 0.2 - - - -
502D GLY* 1.3 76.5 - - - +
504D ILE* 1.3 63.7 + - - +
506D ASP* 3.1 8.2 + - - +
507D ILE 5.2 3.4 - - - +
510D PHE* 6.1 1.1 - - + -
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Residues in contact with ILE 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.7 32.0 - - + +
71D LEU* 4.2 11.7 - - + -
72D ALA* 4.4 5.6 - - - -
75D ARG* 2.8 37.0 + - + +
77D VAL* 4.0 17.3 - - + -
322D LEU* 3.6 31.0 - - + -
325D ILE* 4.1 25.8 - - + -
500D VAL* 3.0 32.3 + - + +
501D GLN 3.7 4.3 - - - +
503D ILE* 1.3 77.3 - - - +
505D TRP* 1.3 59.2 + - - +
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Residues in contact with TRP 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 5.7 0.2 - - - +
4D LEU* 3.8 10.8 + - + +
325D ILE* 3.5 21.1 - - + +
328D ILE* 3.7 22.7 - - + -
329D ASN* 2.7 25.2 + - - -
360D ASN* 3.7 20.6 - - + -
365D THR* 4.2 4.5 - - - +
373D HIS* 3.6 41.1 + + + -
374D GLN 3.4 8.1 + - - -
375D THR* 3.5 33.4 - - + -
376D GLY* 3.5 18.8 - - - -
501D GLN* 2.9 45.6 + - + +
502D GLY* 4.2 2.5 - - - -
504D ILE* 1.3 75.0 - - - +
506D ASP* 1.3 67.7 + - - +
507D ILE* 3.4 22.0 + - + +
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Residues in contact with ASP 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D ALA* 3.6 26.3 - - + +
75D ARG* 3.5 17.1 + - - +
92D TYR* 3.6 2.3 + - - -
365D THR* 3.2 13.1 + - + -
366D LYS* 2.9 63.2 + - - +
367D SER* 4.4 4.5 + - - -
502D GLY 2.9 6.0 + - - -
503D ILE* 3.1 10.3 + - - +
504D ILE 3.2 0.2 - - - -
505D TRP* 1.3 81.3 - - - +
507D ILE* 1.3 60.0 + - - +
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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