Contacts of the helix formed by residues 410 - 451 (chain H) in PDB entry 5WUA
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 GLY 410 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H ASN 3.4 2.0 + - - -
407H LEU* 2.8 27.5 + - - +
409H MET* 1.3 76.4 - - - +
411H GLU* 1.3 59.3 + - - -
413H THR* 2.9 25.8 + - - -
414H ALA* 2.9 11.6 + - - +
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Residues in contact with GLU 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H MET 3.2 2.6 + - - -
410H GLY* 1.3 71.4 - - - -
412H MET* 1.3 57.4 + - - +
414H ALA* 2.9 11.3 + - + +
415H GLY* 2.9 29.1 + - - -
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Residues in contact with MET 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H MET* 3.5 15.1 + - + +
410H GLY 3.2 0.4 - - - -
411H GLU* 1.3 78.5 - - - +
413H THR* 1.3 53.6 + - - +
416H GLN* 2.7 43.4 + - + +
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Residues in contact with THR 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406H ASN 5.7 0.4 - - - -
409H MET* 4.4 9.9 + - - +
410H GLY 2.9 16.9 + - - -
412H MET* 1.3 77.3 - - - +
414H ALA* 1.3 62.9 + - - +
416H GLN* 4.7 0.4 - - - -
417H ILE* 2.6 42.9 + - - +
418H CYS 3.4 0.5 + - - -
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Residues in contact with ALA 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410H GLY 2.9 6.8 + - - +
411H GLU* 2.9 22.0 + - - +
413H THR* 1.3 75.3 - - - +
415H GLY* 1.3 59.2 + - - +
418H CYS* 2.8 34.6 + - - +
1208H VAL* 5.0 18.6 - - + -
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Residues in contact with GLY 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411H GLU 2.9 14.8 + - - -
414H ALA* 1.3 74.9 - - - +
416H GLN* 1.3 55.9 + - - -
418H CYS* 3.4 4.3 - - - +
419H ASN* 2.9 28.8 + - - +
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Residues in contact with GLN 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412H MET* 2.7 29.6 + - + +
413H THR* 4.7 0.4 - - - -
415H GLY* 1.3 70.9 - - - +
417H ILE* 1.3 52.7 + - - +
419H ASN* 2.7 29.5 + - - +
420H LEU* 2.9 10.4 + - - +
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Residues in contact with ILE 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413H THR* 2.6 36.1 + - - +
416H GLN* 1.3 71.3 - - - +
418H CYS* 1.3 64.9 + - - +
420H LEU* 3.0 25.2 - - + +
421H VAL* 3.5 4.9 + - - +
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Residues in contact with CYS 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413H THR 3.4 0.4 + - - -
414H ALA 2.8 23.9 + - - +
415H GLY* 3.4 6.3 - - - +
417H ILE* 1.3 72.0 - - - +
419H ASN* 1.3 57.6 + - - +
420H LEU 2.8 9.5 + - - -
421H VAL* 2.9 18.5 + - - +
422H ALA* 2.9 14.7 + - + +
1204H PHE* 5.5 13.7 - - + -
1205H ALA* 5.9 4.9 - - + +
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Residues in contact with ASN 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H GLY 2.9 12.6 + - - +
416H GLN* 2.7 16.6 + - - +
418H CYS* 1.3 71.0 - - - +
420H LEU* 1.3 56.5 + - - +
422H ALA* 4.3 4.9 - - - -
423H ILE* 2.9 27.2 + - + +
424H ASP* 2.8 23.6 + - - +
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Residues in contact with LEU 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416H GLN 2.9 6.1 + - - +
417H ILE* 3.0 24.7 - - + +
418H CYS 2.8 2.0 + - - -
419H ASN* 1.3 74.5 - - - +
421H VAL* 1.3 51.7 + - - +
424H ASP* 2.7 34.2 + - + +
425H THR* 2.7 17.0 + - - -
609H LYS* 5.6 11.0 - - + +
610H LEU* 6.5 0.4 - - - -
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Residues in contact with VAL 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H GLN* 6.0 5.2 - - + -
395H ILE* 5.0 16.4 - - + -
417H ILE 3.5 3.7 + - - +
418H CYS* 2.9 8.9 + - - +
420H LEU* 1.3 75.4 - - - +
422H ALA* 1.3 62.6 + - - +
425H THR* 2.4 37.6 + - - -
1204H PHE* 5.8 7.4 - - + -
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Residues in contact with ALA 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418H CYS 2.9 18.9 + - - +
419H ASN* 4.3 5.8 - - - -
421H VAL* 1.3 77.8 - - - +
423H ILE* 1.3 63.1 + - + +
425H THR* 4.3 0.2 - - - -
426H ASN* 3.7 14.7 + - - +
1201H LEU* 6.0 5.6 - - + -
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Residues in contact with ILE 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419H ASN* 2.9 30.2 + - + +
422H ALA* 1.3 73.2 - - + +
424H ASP* 1.3 63.7 + - - +
425H THR 3.1 1.8 - - - -
426H ASN* 2.9 8.1 + - - +
427H GLN* 2.9 22.0 + - - +
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Residues in contact with ASP 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419H ASN 2.8 10.0 + - - +
420H LEU* 2.7 28.7 + - + +
423H ILE* 1.3 72.8 - - - +
425H THR* 1.3 61.0 + - - +
427H GLN* 3.3 10.8 - - - +
428H LEU* 2.9 22.9 + - - +
606H SER* 4.3 23.4 - - - +
609H LYS* 6.3 2.2 - - + -
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Residues in contact with THR 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ARG* 5.1 15.6 - - - +
391H ILE* 5.7 7.9 - - - -
420H LEU 2.7 10.1 + - - -
421H VAL* 2.4 33.4 + - - -
422H ALA 4.3 0.4 - - - -
424H ASP* 1.3 72.2 - - - +
426H ASN* 1.3 54.2 + - - +
428H LEU* 2.5 30.1 + - - +
429H MET* 2.9 14.7 + - - +
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Residues in contact with ASN 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ARG* 6.2 0.2 - - - -
422H ALA 3.7 10.8 + - - +
423H ILE* 2.9 8.7 + - - +
425H THR* 1.3 76.7 - - - +
427H GLN* 1.3 66.0 + - - +
429H MET* 4.6 4.5 - - - +
430H TRP* 2.9 25.2 + - - +
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Residues in contact with GLN 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423H ILE 2.9 11.9 + - - +
424H ASP* 3.3 16.6 - - - +
426H ASN* 1.3 78.3 - - - +
428H LEU* 1.3 65.4 + - - +
430H TRP* 3.3 4.6 - - - +
431H PHE* 2.9 23.2 + - - +
602H LYS* 4.7 26.0 - - + +
603H ALA* 5.8 0.9 - - - -
606H SER* 5.2 2.5 - - - -
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Residues in contact with LEU 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H ARG* 6.4 0.9 - - + -
424H ASP 2.9 13.7 + - - +
425H THR* 2.5 16.6 + - - +
427H GLN* 1.3 70.4 - - - +
429H MET* 1.3 58.3 + - - +
431H PHE* 3.0 9.1 + - - +
432H PHE* 2.9 28.4 + - - +
603H ALA* 5.5 4.7 - - - +
606H SER* 5.1 9.6 - - - -
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Residues in contact with MET 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384H GLY* 4.1 20.5 - - - +
387H LEU* 5.6 2.7 - - - -
388H ARG* 3.8 31.4 - - + +
425H THR 2.9 12.3 + - - +
426H ASN* 4.5 4.0 - - - +
428H LEU* 1.3 73.3 - - - +
430H TRP* 1.3 57.9 + - - +
432H PHE* 3.9 7.4 - - - +
433H PHE* 2.9 29.6 + - - +
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Residues in contact with TRP 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426H ASN 2.9 22.1 + - - +
427H GLN* 3.3 5.6 - - - +
429H MET* 1.3 76.9 - - - +
431H PHE* 1.3 62.8 + - - +
433H PHE* 3.0 7.7 + - - +
434H LEU* 3.0 24.9 + - - +
599H SER* 5.6 3.1 - - - -
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Residues in contact with PHE 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H GLN 2.9 12.4 + - - +
428H LEU 3.0 8.3 + - - +
430H TRP* 1.3 75.6 - - - +
432H PHE* 1.3 58.0 + - - +
434H LEU* 3.5 2.7 + - - +
435H CYS* 2.9 30.2 + - - +
599H SER* 3.9 36.5 - - - +
600H THR* 5.1 0.9 - - - +
603H ALA* 3.9 16.4 - - + -
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Residues in contact with PHE 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H LEU* 6.5 0.7 - - + -
299H LEU* 5.5 14.9 - - + +
380H ALA* 5.2 2.2 - - - +
383H THR* 6.2 1.1 - - - -
384H GLY* 5.5 4.7 - - - +
387H LEU* 5.4 10.8 - - + -
428H LEU 2.9 15.1 + - - +
429H MET* 3.9 8.3 - - - +
431H PHE* 1.3 76.7 - - - +
433H PHE* 1.3 64.3 + - - +
435H CYS* 3.0 21.9 + - - +
436H PRO* 4.2 1.7 - - - +
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Residues in contact with PHE 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H ARG* 4.0 6.9 + - - -
380H ALA* 3.2 33.0 - - + +
381H ILE* 4.5 19.7 - - + +
384H GLY* 5.6 2.4 - - - -
429H MET 2.9 20.5 + - - +
430H TRP* 3.0 9.4 + - - +
432H PHE* 1.3 78.4 - - - +
434H LEU* 1.3 59.7 + - - +
435H CYS 3.3 0.2 + - - -
436H PRO* 4.4 1.4 - - - +
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Residues in contact with LEU 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 4.7 0.4 - - - +
430H TRP 3.0 14.2 + - - +
431H PHE* 3.6 3.4 - - - +
433H PHE* 1.3 76.1 - - - +
435H CYS* 1.3 62.7 + - - +
436H PRO 3.4 0.9 - - - -
437H ASN* 3.0 18.3 + - + +
438H LEU* 3.0 18.3 + - - +
596H VAL* 5.8 9.4 - - + +
599H SER* 5.9 5.8 - - - -
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Residues in contact with CYS 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H LEU* 6.5 0.9 - - + -
431H PHE 2.9 18.4 + - - +
432H PHE* 3.0 20.1 + - - +
434H LEU* 1.3 78.3 - - - +
436H PRO* 1.3 56.7 - - - +
438H LEU* 2.9 23.4 + - - +
439H TRP* 2.9 12.8 + - - +
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Residues in contact with PRO 436 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299H LEU 5.3 0.4 - - - +
302H SER* 4.4 9.9 - - - +
303H SER* 4.1 20.9 + - - +
306H ARG* 3.3 31.1 - - - +
380H ALA* 5.9 2.0 - - + -
432H PHE 4.2 2.8 - - - +
433H PHE 4.4 1.5 - - - +
434H LEU 3.4 0.4 - - - -
435H CYS* 1.3 74.2 - - - +
437H ASN* 1.3 61.2 + - - +
439H TRP* 3.1 8.7 + - + +
440H ALA* 2.9 32.7 + - - +
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Residues in contact with ASN 437 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ARG* 2.6 36.7 - - - +
310H ASP* 6.0 0.2 - - - -
434H LEU* 3.0 18.8 + - + +
436H PRO* 1.3 74.4 - - - +
438H LEU* 1.3 49.7 + - - +
440H ALA* 5.2 1.6 - - - -
441H MET* 2.5 43.5 + - + +
592H LEU* 6.3 3.1 - - + -
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Residues in contact with LEU 438 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434H LEU 3.0 8.3 + - - +
435H CYS* 2.9 20.1 + - + +
437H ASN* 1.3 77.3 - - - +
439H TRP* 1.3 66.5 + - - +
441H MET* 3.5 10.0 + - - +
442H PRO* 4.4 3.1 - - - +
596H VAL* 5.3 14.8 - - + -
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Residues in contact with TRP 439 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H SER* 4.4 13.5 - - - +
435H CYS 2.9 11.9 + - - +
436H PRO* 3.1 11.4 + - + +
438H LEU* 1.3 79.8 - - - +
440H ALA* 1.3 62.3 + - - +
441H MET 3.4 0.2 + - - -
442H PRO* 4.3 6.4 - - - +
443H VAL* 4.7 3.1 + - - +
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Residues in contact with ALA 440 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H SER* 5.5 4.3 - - - +
306H ARG* 5.5 4.0 - - + +
307H ILE* 3.5 34.1 - - + +
310H ASP* 4.2 13.2 - - - +
436H PRO 2.9 17.3 + - - +
437H ASN* 4.9 1.3 - - - +
439H TRP* 1.3 73.7 - - + +
441H MET* 1.3 66.7 + - - +
442H PRO 3.3 0.4 - - - -
443H VAL* 2.8 20.5 + - - +
444H GLN* 3.0 11.2 + - + +
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Residues in contact with MET 441 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437H ASN* 2.5 24.8 + - + +
438H LEU* 3.9 7.2 - - - +
439H TRP 3.3 1.4 - - - -
440H ALA* 1.3 75.7 - - - +
442H PRO* 1.3 63.7 - - - +
444H GLN* 3.3 8.1 + - - +
445H ILE* 3.0 20.6 + - - +
589H PRO* 4.9 15.9 - - + +
592H LEU* 6.5 1.1 - - + -
593H LEU* 5.4 12.6 - - + -
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Residues in contact with PRO 442 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438H LEU 4.4 3.2 - - - +
439H TRP 4.3 6.3 - - - +
440H ALA 3.3 0.4 - - - -
441H MET* 1.3 77.9 - - - +
443H VAL* 1.3 57.8 + - - +
445H ILE* 2.7 27.5 + - + -
446H ILE* 2.9 18.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 443 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ILE* 4.4 16.4 - - + -
311H LEU* 5.8 2.1 - - - +
439H TRP 4.7 2.6 + - - +
440H ALA* 2.8 19.2 + - - +
442H PRO* 1.3 74.7 - - - +
444H GLN* 1.3 60.6 + - - +
446H ILE* 5.1 1.5 - - - +
447H VAL* 3.3 22.6 + - - +
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Residues in contact with GLN 444 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307H ILE* 5.0 3.2 - - + +
310H ASP* 4.8 22.7 - - + +
311H LEU* 6.4 2.5 - - - +
314H PHE* 4.3 5.5 - - - -
440H ALA 3.0 9.0 + - - +
441H MET* 3.5 11.2 - - - +
443H VAL* 1.3 77.8 - - - +
445H ILE* 1.3 60.1 + - - +
447H VAL* 3.6 3.8 - - - +
448H GLY* 2.8 24.8 + - - -
589H PRO* 5.5 7.9 - - + -
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Residues in contact with ILE 445 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441H MET 3.0 13.5 + - - +
442H PRO* 2.7 18.8 + - + +
444H GLN* 1.3 69.8 - - - +
446H ILE* 1.3 55.4 + - - +
448H GLY* 2.3 33.4 + - - -
449H VAL* 3.0 6.2 + - - +
586H LEU* 6.2 4.0 - - - +
589H PRO* 5.6 8.2 - - + +
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Residues in contact with ILE 446 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442H PRO* 2.9 16.2 + - + +
443H VAL* 5.1 1.1 - - - +
445H ILE* 1.3 72.8 - - - +
447H VAL* 1.3 57.0 + - - +
449H VAL* 3.4 5.4 + - - +
450H ILE* 2.9 33.7 + - - +
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Residues in contact with VAL 447 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H LEU* 5.2 10.1 - - + -
314H PHE* 3.0 15.6 - - + -
443H VAL 3.3 21.7 + - - +
444H GLN* 3.8 3.8 - - - +
445H ILE 3.2 0.4 - - - -
446H ILE* 1.3 78.2 - - - +
448H GLY* 1.3 51.9 + - - +
450H ILE* 4.6 4.9 - - - -
451H LEU* 2.6 40.6 + - + +
----------------------------------------------------------
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Residues in contact with GLY 448 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 3.4 17.9 - - - -
444H GLN 2.8 8.6 + - - -
445H ILE* 2.3 24.6 + - - -
447H VAL* 1.3 67.9 - - - +
449H VAL* 1.3 64.6 + - - +
451H LEU* 3.5 4.7 + - - +
452H LEU* 3.7 9.4 + - - +
582H LEU* 5.3 7.0 - - - +
586H LEU* 5.1 16.8 - - - -
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Residues in contact with VAL 449 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445H ILE 3.0 7.1 + - - +
446H ILE* 3.4 6.3 + - - +
448H GLY* 1.3 73.7 - - - +
450H ILE* 1.3 65.3 + - - +
452H LEU* 3.0 22.7 + - - +
460H ALA* 6.1 0.3 - - - +
461H LEU* 6.5 0.4 - - - -
464H ALA* 4.7 21.4 - - + +
586H LEU* 5.8 0.2 - - - +
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Residues in contact with ILE 450 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446H ILE 2.9 18.5 + - - +
447H VAL* 4.5 4.0 - - - +
449H VAL* 1.3 79.2 - - - +
451H LEU* 1.3 58.5 + - - +
452H LEU 3.0 11.8 + - - +
455H ILE* 5.3 5.0 - - - +
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Residues in contact with LEU 451 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 3.4 28.0 - - + -
447H VAL* 2.6 24.7 + - + +
448H GLY 4.0 2.5 - - - +
449H VAL 3.1 0.6 + - - -
450H ILE* 1.3 76.8 - - - +
452H LEU* 1.3 61.6 + - - +
453H TYR* 3.4 3.1 + - - +
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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) + - + + + + + -
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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