Contacts of the helix formed by residues 394 - 424 (chain D) in PDB entry 6X34
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 GLN 394 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D HIS* 5.6 0.7 - - - -
219D VAL* 4.4 3.5 - - - +
221D ARG* 5.4 4.8 - - - +
393D CYS* 1.3 88.1 - - - +
395D GLN* 1.3 63.4 + - - +
396D GLU* 3.7 20.5 - - + +
397D GLU* 3.3 40.5 + - - +
398D SER* 3.7 4.5 + - - -
477D LEU* 6.0 0.8 - - - +
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Residues in contact with GLN 395 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D HIS* 5.5 6.5 + - + +
219D VAL* 5.6 0.4 - - - -
393D CYS 4.3 0.2 + - - -
394D GLN* 1.3 71.2 - - - +
396D GLU* 1.3 61.2 + - - +
398D SER* 2.6 24.3 + - - +
399D GLN* 2.9 18.2 + - - +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394D GLN* 3.2 15.3 - - + +
395D GLN* 1.3 77.4 - - - +
397D GLU* 1.3 56.9 + - - +
399D GLN* 3.4 7.1 + - - +
400D ALA* 2.9 30.3 + - - +
451D TYR* 5.3 5.1 + - - +
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Residues in contact with GLU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ARG* 5.5 6.5 - - - +
259D LEU* 5.7 5.6 - - + -
393D CYS* 4.7 13.7 - - + -
394D GLN* 3.3 32.1 + - - +
395D GLN 3.2 0.6 - - - -
396D GLU* 1.3 79.2 - - - +
398D SER* 1.3 56.9 + - - +
400D ALA* 3.3 6.1 + - - +
401D ALA* 2.9 29.3 + - - +
477D LEU* 4.8 17.3 - - + +
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Residues in contact with SER 398 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D VAL* 3.6 36.8 - - - +
285D VAL* 5.2 2.2 - - - +
394D GLN 3.7 1.7 + - - -
395D GLN* 2.6 33.3 + - - +
397D GLU* 1.3 77.0 - - - +
399D GLN* 1.3 54.9 + - - +
401D ALA* 3.3 7.4 + - - +
402D ARG* 2.9 29.5 + - - +
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Residues in contact with GLN 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 5.3 2.1 - - + -
113D HIS* 4.1 22.4 - - - +
395D GLN 2.9 16.3 + - - +
396D GLU* 3.7 7.6 - - - +
397D GLU 3.3 0.2 - - - -
398D SER* 1.3 78.3 + - - +
400D ALA* 1.3 56.3 + - - +
402D ARG* 3.3 6.9 + - - +
403D MET* 2.9 39.9 + - + +
451D TYR* 5.8 2.5 - - - +
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Residues in contact with ALA 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D GLU 2.9 17.6 + - - +
397D GLU* 3.7 6.5 - - - +
399D GLN* 1.3 77.0 - - - +
401D ALA* 1.3 59.4 + - - +
403D MET* 3.3 11.7 + - - +
404D ILE* 2.9 38.6 + - + +
451D TYR* 5.1 10.9 + - + +
474D ARG* 5.9 6.3 - - + -
477D LEU* 4.7 18.4 - - + -
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Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ALA* 5.4 6.5 - - + +
259D LEU* 5.2 6.5 - - + -
285D VAL* 3.8 34.2 - - + +
286D THR* 5.0 1.6 - - + -
397D GLU 2.9 16.9 + - - +
398D SER* 3.6 8.1 - - - +
399D GLN 3.3 0.2 - - - -
400D ALA* 1.3 73.8 - - - +
402D ARG* 1.3 59.5 + - - +
404D ILE* 3.0 19.1 - - + +
405D TYR* 2.9 29.5 + - - +
477D LEU* 6.1 0.2 - - - +
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Residues in contact with ARG 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 6.1 1.3 - - + -
64D ILE* 5.9 6.7 - - + -
113D HIS* 5.2 13.5 - - + -
285D VAL* 4.4 8.4 - - + +
398D SER 2.9 16.9 + - - +
399D GLN* 3.6 7.6 - - - +
401D ALA* 1.3 75.7 - - - +
403D MET* 1.3 58.5 + - + +
405D TYR* 3.3 8.4 + - - +
406D SER* 2.9 30.0 + - - -
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Residues in contact with MET 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.6 53.4 - - + -
399D GLN* 2.9 25.0 + - - +
400D ALA* 3.5 9.9 - - - +
402D ARG* 1.3 76.5 - - + +
404D ILE* 1.3 59.4 + - + +
406D SER* 2.6 20.8 + - - -
407D THR* 2.9 19.9 + - - +
448D LEU* 5.3 8.7 - - + -
451D TYR* 3.6 50.5 - - + -
452D PHE* 4.6 9.6 - - + -
478D PHE* 6.0 2.5 - - + -
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Residues in contact with ILE 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ALA* 4.1 23.6 - - + -
286D THR* 4.3 17.5 - - + -
400D ALA* 2.9 21.3 + - + +
401D ALA* 3.0 28.7 - - - +
403D MET* 1.3 77.5 - - + +
405D TYR* 1.3 58.1 + - - +
407D THR* 3.3 9.5 - - + +
408D ALA* 2.9 33.5 + - - +
477D LEU* 4.8 10.8 - - + +
478D PHE* 4.4 26.2 - - + -
481D GLU* 4.5 18.8 - - + -
483D MET* 4.8 10.4 - - - +
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Residues in contact with TYR 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D VAL* 3.2 23.3 - - + +
286D THR* 3.3 23.1 - - - +
287D THR 3.8 17.7 - - - -
288D GLY* 4.1 12.6 - - - -
401D ALA 2.9 14.4 + - - +
402D ARG* 3.6 7.9 - - - +
404D ILE* 1.3 78.3 - - - +
406D SER* 1.3 69.2 + - - +
408D ALA* 3.7 4.1 - - + +
409D GLY* 2.9 23.7 + - - -
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Residues in contact with SER 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D GLU* 5.7 7.4 - - - -
42D PHE* 4.5 23.1 + - - +
402D ARG 2.9 14.4 + - - -
403D MET* 2.6 26.0 + - - -
405D TYR* 1.3 82.5 - - - +
407D THR* 1.3 55.4 + - - -
409D GLY* 3.3 2.3 + - - -
410D LEU* 3.0 28.1 + - - +
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Residues in contact with THR 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D MET 2.9 22.3 + - - +
404D ILE* 3.3 14.8 - - + +
406D SER* 1.3 77.1 + - - +
408D ALA* 1.3 59.6 + - - +
410D LEU* 3.4 6.7 + - - +
411D TYR* 2.9 58.3 + - - -
444D SER* 5.8 8.0 - - - -
448D LEU* 6.1 4.5 - - - -
478D PHE* 5.0 5.8 - - + -
483D MET* 3.7 20.4 - - + +
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Residues in contact with ALA 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D THR 5.6 3.4 - - - +
404D ILE 2.9 19.7 + - - +
405D TYR* 3.7 6.1 - - + +
407D THR* 1.3 76.6 - - + +
409D GLY* 1.3 55.9 + - - +
411D TYR* 3.2 6.3 + - - +
412D ASN* 2.6 44.4 + - - +
483D MET* 5.5 5.8 - - + -
486D LEU* 4.4 13.0 - - + -
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Residues in contact with GLY 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D TYR* 2.9 17.3 + - - -
406D SER 3.7 3.1 - - - -
408D ALA* 1.3 76.2 - - - +
410D LEU* 1.3 60.8 + - - +
412D ASN* 3.3 9.1 + - - +
413D HIS* 3.0 23.9 + - - +
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Residues in contact with LEU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D SER 3.0 16.5 + - - +
407D THR* 3.7 9.0 - - - +
409D GLY* 1.3 75.5 - - - +
411D TYR* 1.3 64.8 + - + +
413D HIS* 3.3 8.4 + - - +
414D PHE* 2.9 28.2 + - - +
441D VAL* 5.7 8.9 - - + +
444D SER* 4.8 16.2 - - - +
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Residues in contact with TYR 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D THR* 2.9 39.1 + - - +
408D ALA 3.2 1.1 + - - +
410D LEU* 1.3 77.8 - - + +
412D ASN* 1.3 61.7 + - - +
414D PHE* 3.3 7.1 + + + +
415D ILE* 2.9 33.1 + - - +
441D VAL* 4.9 11.4 - - + -
444D SER* 5.6 1.3 - - - -
445D LEU* 3.2 34.2 - - + +
448D LEU* 6.0 0.3 - - - +
483D MET* 3.7 12.1 - - + -
486D LEU* 3.5 42.8 - - + -
487D VAL* 3.7 23.1 - - + +
490D CYS* 4.6 12.0 - - - -
522D LEU* 5.4 7.9 - - + +
525D ILE* 3.7 20.5 - - + +
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Residues in contact with ASN 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D ALA* 2.6 33.3 + - - +
409D GLY* 3.8 7.7 - - - +
411D TYR* 1.3 73.2 - - - +
413D HIS* 1.3 60.6 + - - +
415D ILE* 3.8 7.0 - - - +
416D LYS* 2.9 30.0 + - - +
486D LEU* 3.9 19.8 - - - +
----------------------------------------------------------
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Residues in contact with HIS 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D GLY 3.0 13.6 + - - +
410D LEU* 3.6 10.5 - - - +
412D ASN* 1.3 77.0 - - - +
414D PHE* 1.3 57.7 + - - +
416D LYS* 3.3 8.4 + - + +
417D GLY* 2.9 27.9 + - - -
436D LEU* 5.8 1.9 - - + +
437D PRO* 3.8 37.7 - - + +
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Residues in contact with PHE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D LEU 2.9 17.3 + - - +
411D TYR* 3.6 10.8 - + + +
413D HIS* 1.3 77.0 - - - +
415D ILE* 1.3 59.1 + - + +
417D GLY* 3.3 2.1 + - - -
418D LEU* 2.9 36.8 + - + +
436D LEU* 3.8 40.2 - - + +
437D PRO* 5.7 2.0 - - + -
441D VAL* 4.3 34.3 - - + -
490D CYS* 4.6 26.9 - - + -
494D LEU* 4.4 32.1 - - + -
518D ILE* 4.6 15.5 - - + -
522D LEU* 6.0 3.4 - - + -
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Residues in contact with ILE 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D TYR 2.9 15.3 + - - +
412D ASN* 3.3 7.8 + - - +
414D PHE* 1.3 73.2 - - + +
416D LYS* 1.3 63.5 + - - +
418D LEU* 3.3 5.5 + - - +
419D ASP* 2.9 33.0 + - + +
486D LEU* 3.5 33.2 - - + +
489D ASN* 3.5 33.0 - - + +
490D CYS* 3.8 20.6 - - + -
493D ARG* 5.2 6.6 + - + +
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Residues in contact with LYS 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D ASN 2.9 16.9 + - - +
413D HIS* 3.6 11.9 - - + +
415D ILE* 1.3 78.9 - - - +
417D GLY* 1.3 57.2 + - - +
419D ASP* 3.3 6.0 + - - +
420D SER* 2.8 31.3 + - - -
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Residues in contact with GLY 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D HIS* 2.9 17.4 + - - -
414D PHE 3.7 3.1 - - - -
415D ILE 3.3 0.2 - - - -
416D LYS* 1.3 77.0 - - - +
418D LEU* 1.3 56.8 + - - +
420D SER* 2.8 19.0 + - - -
421D PHE* 2.9 21.1 + - - +
434D THR* 5.0 10.4 - - - +
436D LEU* 4.7 20.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D PHE* 2.9 30.5 + - + +
415D ILE* 3.8 6.3 - - - +
417D GLY* 1.3 76.2 - - - +
419D ASP* 1.3 56.9 + - - +
421D PHE* 3.9 4.4 - - - +
422D SER* 2.8 35.1 + - - -
436D LEU* 4.9 5.1 - - + +
493D ARG* 4.7 24.5 - - + +
494D LEU* 6.3 2.9 - - + -
503D PHE* 6.5 0.9 - - + -
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Residues in contact with ASP 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D ILE* 2.9 20.4 + - + +
416D LYS* 3.8 5.4 - - - +
418D LEU* 1.3 78.4 - - - +
420D SER* 1.3 60.5 + - - +
422D SER* 3.9 6.3 + - - -
423D GLY* 3.1 21.3 + - - -
493D ARG* 4.1 17.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D LYS 2.8 19.0 + - - -
417D GLY* 2.8 17.5 + - - -
419D ASP* 1.3 77.0 - - - +
421D PHE* 1.3 59.0 + - - +
423D GLY* 4.7 0.2 - - - -
424D LYS* 3.8 18.2 + - - +
432D ALA 4.8 2.4 - - - +
433D GLY* 4.9 4.0 - - - -
434D THR* 4.0 18.4 - - - +
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Residues in contact with PHE 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D GLY 2.9 17.3 + - - +
418D LEU* 3.9 5.6 - - - +
420D SER* 1.3 77.4 + - - +
422D SER* 1.3 63.5 + - - +
423D GLY 3.3 0.2 - - - -
424D LYS* 3.3 20.5 + - - +
433D GLY* 5.1 10.8 - - - -
434D THR 5.5 5.4 - - - +
436D LEU* 5.8 5.2 - - + -
497D TYR* 4.4 4.6 + - - +
503D PHE* 5.6 4.0 - - + -
506D PHE* 5.1 1.9 - - - +
507D ALA* 3.9 32.6 + - + +
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Residues in contact with SER 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418D LEU* 2.8 22.8 + - - -
419D ASP* 3.9 6.9 + - - -
421D PHE* 1.3 70.4 - - - +
423D GLY* 1.3 67.8 + - - +
424D LYS 3.4 6.1 + - - +
425D PRO* 5.5 0.2 - - - +
493D ARG* 4.9 11.9 + - - -
496D VAL* 5.7 4.3 - - - -
497D TYR* 3.6 28.5 + - - -
----------------------------------------------------------
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Residues in contact with GLY 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ASP 3.1 15.4 + - - -
420D SER 4.7 0.2 - - - -
422D SER* 1.3 85.0 + - - +
424D LYS* 1.3 58.2 + - - +
425D PRO* 3.6 8.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D SER 3.8 14.8 + - - +
421D PHE 3.3 15.3 + - - +
422D SER 3.3 6.1 - - - +
423D GLY* 1.3 78.0 - - - +
425D PRO* 1.3 74.7 - - + +
431D PRO 5.5 0.7 - - - +
432D ALA* 3.3 30.1 - - + +
506D PHE* 5.0 6.2 - - - +
----------------------------------------------------------
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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