Contacts of the helix formed by residues 386 - 419 (chain A) in PDB entry 4FE1
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 ASP 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 3.4 33.5 - - - +
138A GLN* 4.8 4.5 + - - -
139A ILE 4.8 1.4 - - - +
145A GLN* 3.8 7.9 + - - +
382A TYR 4.3 13.2 + - - +
383A LEU 2.8 15.8 + - - +
385A THR* 1.3 76.2 - - - +
387A TYR* 1.3 60.6 + - - +
388A PRO* 3.4 17.4 - - - +
389A THR* 2.8 39.6 + - - +
390A GLN* 3.1 9.9 + - - +
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Residues in contact with TYR 387 (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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384A ALA 3.1 25.6 - - - -
385A THR* 3.0 10.1 + - - -
386A ASP* 1.3 73.5 - - - +
388A PRO* 1.4 73.4 - - + +
389A THR 3.1 0.2 + - - -
390A GLN* 3.1 5.8 + - - +
391A LEU* 2.9 26.3 + - - +
523A LYS* 3.8 12.7 - - + +
524A VAL* 2.7 41.6 + - - +
622A TRP* 3.3 47.2 - + + -
623A GLY* 3.1 19.4 + - - -
634A ILE* 4.3 7.9 - - + -
751A ILE* 3.7 17.7 - - + +
754A VAL 5.2 0.2 - - - -
755A GLY* 3.4 29.8 + - - -
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Residues in contact with PRO 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 4.2 10.8 - - - +
139A ILE 5.5 0.2 - - - +
140A THR* 3.6 22.0 - - + -
386A ASP* 3.4 13.9 - - - +
387A TYR* 1.4 93.7 - - + +
389A THR* 1.3 53.1 + - - +
391A LEU* 3.9 1.0 - - - +
392A SER* 2.7 37.9 + - - -
748A LEU* 4.8 0.2 - - - +
751A ILE* 3.4 35.3 - - + +
752A ILE* 3.6 22.7 - - + -
755A GLY* 4.1 9.6 - - - +
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO* 5.2 0.2 - - - +
139A ILE 4.1 1.4 + - - -
140A THR* 3.5 23.6 - - - +
142A GLY* 3.5 31.7 + - - +
145A GLN* 4.2 3.1 + - - +
383A LEU* 3.6 20.4 - - + -
386A ASP* 2.8 35.6 + - - -
388A PRO* 1.3 76.0 - - - +
390A GLN* 1.3 65.7 + - - +
392A SER* 3.8 0.3 - - - -
393A LEU* 2.9 31.7 + - + +
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 3.8 10.4 - - - +
375A TYR* 3.4 32.2 + - - +
378A PRO* 3.7 20.6 - - - +
383A LEU* 3.4 44.9 - - + +
384A ALA* 3.7 13.6 + - - +
386A ASP 3.1 8.2 + - - +
387A TYR* 3.6 6.7 - - - +
389A THR* 1.3 74.5 - - - +
391A LEU* 1.3 63.5 + - - +
393A LEU* 3.4 4.2 + - - +
394A PHE* 3.0 25.7 + - - +
525A ALA 5.2 0.4 + - - -
526A MET* 5.1 2.4 - - - +
613A PHE* 4.6 4.5 - - + -
617A MET* 5.9 0.4 - - - +
622A TRP* 3.9 23.7 - - + +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A TYR 2.9 16.0 + - - +
388A PRO 3.9 3.4 - - - +
390A GLN* 1.3 78.0 - - - +
392A SER* 1.3 65.1 + - - +
394A PHE* 3.2 2.8 + - - +
395A THR* 2.9 38.2 + - + +
613A PHE* 3.6 32.5 - - + -
614A SER* 4.2 16.8 - - - +
618A GLN* 4.6 3.6 - - - +
622A TRP* 4.2 7.5 - - + -
747A PHE* 3.9 40.2 - - + +
748A LEU* 5.8 2.0 - - + -
751A ILE* 3.6 31.9 - - + -
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 2.9 36.9 + - - -
388A PRO 2.7 23.4 + - - -
389A THR 3.8 0.2 - - - -
391A LEU* 1.3 76.0 - - - +
393A LEU* 1.3 58.4 + - - +
395A THR* 4.1 4.6 + - - -
396A HIS* 2.9 34.6 + - - +
748A LEU* 3.2 20.7 - - - +
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Residues in contact with LEU 393 (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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140A THR 4.5 2.7 - - - +
141A SER* 3.8 24.5 - - - +
142A GLY* 4.8 1.8 - - - -
371A ALA* 5.6 0.7 - - - -
374A MET* 3.6 30.7 - - + -
380A TYR* 6.0 1.8 - - + -
383A LEU* 4.5 9.0 - - + -
389A THR* 2.9 38.7 + - + +
390A GLN* 3.9 4.5 - - - +
392A SER* 1.3 75.1 - - - +
394A PHE* 1.3 64.3 + - - +
396A HIS* 4.2 6.3 - - + -
397A HIS* 2.6 54.8 + - + +
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Residues in contact with PHE 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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371A ALA* 3.0 43.0 - - - +
372A GLN* 4.1 10.1 - - - -
375A TYR* 4.0 13.9 - + + -
390A GLN 3.0 18.3 + - - +
391A LEU 3.6 2.9 - - - +
393A LEU* 1.3 77.0 - - - +
395A THR* 1.3 71.4 + - + +
397A HIS 3.4 0.2 + - - -
398A MET* 3.0 54.7 + - + +
609A VAL* 4.2 14.6 - - + -
610A ILE* 4.3 7.0 - - + -
613A PHE* 3.4 63.3 - + + -
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Residues in contact with THR 395 (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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391A LEU* 2.9 26.4 + - + +
392A SER* 4.1 3.6 + - - +
394A PHE* 1.3 77.4 - - + +
396A HIS* 1.3 59.0 + - - +
398A MET* 3.2 1.4 + - - +
399A TRP* 2.9 45.8 + - - -
610A ILE* 3.5 32.6 - - + +
743A THR* 5.6 1.0 - - - +
747A PHE* 3.8 31.8 - - + -
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Residues in contact with HIS 396 (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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392A SER 2.9 21.4 + - - +
393A LEU* 3.6 6.5 - - + +
395A THR* 1.3 79.0 + - - +
397A HIS* 1.3 86.8 + + - +
399A TRP* 3.2 8.5 + - - +
400A ILE* 3.0 57.4 + - + +
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Residues in contact with HIS 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 2.5 46.9 + - - +
370A VAL* 3.5 28.4 - - + +
371A ALA* 3.7 11.0 - - + -
374A MET* 4.5 9.1 - - - -
393A LEU* 2.6 57.7 + - + +
396A HIS* 1.3 91.8 + + - +
398A MET* 1.3 65.5 + - - +
400A ILE* 4.4 2.7 - - + -
401A GLY 3.0 7.8 + - - -
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Residues in contact with MET 398 (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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368A ILE* 3.6 48.3 - - + +
371A ALA* 3.7 7.9 - - + -
372A GLN* 3.7 26.0 - - + +
394A PHE* 3.0 46.4 + - + +
395A THR* 3.3 8.7 - - - +
397A HIS* 1.3 79.0 - - - +
399A TRP* 1.3 57.8 + - - +
401A GLY* 3.2 2.6 + - - -
402A GLY* 2.9 26.2 + - - -
606A ILE* 3.8 27.8 - - + +
609A VAL* 4.0 17.7 - - + -
610A ILE* 4.2 1.6 - - + -
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Residues in contact with TRP 399 (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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395A THR* 2.9 35.5 + - - +
396A HIS* 3.5 7.2 - - - +
398A MET* 1.3 74.8 - - - +
400A ILE* 1.3 68.4 + - + +
402A GLY* 3.2 1.8 + - - +
403A PHE* 3.0 35.7 + + + -
602A MET* 4.1 11.7 - - + -
603A TYR* 3.3 42.6 - + - -
606A ILE* 3.5 28.9 - - + -
607A SER* 3.5 17.3 - - - -
610A ILE* 3.6 25.4 - - + +
740A ILE* 3.6 50.9 - - + +
743A THR* 5.0 6.7 - - - +
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Residues in contact with ILE 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 3.8 13.5 - - - +
396A HIS* 3.0 46.7 + - + +
397A HIS* 4.4 1.1 - - + -
399A TRP* 1.3 79.1 - - + +
401A GLY* 1.3 64.0 + - - +
403A PHE* 3.3 6.1 + - + +
404A LEU* 3.0 49.0 + - + +
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Residues in contact with GLY 401 (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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364A GLY* 3.2 28.6 - - - -
367A SER* 3.5 6.9 + - - -
368A ILE* 3.6 10.8 - - - -
397A HIS 3.0 10.9 + - - -
398A MET 3.6 3.4 - - - -
400A ILE* 1.3 77.5 - - - +
402A GLY* 1.3 61.3 + - - +
404A LEU 3.3 0.7 + - - -
405A VAL* 3.0 29.6 + - - +
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Residues in contact with GLY 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ILE* 4.0 3.7 - - - +
398A MET 2.9 14.7 + - - -
399A TRP 3.2 3.8 + - - -
401A GLY* 1.3 77.8 - - - +
403A PHE* 1.3 62.5 + - - +
405A VAL* 3.5 4.4 + - - +
406A VAL* 3.4 24.1 + - - +
602A MET* 3.5 24.7 - - - +
606A ILE* 4.3 9.6 - - - -
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Residues in contact with PHE 403 (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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399A TRP* 3.0 31.6 + + + -
400A ILE* 3.8 8.5 - - + +
402A GLY* 1.3 75.5 - - - +
404A LEU* 1.3 67.9 + - + +
406A VAL* 3.4 5.6 + - - +
407A GLY* 3.0 19.6 + - - -
599A LEU* 4.2 10.5 - - + +
602A MET* 3.9 21.5 - - + -
736A LEU* 3.5 35.7 - - + -
740A ILE* 3.7 28.7 - - + -
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Residues in contact with LEU 404 (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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360A LEU* 3.3 38.8 - - + +
363A MET* 3.8 35.7 - - + +
364A GLY* 3.5 18.6 - - - +
367A SER* 5.5 1.6 - - - -
400A ILE* 3.0 35.5 + - + +
403A PHE* 1.3 80.8 - - + +
405A VAL* 1.3 56.5 + - - +
407A GLY* 3.2 1.1 + - - -
408A GLY 3.0 23.2 + - - -
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Residues in contact with VAL 405 (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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360A LEU 4.3 3.6 - - - -
361A ALA* 4.1 14.4 - - + +
364A GLY* 3.9 1.8 - - - -
365A SER* 3.9 27.6 - - - +
368A ILE* 4.2 8.1 - - + -
401A GLY 3.0 22.8 + - - +
402A GLY* 3.8 6.5 - - - +
403A PHE 3.3 0.4 - - - -
404A LEU* 1.3 72.4 - - - +
406A VAL* 1.3 70.0 + - + +
408A GLY* 3.0 13.5 + - - -
409A ALA* 3.1 10.9 + - - +
549A THR* 6.1 2.2 - - + -
553A LEU* 5.2 7.2 - - + -
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Residues in contact with VAL 406 (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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402A GLY 3.4 13.9 + - - +
403A PHE* 3.4 7.3 + - - +
405A VAL* 1.3 77.4 - - + +
407A GLY* 1.3 57.3 + - - +
409A ALA* 3.1 5.5 + - - +
410A ALA* 2.9 24.9 + - - +
549A THR* 4.8 3.4 - - + -
553A LEU* 4.0 31.3 - - + +
595A VAL* 4.1 16.6 - - + +
598A GLY 4.4 3.8 - - - +
599A LEU* 3.8 31.4 - - + +
602A MET* 3.7 26.5 - - + -
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Residues in contact with GLY 407 (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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360A LEU* 3.7 15.9 - - - -
403A PHE 3.0 15.0 + - - -
404A LEU 3.5 5.4 - - - -
405A VAL 3.1 0.4 - - - -
406A VAL* 1.3 75.9 - - - +
408A GLY* 1.3 64.4 + - - +
410A ALA* 3.0 8.7 + - - +
411A HIS* 3.0 30.4 + - - +
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Residues in contact with GLY 408 (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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357A ALA* 3.2 37.0 - - - +
360A LEU* 3.5 11.1 - - - +
361A ALA* 4.0 6.3 - - - -
404A LEU 3.0 10.9 + - - -
405A VAL 3.0 5.7 + - - -
407A GLY* 1.3 75.4 - - - +
409A ALA* 1.3 64.1 + - - +
412A GLY* 3.0 18.7 + - - -
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Residues in contact with ALA 409 (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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361A ALA* 5.6 0.2 - - - +
405A VAL 3.1 8.6 + - - +
406A VAL 3.1 9.4 + - - +
408A GLY* 1.3 75.9 - - - +
410A ALA* 1.3 62.6 + - - +
412A GLY* 3.1 3.5 + - - -
413A ALA* 3.0 18.7 + - - +
553A LEU* 3.6 41.3 - - + -
557A VAL* 3.4 17.4 - - + +
595A VAL* 4.8 1.6 - - + -
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Residues in contact with ALA 410 (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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406A VAL 2.9 11.7 + - - +
407A GLY* 3.0 13.0 + - - +
409A ALA* 1.3 76.8 - - - +
411A HIS* 1.3 63.5 + - + +
413A ALA* 3.0 6.5 + - - +
414A ILE* 3.0 32.2 + - + +
574A PHE* 3.8 7.7 - - + -
595A VAL* 3.5 36.3 - - + +
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Residues in contact with HIS 411 (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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353A HIS* 3.2 47.3 + + - +
356A LEU* 3.2 35.1 - - + +
357A ALA* 4.0 7.0 - - - +
360A LEU* 4.1 7.2 - - + -
407A GLY* 3.0 21.1 + - - +
410A ALA* 1.3 78.4 - - + +
412A GLY* 1.3 59.7 + - - +
414A ILE* 3.2 28.9 - - + +
415A PHE* 3.0 23.7 + - - +
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Residues in contact with GLY 412 (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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357A ALA* 3.5 17.9 - - - +
408A GLY 3.0 10.5 + - - -
409A ALA* 3.4 5.8 - - - -
410A ALA 3.0 0.4 - - - -
411A HIS* 1.3 79.7 - - - +
413A ALA* 1.3 59.3 + - - +
415A PHE* 3.5 10.0 - - - +
416A MET* 3.3 23.4 + - - +
557A VAL* 3.9 11.1 - - - +
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Residues in contact with ALA 413 (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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409A ALA 3.0 11.6 + - - +
410A ALA* 3.5 9.4 - - - +
412A GLY* 1.3 75.0 - - - +
414A ILE* 1.3 65.4 + - - +
415A PHE 3.2 0.2 - - - -
416A MET* 3.1 8.0 + - - +
417A VAL* 3.0 25.1 + - - +
556A GLY 4.5 0.7 - - - +
557A VAL* 3.8 25.5 - - + +
560A ALA* 4.1 3.7 - - + +
574A PHE* 3.9 17.9 - - + -
591A GLY* 4.4 14.8 - - - +
595A VAL* 5.5 0.7 - - + -
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Residues in contact with ILE 414 (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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353A HIS* 3.4 33.2 - - + +
410A ALA* 3.0 17.1 + - + +
411A HIS* 3.2 38.6 - - + +
413A ALA* 1.3 75.8 - - - +
415A PHE* 1.3 64.2 + - - +
417A VAL* 3.1 2.4 + - - +
418A ARG* 2.9 42.8 + - + +
574A PHE* 3.6 43.3 - - + -
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Residues in contact with PHE 415 (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 VAL* 3.5 36.8 - - + -
351A SER* 3.1 28.0 - - - -
353A HIS* 3.9 13.7 - - + +
354A ALA* 3.8 13.7 - - + +
411A HIS 3.0 14.4 + - - +
412A GLY* 3.5 11.9 - - - +
414A ILE* 1.3 76.7 - - - +
416A MET* 1.3 88.4 + - + +
419A ASP* 2.9 16.7 + - + +
420A TYR* 2.9 46.9 + + + -
425A ASN* 5.1 0.9 - - - -
430A LEU* 4.1 19.1 - - + -
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Residues in contact with MET 416 (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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412A GLY 3.3 12.5 + - - +
413A ALA 3.1 10.4 + - - +
415A PHE* 1.3 99.4 - - + +
417A VAL* 1.3 51.4 + - - +
420A TYR* 3.1 29.4 - - + +
430A LEU* 4.2 15.7 - - - -
434A LEU* 3.7 27.8 - - + -
557A VAL* 3.7 24.9 - - + +
560A ALA* 4.0 13.5 - - + -
561A ARG* 2.7 63.4 + - + +
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Residues in contact with VAL 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ALA 3.0 14.3 + - - +
414A ILE 3.8 4.3 - - - +
416A MET* 1.3 79.0 - - - +
418A ARG* 1.3 68.2 + - + +
420A TYR 5.3 0.5 - - - +
560A ALA* 4.0 27.6 - - + +
561A ARG* 3.2 19.1 + - + +
570A ALA* 3.7 25.8 - - - +
573A GLY* 3.7 6.5 - - - +
574A PHE* 3.7 39.9 - - + +
591A GLY 6.1 0.9 - - - +
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Residues in contact with ARG 418 (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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57A ASP* 3.0 39.6 + - - -
59A ASP* 3.5 30.4 + - - +
60A THR* 4.2 9.1 - - - +
353A HIS* 4.3 6.2 + - + -
414A ILE* 2.9 34.6 + - + +
417A VAL* 1.3 84.7 - - + +
419A ASP* 1.3 71.4 + - - +
420A TYR 5.1 0.8 - - - +
574A PHE* 5.1 13.8 - - + +
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 4.8 2.8 - - - +
350A THR 5.3 1.8 - - - +
351A SER* 2.6 42.5 + - - +
352A TRP 4.2 0.9 + - - -
353A HIS* 3.8 23.3 + - - +
415A PHE* 2.9 19.0 + - + -
418A ARG* 1.3 87.0 - - - +
420A TYR* 1.3 69.3 + - - +
421A ASP* 3.3 8.1 + - - +
424A MET* 5.8 1.7 - - - +
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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