Contacts of the helix formed by residues 382 - 415 (chain A) in PDB entry 4L6V
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 382 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A PRO* 4.2 9.4 - - - +
138A GLN* 4.7 9.0 + - - -
139A ILE 4.5 4.0 - - - +
145A TYR* 2.7 33.0 + - + +
378A TYR 3.7 1.4 + - - +
379A GLN 3.0 15.4 + - - +
381A ILE* 1.3 77.6 - - + +
383A TYR* 1.3 59.0 + - - +
384A ALA* 3.0 23.4 + - - +
385A THR* 2.8 26.4 + - - +
386A GLN* 3.0 23.7 + - - +
751A GLY* 4.3 6.5 - - - +
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Residues in contact with TYR 383 (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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380A ALA 3.2 22.7 - - - -
381A ILE* 2.9 20.2 + - - -
382A ASP* 1.3 74.0 + - - +
384A ALA* 1.3 57.2 + - - +
386A GLN* 3.8 5.8 - - + -
387A LEU* 3.0 29.3 + - - +
519A LYS* 3.4 19.5 - - + +
520A VAL 3.0 33.7 + - - -
618A TRP* 3.3 62.9 - + + -
619A GLY* 3.1 19.9 + - - -
630A VAL* 5.1 4.5 - - + -
747A SER* 4.2 4.0 - - - -
750A ILE* 4.5 17.0 - - + -
751A GLY* 3.4 22.0 + - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLN* 5.0 0.2 - - - +
140A THR* 3.9 8.1 - - + -
382A ASP* 3.0 10.6 + - - +
383A TYR* 1.3 76.9 - - - +
385A THR* 1.3 53.3 + - - +
387A LEU* 3.3 2.3 + - - +
388A SER* 2.5 42.7 + - - -
747A SER* 3.3 25.5 + - - +
748A LEU* 3.2 34.3 - - + -
751A GLY* 4.0 4.0 + - - +
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Residues in contact with THR 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO* 5.5 0.2 - - - +
139A ILE 4.3 0.7 + - - -
140A THR* 3.7 29.0 - - - +
142A GLY* 3.6 28.3 + - - +
145A TYR* 3.6 12.9 - - + -
379A GLN* 4.5 7.6 - - + -
382A ASP* 2.8 36.8 + - - -
384A ALA* 1.3 75.5 - - - +
386A GLN* 1.3 58.3 + - - +
389A LEU* 2.8 43.2 + - + +
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Residues in contact with GLN 386 (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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370A MET 4.4 0.5 - - - -
371A TYR* 3.1 45.8 + - - +
374A PRO* 4.0 13.7 - - - +
379A GLN* 3.1 46.3 + - + +
380A ALA* 4.1 12.4 - - - +
382A ASP 3.0 12.2 + - - +
383A TYR* 3.9 5.2 - - - +
385A THR* 1.3 76.0 - - - +
387A LEU* 1.3 61.2 - - - +
389A LEU* 4.7 1.5 - - - +
390A PHE* 3.2 24.6 + - - +
521A ALA 4.9 3.8 + - - -
522A MET* 5.0 1.8 - - - +
609A PHE* 4.0 6.1 - - + -
613A MET* 5.7 1.4 - - - +
618A TRP* 4.0 21.4 - - + +
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR 3.0 18.0 + - - +
384A ALA 3.7 2.9 - - - +
386A GLN* 1.3 77.0 - - - +
388A SER* 1.3 62.4 + - - +
391A THR* 3.1 40.3 + - + +
609A PHE* 3.6 29.2 - - + -
610A SER* 3.9 26.5 - - - +
614A GLN* 5.4 4.0 - - - +
618A TRP* 4.2 9.1 - - + -
743A PHE* 3.6 49.6 - - + +
746A ARG* 5.9 1.1 - - + -
747A SER* 3.9 11.7 - - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 3.3 39.6 + - - +
384A ALA* 2.5 24.4 + - - -
385A THR 3.8 0.2 - - - -
387A LEU* 1.3 79.2 - - - +
389A LEU* 1.3 60.9 + - - +
391A THR* 3.8 4.0 + - - -
392A HIS* 3.0 29.5 + - - +
744A LEU* 3.8 20.0 - - - +
747A SER* 5.0 0.2 + - - -
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Residues in contact with LEU 389 (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 2.2 - - - +
141A SER* 3.8 24.9 - - - +
142A GLY* 4.7 2.9 - - - -
367A ALA* 5.1 0.3 - - - -
370A MET* 4.3 20.0 - - + -
376A TYR* 5.6 4.0 - - + -
379A GLN* 4.3 19.5 - - - +
385A THR* 2.8 38.8 + - + +
386A GLN* 4.7 2.5 - - - +
388A SER* 1.3 73.1 - - - +
390A PHE* 1.3 63.9 + - - +
392A HIS* 3.8 7.1 - - + +
393A HIS* 3.3 51.9 + - + +
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Residues in contact with PHE 390 (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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367A ALA* 3.3 47.2 - - + +
368A GLN* 4.0 21.3 - - + -
371A TYR* 4.2 4.9 - + + -
386A GLN 3.2 19.8 + - - +
387A LEU 4.0 2.0 - - - +
388A SER 3.3 0.6 - - - -
389A LEU* 1.3 78.7 - - - +
391A THR* 1.3 71.8 + - + +
393A HIS 3.4 0.2 + - - -
394A MET* 3.0 54.8 + - + +
605A VAL* 4.5 10.8 - - + -
606A ILE* 4.5 2.5 - - - -
609A PHE* 3.4 60.1 - + + -
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Residues in contact with THR 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 3.1 27.3 + - + +
388A SER* 3.8 4.7 + - - -
390A PHE* 1.3 87.4 - - + +
392A HIS* 1.3 63.4 + - - +
394A MET* 3.4 3.0 - - - +
395A TRP* 3.1 32.2 + - - -
606A ILE* 3.4 40.8 - - + -
743A PHE* 3.6 23.8 - - + -
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Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER 3.0 19.4 + - - +
389A LEU* 3.8 9.6 - - + +
390A PHE 3.1 0.4 - - - -
391A THR* 1.3 82.0 + - - +
393A HIS* 1.3 103.9 + + - +
394A MET 3.0 0.2 - - - -
395A TRP* 3.0 19.6 + - - +
396A ILE* 3.2 38.4 + - + +
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A THR* 3.3 44.8 - - + +
366A VAL* 3.6 23.9 - - + +
367A ALA* 4.0 10.4 + - + +
370A MET* 4.5 10.8 - - - -
389A LEU* 3.3 37.2 + - + +
392A HIS* 1.3 103.0 + + - +
394A MET* 1.3 61.6 + - - +
396A ILE* 4.1 3.6 - - + -
397A GLY* 3.1 17.3 + - - -
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Residues in contact with MET 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ILE* 3.6 37.5 - - + +
367A ALA* 4.2 4.0 - - + +
368A GLN* 4.0 16.8 - - + +
390A PHE* 3.0 44.0 + - + +
391A THR* 3.4 13.9 - - - +
392A HIS 3.0 0.2 - - - -
393A HIS* 1.3 79.6 - - - +
395A TRP* 1.3 56.5 + - - +
397A GLY* 3.7 1.0 - - - -
398A GLY 2.8 23.0 + - - -
602A LEU* 3.0 25.5 - - + +
605A VAL* 3.5 29.4 - - + -
606A ILE* 4.3 11.2 - - + -
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Residues in contact with TRP 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 THR* 3.1 24.2 + - - -
392A HIS* 3.0 9.6 + - - +
394A MET* 1.3 76.4 - - + +
396A ILE* 1.3 60.0 + - + +
398A GLY* 2.8 3.3 + - - -
399A PHE* 2.7 49.4 + + + -
598A MET* 4.0 12.6 - - + -
599A TYR* 3.5 46.9 - + - -
602A LEU* 3.5 29.4 - - + -
603A SER* 3.6 12.1 - - - -
606A ILE* 3.9 33.4 - - + +
736A ILE* 4.0 42.7 - - + +
739A THR* 5.5 4.5 - - - -
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Residues in contact with ILE 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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363A THR* 4.1 16.4 - - + +
392A HIS* 3.2 41.7 + - + +
393A HIS* 5.2 0.9 - - + -
395A TRP* 1.3 79.5 - - + +
397A GLY* 1.3 64.5 + - - +
398A GLY 3.2 0.2 + - - -
399A PHE* 3.2 9.0 + - + +
400A LEU* 3.0 47.1 + - + +
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Residues in contact with GLY 397 (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 GLY* 3.1 30.5 - - - +
363A THR* 3.7 12.9 - - - -
364A ILE* 4.0 4.9 - - - -
393A HIS 3.1 12.8 + - - -
394A MET 3.7 1.6 - - - -
396A ILE* 1.3 79.6 - - - +
398A GLY* 1.3 61.0 + - - +
401A ILE* 3.2 28.2 + - - +
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Residues in contact with GLY 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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364A ILE* 4.9 0.7 - - - -
394A MET 2.8 12.5 + - - -
395A TRP 2.8 8.8 + - - -
397A GLY* 1.3 76.6 - - - +
399A PHE* 1.3 63.7 + - - +
401A ILE* 3.2 25.7 - - - +
402A VAL* 3.5 2.9 - - - +
598A MET* 3.2 31.0 - - - +
602A LEU* 3.8 7.9 - - - -
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Residues in contact with PHE 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 TRP* 2.7 36.3 + + + +
396A ILE* 3.9 9.4 - - + +
398A GLY* 1.3 72.3 - - - +
400A LEU* 1.3 64.3 + - + +
402A VAL* 3.1 14.7 + - - +
403A GLY* 3.2 9.0 + - - -
595A LEU* 4.1 13.5 - - + -
598A MET* 3.6 18.4 - - + -
732A LEU* 3.8 32.5 - - + -
736A ILE* 4.3 23.6 - - + -
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Residues in contact with LEU 400 (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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356A LEU* 3.3 38.9 - - + +
359A LEU* 4.0 22.0 - - + -
360A GLY* 3.5 26.7 - - - +
363A THR* 4.0 9.9 - - - +
396A ILE* 3.0 37.7 + - + +
398A GLY 3.3 0.2 - - - -
399A PHE* 1.3 77.7 - - + +
401A ILE* 1.3 57.9 + - - +
402A VAL 3.1 0.3 + - - -
403A GLY 3.1 2.4 + - - -
404A ALA 3.0 21.7 + - - -
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Residues in contact with ILE 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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356A LEU 4.1 0.4 - - - +
357A ALA* 3.5 15.0 - - - +
360A GLY* 3.5 2.5 - - - -
361A SER* 3.4 35.4 - - - +
364A ILE* 3.7 21.1 - - + -
397A GLY 3.2 12.8 + - - +
398A GLY* 3.2 20.2 - - - +
400A LEU* 1.3 74.7 - - - +
402A VAL* 1.3 59.6 + - + +
404A ALA* 3.6 17.6 - - + +
405A GLY 4.1 1.0 + - - -
549A LEU* 3.8 13.2 - - + +
598A MET* 5.1 3.6 - - + -
602A LEU* 5.8 3.6 - - + -
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Residues in contact with VAL 402 (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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398A GLY 3.5 3.1 + - - +
399A PHE 3.1 8.9 + - - +
400A LEU 3.0 0.6 - - - -
401A ILE* 1.3 78.1 - - + +
403A GLY* 1.3 61.1 + - - +
404A ALA 3.0 1.6 - - - -
405A GLY* 2.9 17.7 + - - -
406A ALA* 3.2 8.8 + - - +
545A THR* 5.0 0.7 - - + -
549A LEU* 4.0 22.9 - - + +
591A VAL* 4.0 21.0 - - + +
594A GLY 4.1 6.1 - - - +
595A LEU* 3.8 26.0 - - + -
598A MET* 3.4 45.1 - - + -
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Residues in contact with GLY 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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356A LEU* 3.4 19.7 - - - -
399A PHE 3.2 5.8 + - - -
400A LEU 3.1 3.8 + - - -
402A VAL* 1.3 77.5 - - - +
404A ALA* 1.3 60.2 + - - +
406A ALA* 2.9 27.2 + - - +
407A HIS* 3.0 22.1 + - - +
591A VAL* 5.7 0.4 - - - -
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Residues in contact with ALA 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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353A ALA* 3.6 18.8 - - - +
356A LEU* 3.5 4.9 - - - +
357A ALA* 3.3 41.7 - - + +
400A LEU 3.0 9.4 + - - +
401A ILE 3.6 14.8 - - - +
403A GLY* 1.3 76.7 - - - +
405A GLY* 1.3 56.5 + - - +
408A GLY* 3.4 19.6 + - - -
553A VAL* 5.4 0.2 - - - +
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Residues in contact with GLY 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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401A ILE 4.1 2.6 + - - -
402A VAL 2.9 11.3 + - - -
404A ALA* 1.3 79.9 - - - +
406A ALA* 1.3 62.3 + - - +
408A GLY 3.8 0.7 - - - -
409A ALA* 3.2 22.0 + - - +
549A LEU* 4.5 23.5 - - - +
552A GLY 5.6 0.2 - - - -
553A VAL* 3.5 14.9 - - - +
591A VAL* 4.4 4.6 - - - +
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Residues in contact with ALA 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 VAL 3.2 4.6 + - - +
403A GLY* 2.9 19.3 + - - +
405A GLY* 1.3 77.9 - - - +
407A HIS* 1.3 63.7 - - + +
409A ALA* 3.0 8.0 + - - +
410A ILE* 2.9 32.2 + - + +
570A PHE* 3.9 8.6 - - + -
591A VAL* 3.5 31.1 - - + +
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Residues in contact with HIS 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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349A HIS* 3.0 51.5 + + - +
352A LEU* 3.2 33.7 - - + +
353A ALA* 3.8 12.1 - - - +
356A LEU* 4.1 10.6 - - + +
403A GLY* 3.0 22.7 + - - +
406A ALA* 1.3 76.7 - - + +
408A GLY* 1.3 64.7 + - - +
409A ALA 3.1 1.8 - - - -
410A ILE* 3.6 15.7 - - + +
411A PHE* 3.1 23.9 + - - +
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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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353A ALA* 3.5 16.7 - - - +
404A ALA 3.4 15.8 + - - -
405A GLY 4.0 2.0 - - - -
406A ALA 3.2 1.2 - - - -
407A HIS* 1.3 79.3 - - - +
409A ALA* 1.3 57.8 + - - +
411A PHE* 4.0 7.6 - - - +
412A MET* 3.8 12.1 + - - +
553A VAL* 3.3 26.5 - - - +
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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
----------------------------------------------------------
405A GLY 3.2 12.6 + - - +
406A ALA* 3.0 10.1 + - - +
408A GLY* 1.3 76.2 - - - +
410A ILE* 1.3 64.1 + - - +
411A PHE 3.2 1.6 - - - -
412A MET* 3.0 14.7 + - - +
413A VAL* 3.1 15.4 + - - +
552A GLY 3.7 23.6 - - - +
553A VAL* 4.0 10.1 - - + +
556A ALA* 4.0 4.6 - - + +
570A PHE* 4.0 18.6 - - + -
587A GLY* 4.6 4.3 - - - +
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Residues in contact with ILE 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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349A HIS* 3.3 33.9 - - + +
406A ALA* 2.9 20.7 + - + +
407A HIS* 3.5 29.8 + - + +
409A ALA* 1.3 74.8 - - - +
411A PHE* 1.3 56.7 + - - +
413A VAL* 3.2 3.1 + - - +
414A ARG* 2.8 55.7 + - + +
570A PHE* 3.5 43.7 - - + -
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Residues in contact with PHE 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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343A ILE* 3.8 34.5 - - + -
347A SER* 3.5 20.2 - - - -
349A HIS* 4.2 6.2 - - - +
350A ALA* 3.8 31.6 - - + +
353A ALA* 5.8 0.2 - - + -
407A HIS 3.1 17.1 + - - +
408A GLY* 4.0 7.2 - - - +
410A ILE* 1.3 77.9 - - - +
412A MET* 1.3 78.7 + - + +
414A ARG* 5.3 0.2 - - - -
415A ASP* 3.0 28.8 + - + +
416A TYR* 2.9 36.1 + + + -
426A LEU* 3.9 24.2 - - + -
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Residues in contact with MET 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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408A GLY 3.8 13.5 - - - +
409A ALA 3.0 9.6 + - - +
411A PHE* 1.3 97.1 - - + +
413A VAL* 1.3 52.2 + - - +
416A TYR* 3.5 15.6 - - + +
426A LEU* 4.3 14.8 - - - -
430A LEU* 3.4 38.1 - - + -
553A VAL* 3.5 30.3 - - + +
554A LEU 5.1 1.8 - - - +
556A ALA* 4.1 6.5 - - + -
557A ARG* 2.6 64.5 + - + -
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Residues in contact with VAL 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA 3.1 13.2 + - - +
410A ILE 3.2 5.1 + - - +
412A MET* 1.3 76.6 - - - +
414A ARG* 1.3 72.3 + - + +
556A ALA* 3.8 29.2 - - + +
557A ARG* 3.1 20.6 + - - +
566A ALA* 4.2 15.0 - - - +
569A GLY* 3.9 12.3 - - - +
570A PHE* 3.6 46.4 - - + +
587A GLY 6.1 0.7 - - - +
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.0 41.0 + - - -
59A ASP* 3.4 31.8 + - - +
60A SER* 4.2 11.0 - - - -
349A HIS* 3.9 12.5 + - - -
410A ILE* 2.8 35.0 + - + +
413A VAL* 1.3 88.5 - - + +
415A ASP* 1.3 74.2 + - - +
416A TYR 3.6 4.6 + - - +
557A ARG* 5.3 0.2 + - - -
570A PHE* 5.8 4.8 - - + +
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Residues in contact with ASP 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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59A ASP* 4.7 4.5 - - - +
343A ILE* 5.4 4.0 - - - +
346A THR 5.1 1.1 - - - +
347A SER* 2.9 40.3 + - - +
348A TRP 4.6 0.9 + - - -
349A HIS* 4.4 14.7 - - - +
411A PHE* 3.0 23.2 + - + +
414A ARG* 1.3 90.0 - - - +
416A TYR* 1.3 61.4 + - - +
417A ASP* 3.6 5.7 + - - +
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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) + - + + + + + -
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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