Contacts of the helix formed by residues 333 - 373 (chain A) in PDB entry 3BNF
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 SER 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A MET* 3.6 1.2 - - - +
332A GLU* 1.3 100.5 + - - +
334A GLU* 1.3 66.0 + - - +
335A GLN* 3.7 10.1 - - - -
336A LYS* 2.7 53.5 + - - +
337A LEU* 3.4 9.5 + - - +
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Residues in contact with GLU 334 (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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322A MET* 3.4 25.4 + - + +
323A ASP* 3.7 27.9 + - - +
327A MET* 3.2 26.8 - - + +
332A GLU 3.7 0.2 + - - -
333A SER* 1.3 72.8 - - - +
335A GLN* 1.3 52.2 + - - +
337A LEU* 3.1 5.4 + - - +
338A LYS* 2.7 43.3 + - + +
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Residues in contact with GLN 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A SER* 3.2 7.5 - - - +
334A GLU* 1.3 77.8 - - - +
336A LYS* 1.3 70.0 + - + +
338A LYS* 3.2 23.2 + - - +
339A ASP* 2.7 50.6 + - - +
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Residues in contact with LYS 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLU* 3.5 16.6 - - + +
333A SER* 2.7 28.2 + - - +
335A GLN* 1.3 78.3 - - + +
337A LEU* 1.3 57.9 + - - +
339A ASP* 3.2 11.4 + - - +
340A ILE* 2.9 41.1 + - + +
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Residues in contact with LEU 337 (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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322A MET* 3.6 22.7 - - + -
326A CYS* 4.0 9.6 - - + -
327A MET* 3.9 11.9 - - + -
330A HIS* 3.9 28.7 - - + +
332A GLU* 3.3 17.6 + - - +
333A SER 3.4 9.6 + - - +
334A GLU 3.1 8.8 + - - +
336A LYS* 1.3 76.8 - - - +
338A LYS* 1.3 64.8 + - - +
340A ILE* 3.4 16.8 + - + +
341A VAL* 3.3 28.9 + - - +
512A HEM 3.9 36.1 - - + -
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Residues in contact with LYS 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.5 42.8 + - + +
320A ASP* 5.8 0.4 - - - +
322A MET* 3.6 20.6 - - - +
334A GLU* 2.7 23.6 + - + +
335A GLN* 3.6 27.6 + - - +
337A LEU* 1.3 72.7 - - - +
339A ASP* 1.3 58.2 + - - +
341A VAL* 3.2 8.1 + - - +
342A LYS* 3.0 27.3 + - - +
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Residues in contact with ASP 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A GLN* 2.7 48.0 + - - +
336A LYS* 3.5 9.7 - - - +
338A LYS* 1.3 78.0 - - - +
340A ILE* 1.3 61.2 + - - +
342A LYS* 3.4 16.4 + - + +
343A GLN* 3.1 37.3 + - - +
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Residues in contact with ILE 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A GLU* 5.5 2.2 - - - +
336A LYS* 2.9 32.9 + - + +
337A LEU* 3.7 18.8 - - + +
338A LYS 3.3 0.4 - - - -
339A ASP* 1.3 76.0 - - - +
341A VAL* 1.3 60.2 + - - +
343A GLN* 3.4 18.3 + - + +
344A LYS* 3.2 32.7 + - + +
347A ARG* 4.8 1.3 + - - +
512A HEM 3.8 26.5 - - + -
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Residues in contact with VAL 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 4.1 25.6 - - + -
337A LEU 3.3 14.8 + - - +
338A LYS 3.2 7.7 + - - +
340A ILE* 1.3 75.5 - - - +
342A LYS* 1.3 61.7 + - - +
344A LYS* 3.2 8.7 + - + +
345A PHE* 2.9 28.0 + - + +
403A PHE* 3.7 25.1 - - + -
404A PHE* 3.7 37.2 - - + -
511A HEM 4.9 2.0 - - + -
512A HEM 3.9 18.2 - - + -
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Residues in contact with LYS 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LYS 3.0 13.1 + - - +
339A ASP* 3.5 19.5 - - + +
341A VAL* 1.3 75.7 - - - +
343A GLN* 1.3 59.1 + - + +
345A PHE* 3.2 8.4 + - + +
346A GLU* 3.0 50.4 + - + +
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Residues in contact with GLN 343 (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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339A ASP* 3.1 34.8 + - - +
340A ILE* 3.6 19.2 - - - +
341A VAL 3.1 0.4 - - - -
342A LYS* 1.3 79.3 - - + +
344A LYS* 1.3 63.2 + - - +
346A GLU* 3.2 7.1 + - - +
347A ARG* 3.0 46.7 + - - +
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Residues in contact with LYS 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A Y1 4.1 4.4 - - - -
340A ILE* 3.2 21.6 - - - +
341A VAL* 3.2 8.4 + - - +
343A GLN* 1.3 77.4 - - - +
345A PHE* 1.3 64.6 + - - +
347A ARG* 3.3 29.1 + - - +
348A LYS* 3.0 23.2 + - - +
403A PHE* 3.8 18.7 - - + +
404A PHE* 4.5 16.4 - - + -
407A PRO* 3.7 23.4 - - + +
411A LEU* 5.4 0.7 - - - +
512A HEM 2.9 58.9 + - - +
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Residues in contact with PHE 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A VAL 2.9 13.3 + - - +
342A LYS* 3.2 11.9 + - - +
344A LYS* 1.3 75.7 - - - +
346A GLU* 1.3 80.9 + - - +
348A LYS* 3.2 22.5 + - - +
349A GLU* 2.9 62.5 + - + +
400A HIS 5.5 1.1 - - - -
403A PHE* 3.6 40.1 - + + -
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Residues in contact with GLU 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A LYS* 3.0 42.1 + - + +
343A GLN* 3.2 6.0 + - - +
345A PHE* 1.3 98.8 - - - +
347A ARG* 1.3 63.6 + - - +
349A GLU* 3.7 11.6 - - - +
350A PHE* 3.0 23.6 + - - +
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Residues in contact with ARG 347 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ILE* 4.8 1.4 + - - +
343A GLN* 3.0 36.1 + - - +
344A LYS* 3.5 44.8 - - - +
346A GLU* 1.3 75.3 - - - +
348A LYS* 1.3 63.4 + - - +
350A PHE* 3.3 9.5 + - - +
351A LEU* 3.2 20.4 + - - +
407A PRO* 5.8 1.8 - - - +
411A LEU* 3.8 35.2 - - + +
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Residues in contact with LYS 348 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A LYS 3.0 13.0 + - - +
345A PHE* 3.4 29.3 - - - +
347A ARG* 1.3 77.7 - - - +
349A GLU* 1.3 80.3 + - - +
351A LEU 3.4 0.2 + - - -
352A GLN* 2.9 57.2 + - + +
396A ALA 5.4 1.1 - - - +
397A ILE* 4.4 10.7 - - + +
403A PHE* 3.8 23.1 - - + -
410A VAL* 3.6 28.0 - - + -
411A LEU* 3.9 10.6 - - + +
414A LEU* 3.8 6.2 - - + +
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Residues in contact with GLU 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 3.0 36.3 + - - -
345A PHE* 2.9 52.3 + - + +
346A GLU* 3.7 16.6 - - - +
348A LYS* 1.3 95.1 + - - +
350A PHE* 1.3 63.8 + - - +
352A GLN* 3.2 5.3 + - - +
353A ASP* 2.9 34.6 + - - +
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Residues in contact with PHE 350 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A GLU 3.0 13.9 + - - +
347A ARG* 3.4 11.2 - - - +
348A LYS 3.3 0.2 - - - -
349A GLU* 1.3 77.5 - - - +
351A LEU* 1.3 95.0 + - + +
353A ASP* 3.9 4.1 - - - +
354A ILE* 3.3 42.4 + - + +
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Residues in contact with LEU 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ARG 3.2 12.2 + - - +
350A PHE* 1.3 103.2 - - + +
352A GLN* 1.3 59.0 - - - +
354A ILE* 3.5 11.9 + - + +
355A ALA* 2.9 31.4 + - - +
411A LEU* 3.8 44.0 - - + +
414A LEU* 3.9 22.2 - - + +
415A ALA* 4.6 13.0 - - + +
418A ASN* 5.5 0.5 - - - +
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Residues in contact with GLN 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 5.4 2.6 - - - +
80A LYS* 3.8 30.5 - - + +
83A LEU* 5.0 2.4 - - - +
348A LYS* 2.9 53.7 + - + +
349A GLU* 3.2 7.7 + - - +
351A LEU* 1.3 76.3 - - - +
353A ASP* 1.3 65.6 + - - +
355A ALA* 3.4 0.5 + - - -
356A PHE* 2.9 40.5 + - + +
397A ILE* 3.4 38.6 - - + +
414A LEU* 3.9 11.6 - - + +
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Residues in contact with ASP 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LYS* 2.7 40.0 + - - +
349A GLU* 2.9 21.6 + - - +
350A PHE* 3.9 4.4 - - - +
352A GLN* 1.3 76.4 - - - +
354A ILE* 1.3 66.4 + - + +
356A PHE* 4.6 1.7 - - - +
357A ASP* 3.0 27.8 + - - +
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Residues in contact with ILE 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 3.3 50.3 + - + +
351A LEU* 3.8 14.8 - - + +
353A ASP* 1.3 79.6 - - + +
355A ALA* 1.4 63.4 + - - +
357A ASP* 3.2 5.0 + - - +
358A ASN* 3.1 29.6 + - - +
418A ASN* 3.5 26.9 - - + +
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Residues in contact with ALA 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LEU 2.9 21.6 + - - +
352A GLN 3.4 3.1 + - - +
354A ILE* 1.4 73.9 - - - +
356A PHE* 1.3 59.3 + - + +
358A ASN* 3.4 2.3 + - - +
359A ILE* 2.9 34.1 + - + +
393A ALA* 4.1 21.8 - - + -
414A LEU* 3.9 23.3 - - + +
418A ASN* 3.6 19.2 - - + +
421A ALA* 4.7 0.3 - - - +
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Residues in contact with PHE 356 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 4.0 27.0 - - + +
83A LEU* 3.7 21.3 - - + -
86A ALA* 4.0 24.5 - - + -
87A TRP* 5.5 1.6 - + - -
352A GLN* 2.9 33.3 + - + +
353A ASP* 4.6 2.2 - - - +
355A ALA* 1.3 76.0 - - + +
357A ASP* 1.3 62.0 + - - +
359A ILE* 3.9 14.5 - - + +
360A GLY* 2.9 24.8 + - - -
390A GLN* 4.5 7.9 - - + -
393A ALA* 3.7 29.4 - - + -
394A ASP* 3.9 14.4 - - + -
397A ILE* 3.5 39.3 - - + -
414A LEU* 4.7 0.4 - - + -
445A PHE* 4.3 0.3 - - - -
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Residues in contact with ASP 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 4.9 1.2 - - - +
353A ASP 3.0 20.7 + - - +
354A ILE* 3.5 6.1 - - - +
356A PHE* 1.3 77.7 - - - +
358A ASN* 1.3 61.1 + - - +
360A GLY* 3.8 0.7 - - - -
361A LYS* 2.9 61.1 + - - +
445A PHE* 3.7 24.2 - - - -
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Residues in contact with ASN 358 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ILE* 3.1 20.4 + - - +
355A ALA 4.1 0.2 - - - +
357A ASP* 1.3 75.8 - - - +
359A ILE* 1.3 55.1 + - - +
361A LYS* 4.1 7.3 + - - +
362A ALA* 2.8 35.5 + - - +
418A ASN* 2.7 31.1 + - - +
421A ALA* 4.0 10.8 - - + -
422A GLN* 3.4 31.6 + - - +
425A ARG* 3.2 28.7 + - - +
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Residues in contact with ILE 359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 4.8 2.7 - - + -
355A ALA* 2.9 30.2 + - + +
356A PHE* 3.9 20.2 - - + +
358A ASN* 1.3 72.1 - - - +
360A GLY* 1.3 56.9 + - - +
362A ALA* 3.1 6.3 + - - +
363A HIS* 2.9 37.8 + - + +
386A ILE* 5.0 5.1 - - + +
389A ALA* 3.9 9.4 - - + +
390A GLN* 3.2 46.9 - - + +
393A ALA* 3.7 29.8 - - + -
417A GLY 5.2 1.3 - - - +
421A ALA* 3.8 18.3 - - + +
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Residues in contact with GLY 360 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 5.4 2.0 - - - -
85A VAL* 3.8 18.3 - - - +
86A ALA* 5.5 0.7 - - - -
356A PHE 2.9 20.6 + - - -
357A ASP 3.8 0.9 - - - -
359A ILE* 1.3 73.4 - - - +
361A LYS* 1.3 64.7 + - - +
363A HIS* 3.3 6.2 + - - +
364A LEU* 3.0 26.9 + - - +
445A PHE* 3.8 17.3 - - - -
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Residues in contact with LYS 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ASP* 2.9 44.6 + - - +
358A ASN* 3.6 7.1 + - - +
360A GLY* 1.3 74.2 - - - +
362A ALA* 1.3 59.4 + - - +
364A LEU* 3.2 1.8 + - - +
365A GLU* 2.9 39.8 + - - +
425A ARG* 3.5 44.1 - - - +
442A ALA* 4.2 21.3 - - + -
445A PHE* 4.0 8.6 - - + -
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Residues in contact with ALA 362 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ASN 2.8 18.7 + - - +
359A ILE* 3.1 7.1 + - - +
361A LYS* 1.3 74.5 - - - +
363A HIS* 1.3 66.7 + - - +
365A GLU* 4.1 8.7 + - - -
366A THR* 2.8 29.9 + - - -
386A ILE* 3.9 24.0 - - + -
421A ALA* 4.5 3.1 - - + +
424A ALA* 4.4 5.2 - - + -
425A ARG* 3.9 14.6 - - + -
428A LEU* 3.6 7.9 - - + +
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Residues in contact with HIS 363 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 4.2 11.9 - - + -
86A ALA* 4.2 3.1 - - - -
265A HIS* 3.1 46.4 + + + -
267A ILE* 3.7 6.2 - - + +
268A SER* 2.8 30.1 + - - -
272A MET* 3.6 10.1 - - + -
359A ILE* 2.9 35.9 + - + +
360A GLY* 3.3 7.6 + - - +
362A ALA* 1.3 77.4 - - - +
364A LEU* 1.3 57.7 + - - +
366A THR* 3.1 3.5 + - - -
367A GLY 3.0 23.9 + - - -
386A ILE* 3.3 24.2 - - + +
390A GLN* 2.8 22.6 + - - -
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Residues in contact with LEU 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A VAL* 4.2 8.5 - - + -
267A ILE* 4.1 28.4 - - + +
360A GLY 3.0 22.2 + - - +
361A LYS 3.2 3.3 + - - +
363A HIS* 1.3 73.1 - - - +
365A GLU* 1.3 59.7 + - - +
367A GLY* 3.2 2.3 + - - -
368A LYS* 2.9 29.1 + - - +
440A TYR* 3.7 6.9 + - - +
442A ALA* 4.0 13.0 - - + -
443A PRO* 3.5 46.9 - - + +
445A PHE* 3.5 22.0 - - + -
454A LEU* 4.2 16.6 - - + +
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Residues in contact with GLU 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A LYS* 2.9 22.6 + - - +
362A ALA* 4.1 1.0 - - - -
364A LEU* 1.3 74.7 - - - +
366A THR* 1.3 56.7 + - - +
368A LYS* 3.4 2.6 + - - +
369A ALA* 2.8 28.6 + - - +
425A ARG* 2.8 57.0 + - - +
428A LEU* 3.9 19.0 - - + +
429A VAL* 6.0 2.2 - - - +
432A LEU* 3.9 19.8 - - + +
440A TYR* 3.9 30.0 - - + +
442A ALA* 4.2 10.9 + - + +
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Residues in contact with THR 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A SER* 3.7 31.9 - - - +
362A ALA 2.8 22.5 + - - -
363A HIS 3.1 4.7 + - - -
365A GLU* 1.3 74.5 - - - +
367A GLY* 1.3 54.0 + - - +
369A ALA* 3.1 4.3 + - - +
370A MET* 2.8 40.2 + - - +
379A LEU* 4.3 15.5 - - + -
382A ILE* 3.5 2.2 - - + +
383A ARG* 4.2 16.4 - - + +
386A ILE* 3.4 10.0 - - - +
428A LEU* 3.3 22.6 - - - +
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Residues in contact with GLY 367 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 3.3 29.3 + - - -
363A HIS 3.0 12.2 + - - -
364A LEU 3.2 3.8 + - - -
366A THR* 1.3 74.1 - - - +
368A LYS* 1.3 51.8 + - - +
370A MET* 3.1 10.6 + - - +
371A GLU* 2.8 42.9 + - - +
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Residues in contact with LYS 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A LEU 2.9 6.5 + - - +
365A GLU 3.5 8.7 - - - +
367A GLY* 1.3 75.9 - - - +
369A ALA* 1.4 63.3 + - - +
371A GLU* 3.0 32.9 + - + +
372A LEU* 3.1 43.1 + - + +
432A LEU* 3.8 10.1 - - + -
437A ALA* 4.5 7.2 - - - -
440A TYR* 3.5 60.5 - - + +
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Residues in contact with ALA 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLU 2.8 15.4 + - - +
366A THR* 3.1 8.9 + - - +
368A LYS* 1.4 75.8 - - - +
370A MET* 1.3 59.2 + - - +
372A LEU* 3.2 7.9 + - - +
373A GLY 3.2 5.2 + - - -
374A ALA* 2.9 30.5 + - + +
379A LEU* 4.3 9.6 - - + -
428A LEU* 4.5 3.8 - - + -
431A VAL* 3.8 28.3 - - + -
432A LEU* 3.9 14.1 - - + +
435A TYR* 5.7 0.9 - - + -
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Residues in contact with MET 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE 3.6 14.4 - - - +
268A SER 3.6 11.2 - - - +
269A LYS* 3.2 39.9 - - + +
366A THR 2.8 18.4 + - - +
367A GLY* 3.1 8.3 + - - +
369A ALA* 1.3 73.4 - - - +
371A GLU* 1.3 66.8 + - + +
373A GLY* 2.9 16.3 + - - -
374A ALA 4.0 9.5 + - - +
379A LEU* 3.7 10.5 - - + -
383A ARG* 3.3 27.6 - - - +
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A GLY* 2.8 19.2 + - - +
368A LYS* 3.0 29.1 + - + +
370A MET* 1.3 77.0 - - + +
372A LEU* 1.3 63.1 + - + +
373A GLY* 3.1 1.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LYS* 3.1 39.1 + - + +
369A ALA* 3.7 6.7 - - - +
370A MET 3.1 0.6 - - - -
371A GLU* 1.3 80.0 - - + +
373A GLY* 1.3 57.6 + - - +
374A ALA 3.7 0.2 - - - -
432A LEU* 4.1 14.1 - - + +
435A TYR* 3.6 48.3 - - + +
437A ALA* 3.5 29.8 - - + -
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Residues in contact with GLY 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A MET 2.9 11.5 + - - -
371A GLU 3.1 1.3 - - - -
372A LEU* 1.3 80.8 - - - +
374A ALA* 1.3 68.2 + - - +
375A THR* 3.5 7.8 + - - +
435A TYR* 3.6 13.3 + - - -
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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