Contacts of the helix formed by residues 392 - 428 (chain A) in PDB entry 4N3Z
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 LEU 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A MET 5.2 2.9 - - - +
253A LEU* 4.9 14.6 - - + +
316A LEU* 3.7 28.9 - - + +
317A PRO* 3.6 38.1 - - + -
320A ILE* 5.0 2.2 - - + -
365A PHE* 3.9 49.8 - - + -
391A ASN* 1.3 79.5 + - - +
393A ASP* 1.3 57.1 + - - +
395A LEU* 2.8 29.5 + - + +
396A SER* 3.1 13.5 + - - +
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Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 4.8 11.0 - - - +
391A ASN* 2.9 16.0 + - - +
392A LEU* 1.3 77.4 - - - +
394A LEU* 1.3 53.1 + - + +
396A SER* 3.3 5.6 + - - -
397A GLN* 2.7 67.1 + - - +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN* 3.8 31.3 + - + +
392A LEU 3.2 0.4 - - - -
393A ASP* 1.3 79.0 - - + +
395A LEU* 1.3 58.8 + - + +
397A GLN* 3.9 5.6 - - + +
398A LEU* 2.8 36.3 + - + +
596B ILE* 5.1 15.3 - - + -
597B SER* 6.0 4.3 - - - -
600B VAL* 4.8 19.1 - - + -
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Residues in contact with LEU 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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316A LEU* 3.5 15.9 - - + -
361A CYS* 3.7 30.1 - - + +
364A ALA* 5.9 0.2 - - + -
365A PHE* 3.9 30.5 - - + +
391A ASN 3.3 20.2 - - - +
392A LEU* 2.8 18.3 + - - +
394A LEU* 1.3 72.6 - - + +
396A SER* 1.3 56.1 - - - +
398A LEU* 4.1 4.5 - - - +
399A ASN* 2.2 38.0 + - - +
596B ILE* 5.2 11.2 - - + -
596C ILE* 4.1 18.6 - - + -
599C LEU* 4.3 7.9 - - + -
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ALA 3.9 6.6 + - - -
313A ASP* 3.9 31.6 + - - -
316A LEU* 3.4 28.8 - - - +
317A PRO* 4.4 1.6 - - - +
354A TYR* 5.5 0.2 + - - -
358A ASN* 5.7 1.6 - - - -
392A LEU* 3.1 9.2 + - - +
393A ASP* 3.6 10.7 - - - -
395A LEU* 1.3 72.8 - - - +
397A GLN* 1.3 59.7 + - - +
399A ASN* 3.1 7.6 + - - +
400A GLU* 2.9 36.2 + - - +
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Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASP* 4.8 6.7 - - - +
393A ASP* 2.7 50.3 + - - +
394A LEU* 3.9 6.3 - - + +
396A SER* 1.3 72.5 - - - +
398A LEU* 1.3 57.1 + - - +
400A GLU* 2.9 38.2 + - - +
401A ARG* 2.9 40.4 + - - +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 2.8 21.3 + - + +
395A LEU* 4.1 4.3 - - - +
397A GLN* 1.3 71.0 - - - +
399A ASN* 1.3 64.0 + - - +
401A ARG* 3.1 11.3 - - + +
402A GLN* 3.1 54.0 + - + +
596B ILE* 3.7 28.5 - - + +
599B LEU* 4.1 8.1 - - + +
600B VAL* 3.5 35.0 - - + +
603B ALA* 5.8 1.1 - - + -
599C LEU* 3.6 27.6 - - + -
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Residues in contact with ASN 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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316A LEU* 5.2 1.2 - - - +
354A TYR* 3.8 20.8 - - + +
357A THR* 3.1 26.7 + - - -
358A ASN* 3.5 17.7 + - - +
361A CYS* 3.4 23.0 - - - +
395A LEU 2.2 34.4 + - - +
396A SER* 3.1 7.6 + - - +
398A LEU* 1.3 73.6 - - - +
400A GLU* 1.3 66.1 + - - +
402A GLN* 3.5 7.9 + - - +
403A GLU* 3.0 26.9 + - - +
599C LEU* 3.6 16.5 - - - +
602C ARG* 4.3 2.9 + - - +
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Residues in contact with GLU 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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312A ALA* 3.4 34.3 - - + +
313A ASP* 3.7 12.5 + - - +
354A TYR* 4.6 6.7 - - - +
396A SER* 2.9 23.2 + - - +
397A GLN* 2.9 34.3 - - - +
399A ASN* 1.3 74.6 - - - +
401A ARG* 1.3 64.5 + - - +
403A GLU* 3.3 5.3 + - - +
404A ARG* 2.9 27.0 + - - +
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Residues in contact with ARG 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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397A GLN* 2.9 26.7 + - - +
398A LEU* 3.1 16.8 - - + +
400A GLU* 1.3 79.3 - - - +
402A GLN* 1.3 66.2 + - + +
404A ARG* 3.3 4.8 + - - +
405A ILE* 3.1 26.5 + - + +
600B VAL* 4.1 28.5 + - - +
603B ALA* 4.1 19.2 - - + +
604B GLN* 4.6 13.3 + - - +
607B GLU* 2.7 41.9 + - - +
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Residues in contact with GLN 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 LEU* 3.1 40.6 + - + +
399A ASN* 4.1 4.4 - - - +
401A ARG* 1.3 80.7 - - + +
403A GLU* 1.3 63.8 + - - +
405A ILE* 3.5 12.0 - - + +
406A MET* 3.2 40.9 + - + +
599B LEU* 4.5 6.9 + - - +
603B ALA* 5.2 9.4 - - + -
599C LEU* 3.2 25.4 + - - +
602C ARG* 3.2 31.4 - - - +
603C ALA* 3.5 19.0 - - - +
606C SER* 4.3 6.3 - - - +
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Residues in contact with GLU 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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349A THR* 4.5 3.1 + - - -
350A GLY 4.0 20.1 + - - +
354A TYR* 3.7 29.7 - - + +
399A ASN 3.0 18.9 + - - +
400A GLU* 3.3 5.4 + - - +
402A GLN* 1.3 73.5 - - - +
404A ARG* 1.3 65.6 + - - +
406A MET* 3.4 4.8 + - - +
407A ASN* 3.0 41.6 + - - +
602C ARG* 2.8 37.3 + - - +
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Residues in contact with ARG 404 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A GLU 2.9 17.4 + - - +
401A ARG* 3.5 4.5 - - - +
403A GLU* 1.3 72.9 - - - +
405A ILE* 1.3 60.3 + - + +
406A MET 2.9 4.9 - - - -
407A ASN* 2.6 33.0 + - - +
408A GLU* 2.8 48.1 + - + +
607B GLU* 4.3 25.8 + - - +
610B LEU* 4.2 15.7 - - - +
611B GLU* 6.1 2.2 - - - +
614B GLN* 5.3 3.4 + - - +
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Residues in contact with ILE 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ARG* 3.1 16.8 + - + +
402A GLN* 3.5 13.2 - - + +
404A ARG* 1.3 88.9 - - + +
406A MET* 1.3 59.7 + - - +
408A GLU* 3.9 1.3 - - - +
409A ALA* 2.9 28.6 + - - +
603B ALA* 5.7 2.5 - - + -
606B SER* 3.6 29.2 - - - +
607B GLU* 3.5 31.9 - - + +
610B LEU* 3.9 21.6 - - + +
606C SER* 3.5 31.9 - - - +
610C LEU* 4.4 9.9 - - + +
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Residues in contact with MET 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A LEU 3.5 20.6 - - - +
348A MET* 3.6 17.0 - - - -
349A THR* 4.4 8.9 - - - +
402A GLN* 3.2 27.7 + - + +
403A GLU* 3.6 5.8 - - - +
404A ARG 2.9 0.6 - - - -
405A ILE* 1.3 80.5 - - - +
407A ASN* 1.3 63.0 + - - +
409A ALA* 3.8 3.5 - - - +
410A LYS* 3.0 33.1 + - - +
602C ARG* 3.3 40.8 - - - +
605C ALA* 4.7 2.9 - - - -
606C SER* 3.3 30.1 - - - +
609C LEU* 3.7 21.5 - - + -
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Residues in contact with ASN 407 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A THR* 3.6 17.9 + - - -
403A GLU* 3.0 36.0 + - - +
404A ARG* 2.6 19.7 + - - +
406A MET* 1.3 70.7 - - - +
408A GLU* 1.3 65.8 + - - +
410A LYS* 3.2 7.7 + - - +
411A LYS* 3.1 43.3 + - - +
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Residues in contact with GLU 408 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ARG* 2.8 57.5 + - + +
405A ILE 4.0 0.2 - - - +
407A ASN* 1.3 74.2 - - - +
409A ALA* 1.3 57.9 + - - +
411A LYS* 3.2 25.9 + - - +
412A LEU* 3.0 30.0 + - - +
610B LEU* 3.6 23.1 - - + +
614B GLN* 3.6 20.6 + - - +
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Residues in contact with ALA 409 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ILE 2.9 20.2 + - - +
406A MET 3.9 1.1 - - - +
407A ASN 3.2 0.2 - - - -
408A GLU* 1.3 74.0 - - - +
410A LYS* 1.3 58.3 + - - +
411A LYS 3.0 4.5 - - - -
412A LEU* 3.4 0.8 + - - +
413A GLU* 2.9 30.2 + - - +
610B LEU* 4.0 4.4 - - - +
609C LEU* 3.5 32.1 - - + -
610C LEU* 4.2 10.3 - - + -
613C LEU* 3.7 19.8 - - + +
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Residues in contact with LYS 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A MET* 4.3 19.1 - - + +
349A THR* 3.5 34.5 - - + -
406A MET 3.0 22.0 - - - +
407A ASN* 3.2 5.8 + - - +
409A ALA* 1.3 74.3 - - - +
411A LYS* 1.3 58.7 + - - +
413A GLU* 3.3 30.7 + - - +
414A LYS* 3.4 35.7 + - - +
609C LEU* 3.6 34.9 - - + +
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Residues in contact with LYS 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ASN* 3.1 39.3 + - - +
408A GLU* 3.3 24.8 + - - +
409A ALA 3.0 0.6 - - - -
410A LYS* 1.3 77.0 - - - +
412A LEU* 1.3 58.2 + - - +
413A GLU 3.1 0.9 - - - -
414A LYS* 2.8 29.5 + - + +
415A ASP* 2.9 26.6 + - - +
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Residues in contact with LEU 412 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A GLU 3.0 12.3 + - - +
409A ALA* 4.0 3.8 - - - +
411A LYS* 1.3 78.9 - - - +
413A GLU* 1.3 63.2 + - - +
415A ASP* 4.1 8.9 + - - +
416A LEU* 3.1 39.9 + - + +
610B LEU* 4.5 4.5 - - + +
613B LEU* 3.6 35.9 - - + +
614B GLN* 3.9 31.6 - - + +
617B LEU* 3.6 30.7 - - + -
613C LEU* 4.3 20.4 - - + +
617C LEU* 6.2 1.6 - - + -
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Residues in contact with GLU 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A ALA 2.9 18.4 + - - +
410A LYS* 3.3 45.9 + - - +
411A LYS 3.1 0.2 - - - -
412A LEU* 1.3 75.3 - - - +
414A LYS* 1.3 63.5 + - + +
416A LEU* 3.9 9.3 - - - +
417A ILE* 3.8 18.7 - - + +
609C LEU* 5.7 0.4 - - + -
612C GLU* 4.2 16.9 - - + +
613C LEU* 3.6 23.9 - - + +
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Residues in contact with LYS 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LYS* 3.4 21.9 + - - +
411A LYS* 2.8 12.8 + - + +
413A GLU* 1.3 80.7 - - + +
415A ASP* 1.3 57.8 + - - +
416A LEU 2.9 4.0 - - - -
417A ILE* 2.5 36.4 + - + +
418A ASP* 2.9 21.6 + - - +
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Residues in contact with ASP 415 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A LYS* 2.9 31.8 + - - +
412A LEU* 3.4 9.0 + - - +
414A LYS* 1.3 72.2 - - - +
416A LEU* 1.3 56.9 + - - +
418A ASP* 3.7 17.1 - - - +
419A TRP* 2.9 32.1 + - - +
617B LEU* 3.9 20.5 - - + +
621B LYS* 5.1 7.6 - - - +
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Residues in contact with LEU 416 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 3.1 36.4 + - + +
413A GLU* 3.9 7.9 - - - +
414A LYS 2.8 0.6 + - - -
415A ASP* 1.3 77.3 - - - +
417A ILE* 1.3 58.2 + - + +
419A TRP* 3.8 3.1 - - - +
420A THR* 2.9 34.9 + - - -
617B LEU* 3.7 33.4 - - + -
613C LEU* 4.1 21.1 - - + +
616C GLY* 3.5 38.4 - - - +
617C LEU* 3.6 12.6 - - + +
620C ALA* 4.2 10.5 - - + -
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Residues in contact with ILE 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A GLU* 3.8 17.0 - - + +
414A LYS* 2.5 15.9 + - + +
416A LEU* 1.3 70.9 - - + +
418A ASP* 1.3 64.3 + - - +
420A THR* 4.2 5.6 - - - -
421A ASP* 2.9 49.1 + - - +
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Residues in contact with ASP 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A LYS* 2.9 20.5 + - - +
415A ASP* 3.7 19.3 - - - +
417A ILE* 1.3 81.3 - - - +
419A TRP* 1.3 57.1 + - - +
421A ASP* 4.2 3.1 - - - +
422A GLY* 2.9 27.5 + - - -
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Residues in contact with TRP 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A ASP 2.9 18.4 + - - +
416A LEU 3.8 1.8 - - - +
418A ASP* 1.3 74.1 - - - +
420A THR* 1.3 69.4 + - - +
422A GLY* 4.9 0.7 - - - -
423A ILE* 3.1 42.0 + - + +
617B LEU* 3.9 21.3 - - + -
620B ALA* 3.6 37.2 - - + -
621B LYS* 3.8 39.5 + - + +
624B VAL* 3.6 18.1 - - + +
617C LEU* 5.1 0.7 - - + -
620C ALA* 3.5 41.1 - - + -
621C LYS* 4.1 6.3 - - + -
624C VAL* 3.5 24.9 - - + -
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Residues in contact with THR 420 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A LEU 2.9 23.9 + - - -
417A ILE* 3.3 8.5 + - + -
419A TRP* 1.3 73.6 - - - +
421A ASP* 1.3 75.3 + - - +
423A ILE* 3.7 3.6 - - - +
424A ALA* 3.0 28.6 + - + +
620C ALA* 3.9 23.2 + - - +
623C ASP* 4.7 19.1 - - + +
624C VAL* 4.3 12.5 - - + +
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Residues in contact with ASP 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A ILE* 2.9 35.2 + - - +
418A ASP* 4.2 2.9 - - - +
420A THR* 1.3 84.7 - - - +
422A GLY* 1.3 50.7 + - - +
423A ILE 2.7 2.1 + - - -
424A ALA* 2.6 13.4 + - - +
425A ARG* 2.3 60.0 + - + +
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Residues in contact with GLY 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A ASP 2.9 23.6 + - - -
419A TRP* 3.5 1.8 + - - -
421A ASP* 1.3 71.3 - - - +
423A ILE* 1.3 57.1 + - - +
425A ARG* 4.1 12.5 - - - +
426A GLU* 3.1 34.0 + - - +
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Residues in contact with ILE 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A TRP* 3.1 28.9 + - + +
420A THR 3.7 3.8 - - - +
421A ASP 2.7 5.1 + - - -
422A GLY* 1.3 74.3 - - - +
424A ALA* 1.3 59.3 - - + +
426A GLU* 3.6 12.0 - - - +
427A VAL* 2.8 37.1 + - + +
624B VAL* 3.8 18.6 - - + -
625B GLN* 6.2 1.6 - - - -
628B MET* 3.6 31.0 - - + +
624C VAL* 3.6 39.0 - - + +
627C GLN* 4.6 6.1 - - + -
628C MET* 5.9 0.7 - - - -
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Residues in contact with ALA 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A THR* 3.0 19.9 + - + +
421A ASP* 2.6 9.3 + - - +
423A ILE* 1.3 72.2 - - - +
425A ARG* 1.3 64.4 + - - +
426A GLU 2.9 2.6 + - - -
427A VAL 3.0 9.8 + - - +
428A GLN* 2.6 26.4 - - - +
627C GLN* 3.5 40.2 - - + +
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Residues in contact with ARG 425 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421A ASP* 2.3 57.8 + - + +
422A GLY* 4.1 8.3 - - - +
424A ALA* 1.3 68.2 - - - +
426A GLU* 1.3 57.2 + - - +
428A GLN* 4.1 10.9 + - - +
429A ASP* 4.4 6.1 + - - +
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Residues in contact with GLU 426 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A GLY 3.1 22.2 + - - +
423A ILE* 4.3 8.0 - - - +
424A ALA 2.9 1.6 + - - -
425A ARG* 1.3 77.7 - - + +
427A VAL* 1.3 52.2 + - - +
428A GLN 3.0 6.1 - - - -
429A ASP* 2.5 42.5 - - - +
430A ILE* 4.6 1.0 - - - +
628B MET* 3.4 32.1 - - + +
632B MET* 4.7 6.9 - - - +
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Residues in contact with VAL 427 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A ILE* 2.8 22.0 + - + +
424A ALA 3.0 2.3 + - - +
426A GLU* 1.3 75.1 - - - +
428A GLN* 1.3 68.7 + - + +
429A ASP* 3.8 0.2 - - - -
430A ILE* 3.6 23.8 - - - +
628B MET* 4.4 9.0 - - + -
627C GLN* 3.3 50.0 - - + +
628C MET* 4.3 12.8 - - - -
630C VAL* 3.8 10.3 - - + +
631C LEU* 3.9 33.7 - - + +
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Residues in contact with GLN 428 (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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424A ALA* 2.6 26.6 - - - +
425A ARG* 4.1 7.7 + - - +
426A GLU 3.0 0.4 - - - -
427A VAL* 1.3 88.8 - - + +
429A ASP* 1.3 64.4 + - - +
430A ILE 3.3 7.5 - - - +
627C GLN* 3.2 25.2 + - - +
630C VAL* 5.0 6.8 - - + +
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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