Contacts of the helix formed by residues 439 - 476 (chain A) in PDB entry 1YC9
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 THR 439 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A TYR* 3.8 8.1 - - - -
438A ALA* 1.3 79.4 - - - +
440A TYR* 1.3 64.5 + - - +
441A LEU* 3.4 13.2 + - - +
442A ASP* 3.1 36.5 + - - +
443A VAL* 3.7 9.5 + - - +
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Residues in contact with TYR 440 (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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216A THR* 3.9 18.5 - - + +
220A LEU* 3.4 25.8 - - + -
229A GLU* 4.1 10.0 + - - +
233A SER* 3.8 42.2 - - - +
236A GLN* 3.9 11.0 - - + -
237A ALA* 3.2 26.1 + - + +
240A VAL* 4.0 7.8 - - - +
433A TYR* 3.7 14.3 - + + -
439A THR* 1.3 72.0 - - - +
441A LEU* 1.3 70.8 + - + +
443A VAL* 2.8 22.1 + - + +
444A LEU* 2.8 52.4 + - + +
447A GLU* 4.6 5.5 + - - -
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Residues in contact with LEU 441 (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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236A GLN* 6.4 0.4 - - + -
439A THR* 3.2 13.1 + - + +
440A TYR* 1.3 84.3 - - + +
442A ASP* 1.3 65.2 + - - +
444A LEU* 3.2 27.5 + - + -
445A VAL* 3.0 39.4 + - + +
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Residues in contact with ASP 442 (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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429A ALA* 4.0 14.4 - - + +
438A ALA* 3.5 13.9 - - + +
439A THR* 3.1 34.6 + - - +
440A TYR 3.2 0.8 - - - -
441A LEU* 1.3 78.9 - - - +
443A VAL* 1.3 62.1 + - - +
445A VAL* 3.6 4.6 + - - +
446A ALA* 3.1 24.8 + - - +
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Residues in contact with VAL 443 (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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216A THR* 4.6 7.4 - - + +
426A LEU* 3.9 0.4 - - - +
429A ALA* 3.5 37.0 - - + +
430A THR* 4.1 19.1 - - + +
433A TYR* 3.9 17.5 - - + -
439A THR 3.9 11.0 - - - +
440A TYR* 2.8 21.8 + - + +
442A ASP* 1.3 74.2 - - - +
444A LEU* 1.3 65.3 + - - +
446A ALA* 3.3 2.4 + - - +
447A GLU* 2.8 43.9 + - + +
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Residues in contact with LEU 444 (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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236A GLN* 3.6 32.8 - - + +
240A VAL* 4.0 16.2 - - + -
440A TYR* 2.8 37.2 + - + +
441A LEU* 3.2 22.0 + - + +
443A VAL* 1.3 73.4 - - - +
445A VAL* 1.3 72.3 + - + +
447A GLU* 3.4 12.4 + - - +
448A GLU* 3.0 37.8 + - + +
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Residues in contact with VAL 445 (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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441A LEU* 3.0 31.6 + - + +
442A ASP* 4.0 5.4 - - - +
444A LEU* 1.3 87.8 - - + +
446A ALA* 1.3 59.0 + - - +
448A GLU* 3.4 5.6 + - - +
449A SER* 3.0 30.4 + - - -
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Residues in contact with ALA 446 (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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422A ALA* 4.4 4.6 - - - +
425A ALA* 4.1 13.9 - - + +
426A LEU* 3.6 35.8 - - + +
429A ALA* 4.5 1.8 - - + -
442A ASP 3.1 18.2 + - - +
443A VAL 3.8 2.7 - - - +
445A VAL* 1.3 76.8 - - - +
447A GLU* 1.3 59.2 + - - +
449A SER* 3.4 5.9 + - - -
450A LEU* 2.9 30.8 + - - +
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Residues in contact with GLU 447 (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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212A VAL* 3.8 9.6 - - + +
213A ARG* 3.1 53.1 + - - +
216A THR* 3.1 28.7 + - - +
240A VAL* 4.5 7.6 - - + +
426A LEU* 3.6 27.7 - - + +
430A THR* 5.8 0.7 - - - +
440A TYR* 4.6 5.9 + - - -
443A VAL* 2.8 31.0 + - - +
444A LEU* 3.6 12.5 - - - +
446A ALA* 1.3 73.2 - - - +
448A GLU* 1.3 58.5 + - - +
450A LEU* 3.4 2.0 + - - +
451A LEU* 3.0 24.3 + - - +
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Residues in contact with GLU 448 (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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213A ARG* 5.0 1.3 - - - +
240A VAL* 5.7 5.7 - - - +
444A LEU* 3.0 24.9 + - + +
445A VAL* 3.6 6.1 - - - +
447A GLU* 1.3 75.0 - - - +
449A SER* 1.3 60.0 + - - +
451A LEU* 3.4 7.0 + - - +
452A ASN* 2.9 54.2 + - - +
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Residues in contact with SER 449 (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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422A ALA* 3.6 10.4 - - - +
445A VAL* 3.0 20.3 + - - -
446A ALA* 3.8 6.5 - - - -
448A GLU* 1.3 77.7 - - - +
450A LEU* 1.3 62.1 + - - +
452A ASN* 3.4 7.4 + - - +
453A ASN* 3.0 42.8 + - - -
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Residues in contact with LEU 450 (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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213A ARG* 5.9 2.5 - - - +
419A VAL* 3.6 28.3 - - + +
422A ALA* 3.8 11.8 - - + +
423A GLU* 3.9 25.6 - - + +
426A LEU* 3.8 24.7 - - + -
446A ALA 2.9 18.4 + - - +
447A GLU* 3.7 4.7 - - - +
449A SER* 1.3 73.6 + - - +
451A LEU* 1.3 60.6 + - - +
453A ASN* 3.3 2.3 + - - +
454A GLN* 2.9 66.1 + - + +
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Residues in contact with LEU 451 (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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205A THR* 4.0 24.7 - - + +
206A VAL* 4.4 9.2 - - + -
209A ALA* 3.9 27.1 - - + -
213A ARG* 3.8 12.1 - - - +
244A VAL* 4.3 23.8 - - + -
247A GLU* 6.5 0.9 - - + -
447A GLU 3.0 16.7 + - - +
448A GLU* 3.9 8.1 - - - +
450A LEU* 1.3 76.8 - - - +
452A ASN* 1.3 66.4 + - - +
454A GLN* 3.7 7.0 - - - +
455A ARG* 3.1 39.2 + - - +
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Residues in contact with ASN 452 (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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448A GLU* 2.9 43.2 + - - +
449A SER* 3.8 7.3 - - - +
451A LEU* 1.3 80.5 - - - +
453A ASN* 1.3 61.2 + - - +
455A ARG* 3.4 6.5 + - - +
456A ALA* 3.0 27.2 + - - +
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Residues in contact with ASN 453 (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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415A THR* 3.8 5.0 - - + +
418A ALA* 3.6 34.4 + - + +
419A VAL* 3.3 29.5 - - + +
422A ALA* 3.9 1.6 - - - +
449A SER* 3.0 33.7 + - - +
450A LEU 3.8 2.5 - - - +
452A ASN* 1.3 78.0 - - - +
454A GLN* 1.3 58.4 + - - +
456A ALA* 3.3 8.2 + - - +
457A LEU* 2.9 24.9 + - - +
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Residues in contact with GLN 454 (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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205A THR* 3.7 26.6 - - + +
209A ALA* 5.2 3.5 - - - +
419A VAL* 3.8 18.6 - - + +
423A GLU* 5.7 3.2 + - - -
450A LEU* 2.9 47.8 + - + +
451A LEU* 3.7 18.4 - - - +
453A ASN* 1.3 76.3 - - - +
455A ARG* 1.3 63.0 + - - +
457A LEU* 3.4 3.9 + - - +
458A VAL* 3.0 27.4 + - - +
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Residues in contact with ARG 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 5.9 1.2 - - - +
202A ASN* 2.9 29.3 + - - +
205A THR* 4.0 15.0 - - + -
206A VAL* 3.7 23.8 - - + +
247A GLU* 2.6 38.6 + - - +
251A ILE* 3.7 20.8 - - - +
451A LEU* 3.1 28.8 + - + +
452A ASN* 3.8 7.0 - - - +
453A ASN 3.3 0.2 - - - -
454A GLN* 1.3 74.2 - - - +
456A ALA* 1.3 58.8 + - - +
458A VAL* 3.3 4.6 + - - +
459A ASN* 2.9 39.2 + - - +
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Residues in contact with ALA 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A THR* 3.9 14.4 - - + -
452A ASN 3.0 16.1 + - - +
453A ASN* 3.3 9.2 + - - +
455A ARG* 1.3 75.5 - - - +
457A LEU* 1.3 62.4 + - - +
459A ASN* 3.3 8.3 + - - +
460A LEU* 3.0 28.8 + - + +
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Residues in contact with LEU 457 (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 ILE* 4.1 20.9 - - + +
415A THR* 3.6 12.5 - - + +
416A GLU* 3.8 36.3 - - + +
419A VAL* 4.0 22.9 - - + -
453A ASN 2.9 17.1 + - - +
454A GLN* 3.6 6.1 - - - +
456A ALA* 1.3 76.5 - - - +
458A VAL* 1.3 63.6 + - + +
460A LEU* 3.1 3.0 + - + -
461A GLN* 2.9 48.3 + - + +
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Residues in contact with VAL 458 (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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198A ARG* 4.1 2.7 - - + +
201A ALA* 3.3 31.5 - - + +
202A ASN* 3.3 33.0 - - - +
205A THR* 3.6 23.6 - - - +
454A GLN 3.0 17.8 + - - +
455A ARG* 3.7 3.6 - - - +
457A LEU* 1.3 75.2 - - + +
459A ASN* 1.3 62.8 + - - +
461A GLN* 3.4 17.4 + - - +
462A SER* 3.0 22.7 + - - -
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Residues in contact with ASN 459 (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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198A ARG* 2.9 42.3 + - - +
202A ASN* 3.0 22.9 - - - +
455A ARG* 2.9 23.6 + - - +
456A ALA* 3.7 7.4 - - - +
458A VAL* 1.3 78.4 - - - +
460A LEU* 1.3 57.0 + - + +
462A SER* 3.5 5.9 + - - -
463A ARG* 3.0 25.3 + - - +
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Residues in contact with LEU 460 (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 LEU* 3.7 24.8 - - + +
411A ARG* 3.7 55.6 - - + +
412A ILE* 3.7 17.8 - - + +
415A THR* 3.2 33.4 - - + +
456A ALA* 3.0 16.3 + - + +
457A LEU* 3.1 6.9 + - - +
459A ASN* 1.3 76.5 - - + +
461A GLN* 1.3 63.4 + - - +
463A ARG* 3.2 24.8 + - - +
464A ALA 3.3 5.5 + - - -
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Residues in contact with GLN 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU* 4.6 3.8 - - - +
412A ILE* 4.4 13.6 - - + +
416A GLU* 4.6 8.5 + - - -
457A LEU* 2.9 44.2 + - + +
458A VAL* 3.7 23.9 + - - +
460A LEU* 1.3 75.9 - - - +
462A SER* 1.3 61.8 + - - +
464A ALA* 3.1 20.4 + - - +
465A PHE* 3.8 2.9 + - - +
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Residues in contact with SER 462 (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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194A ALA* 3.7 10.9 + - - +
197A ALA* 5.7 1.2 - - - +
198A ARG* 3.4 40.3 - - - +
201A ALA* 6.4 0.2 - - - -
458A VAL 3.0 16.7 + - - -
459A ASN 3.6 5.6 - - - -
461A GLN* 1.3 72.5 - - - +
463A ARG* 1.3 65.2 + - - +
465A PHE* 3.1 13.2 + - - +
466A SER* 3.0 24.0 + - - -
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Residues in contact with ARG 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A SER* 3.4 30.4 + - - -
408A LEU* 4.0 16.3 - - + +
411A ARG* 4.0 20.0 - - - +
459A ASN 3.0 14.5 + - - +
460A LEU* 3.2 25.5 + - - +
462A SER* 1.3 76.2 - - - +
464A ALA* 1.3 56.6 + - - +
466A SER* 3.6 10.1 - - - -
467A LEU* 2.8 51.1 + - + +
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Residues in contact with ALA 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU* 3.6 17.8 - - + +
408A LEU* 3.5 23.8 - - + +
412A ILE* 5.1 4.0 - - + -
460A LEU 3.3 3.5 + - - +
461A GLN* 3.1 15.3 + - - +
462A SER 3.1 0.6 - - - -
463A ARG* 1.3 80.0 - - - +
465A PHE* 1.3 62.0 + - - +
467A LEU* 3.5 3.0 + - - +
468A ASP* 3.1 22.3 + - - +
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Residues in contact with PHE 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A TYR* 3.7 37.9 - + - -
77A LEU* 4.4 7.2 - - + -
190A ALA 4.4 3.1 - - - -
193A TYR* 4.6 2.9 - + - -
194A ALA* 3.6 39.9 - - + -
197A ALA* 5.3 5.2 - - + -
281A ILE* 3.5 40.4 - - + -
283A LEU* 3.5 30.9 - - + +
461A GLN 3.8 1.5 + - - +
462A SER* 3.1 13.1 + - - +
464A ALA* 1.3 75.7 - - - +
466A SER* 1.3 63.7 + - - +
468A ASP* 3.0 3.1 + - - +
469A LEU* 3.0 36.5 + - + +
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Residues in contact with SER 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN* 4.5 8.4 + - - +
194A ALA* 3.8 16.6 - - - +
462A SER* 3.0 16.3 + - - -
463A ARG* 3.2 14.5 + - - -
465A PHE* 1.3 75.1 - - - +
467A LEU* 1.3 59.5 + - - +
469A LEU* 3.3 12.5 + - - +
470A ALA* 2.8 27.5 + - - +
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Residues in contact with LEU 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A VAL* 3.9 12.9 - - - +
404A SER* 3.6 49.4 - - - +
405A SER* 3.9 17.0 + - - +
408A LEU* 4.1 12.6 - - + -
463A ARG* 2.8 48.8 + - + +
464A ALA* 3.9 4.7 - - - +
466A SER* 1.3 71.8 - - - +
468A ASP* 1.3 66.5 + - - +
470A ALA* 3.5 13.4 - - + +
471A LEU* 3.0 23.4 + - - +
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Residues in contact with ASP 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ARG* 4.3 3.1 + - - -
72A TYR* 2.5 34.2 + - + +
283A LEU* 4.6 6.7 - - + -
284A THR 4.9 5.4 - - - +
286A ARG* 2.8 43.0 + - - +
464A ALA 3.1 12.4 + - - +
465A PHE* 3.0 12.2 + - - +
467A LEU* 1.3 76.0 - - - +
469A LEU* 1.3 62.2 + - - +
471A LEU* 3.2 10.7 + - - +
472A ILE* 3.1 22.7 + - - +
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Residues in contact with LEU 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TRP* 3.5 33.0 - - + -
72A TYR* 3.6 20.6 - - + +
187A THR* 5.1 4.2 - - - +
190A ALA* 3.4 37.0 - - + +
191A ASN* 3.6 27.2 + - - +
194A ALA* 4.1 8.5 - - + -
465A PHE* 3.0 32.0 + - + +
466A SER* 3.5 7.2 - - - +
468A ASP* 1.3 77.5 - - - +
470A ALA* 1.3 54.8 + - - +
472A ILE* 3.2 6.2 + - - +
473A HIS* 2.9 29.0 + - - +
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Residues in contact with ALA 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN* 5.3 0.8 + - - +
401A VAL* 3.5 17.4 - - + +
466A SER 2.8 19.5 + - - +
467A LEU* 3.5 17.5 - - + +
468A ASP 3.3 0.2 - - - -
469A LEU* 1.3 70.8 - - - +
471A LEU* 1.3 59.4 + - - +
473A HIS* 3.5 6.7 + - - +
474A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PRO* 5.6 1.1 - - + -
286A ARG* 4.1 33.2 - - + +
398A ILE* 5.7 6.3 - - + -
401A VAL* 3.8 23.3 - - + +
402A VAL* 6.2 2.9 - - + -
467A LEU 3.0 12.7 + - - +
468A ASP* 3.5 12.6 - - - +
469A LEU 3.2 0.2 - - - -
470A ALA* 1.3 76.5 - - - +
472A ILE* 1.3 66.8 + - + +
474A ALA* 3.2 3.3 + - + +
475A LEU* 2.9 58.5 + - + +
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Residues in contact with ILE 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PRO* 3.9 20.4 - - + -
68A TRP* 3.4 66.2 - - + +
72A TYR* 3.4 14.1 - - + +
183A LEU* 4.6 2.5 - - + -
187A THR* 4.9 1.1 - - + -
286A ARG* 3.4 30.5 - - - +
468A ASP 3.1 8.6 + - - +
469A LEU* 3.6 8.1 - - - +
471A LEU* 1.3 76.6 - - + +
473A HIS* 1.3 64.6 + - - +
475A LEU* 3.3 1.4 + - - +
476A GLY 3.1 3.8 + - - -
477A GLY* 3.0 35.4 + - - -
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Residues in contact with HIS 473 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.8 24.9 - - + +
184A MET* 5.6 4.4 - - - +
187A THR* 3.5 31.4 - - + -
191A ASN* 5.9 3.4 - - - +
301A ARG* 4.2 7.8 + - - -
397A GLU* 4.4 17.6 + - - -
469A LEU 2.9 15.6 + - - +
470A ALA* 3.8 7.2 - - - +
472A ILE* 1.3 79.1 - - - +
474A ALA* 1.3 57.4 + - - +
476A GLY* 3.0 18.9 + - - -
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A ARG* 2.9 34.2 + - - +
397A GLU* 4.2 7.4 - - + -
398A ILE* 3.8 35.2 - - + +
401A VAL* 4.1 15.3 - - + -
470A ALA 2.9 19.1 + - - +
471A LEU* 3.2 5.6 + - + +
473A HIS* 1.3 78.7 + - - +
475A LEU* 1.3 58.8 + - + +
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Residues in contact with LEU 475 (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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63A TRP* 4.3 22.1 - - + -
64A PRO* 3.8 32.8 - - + -
297A LEU* 3.9 40.5 - - + +
300A HIS* 3.4 25.3 + - - +
301A ARG* 4.0 5.0 + - - +
398A ILE* 4.7 8.1 - - + -
471A LEU* 2.9 47.6 + - + +
472A ILE 4.0 3.6 - - - +
474A ALA* 1.3 79.6 - - - +
476A GLY* 1.3 60.2 + - - +
477A GLY 3.4 2.9 - - - +
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Residues in contact with GLY 476 (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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179A VAL* 5.2 8.8 - - - +
183A LEU* 4.0 20.0 - - - +
300A HIS* 3.2 21.3 + - - +
301A ARG* 4.4 8.5 - - - -
302A ALA* 5.3 2.0 + - - +
472A ILE 3.1 0.4 + - - -
473A HIS 3.0 17.0 + - - -
474A ALA 3.3 0.4 - - - -
475A LEU* 1.3 77.8 - - - +
477A GLY* 1.3 63.8 + - - +
478A GLY 4.0 0.3 + - - -
479A PHE* 5.0 2.1 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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