Contacts of the helix formed by residues 444 - 478 (chain A) in PDB entry 5LLU
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 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ILE* 3.6 27.3 - - + +
397A ASN* 3.0 35.1 + - - +
435A LEU* 5.0 1.3 - - + -
441A PRO* 3.4 31.1 - - - +
442A THR 3.1 1.6 - - - -
443A ASP* 1.3 77.9 - - - +
445A ILE* 1.4 62.5 + - - +
446A THR 3.2 2.7 + - - -
447A LEU* 3.5 34.8 + - + +
448A ILE* 4.1 10.6 - - - +
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Residues in contact with ILE 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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428A LEU* 3.4 49.8 - - + +
429A VAL* 5.6 0.2 - - - -
431A MET* 3.8 33.7 - - + -
432A VAL* 3.8 27.4 - - + +
435A LEU* 3.9 11.7 - - + -
442A THR 3.4 19.1 - - - +
443A ASP 3.2 0.8 - - - -
444A ASP* 1.4 76.6 - - - +
446A THR* 1.4 57.5 + - - +
448A ILE* 3.1 7.1 + - + +
449A ILE* 3.1 37.7 + - + +
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Residues in contact with THR 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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443A ASP* 2.7 29.6 + - + +
444A ASP 4.2 0.9 - - - -
445A ILE* 1.4 78.0 - - + +
447A LEU* 1.3 67.3 + - - +
449A ILE* 3.6 30.1 - - + +
450A ALA* 4.5 2.3 + - - +
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Residues in contact with LEU 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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294A LEU* 3.4 28.7 - - + +
392A PHE* 6.3 0.7 - - + -
393A ILE* 5.7 2.0 - - + -
444A ASP* 3.5 38.4 - - + +
445A ILE 3.3 0.8 + - - -
446A THR* 1.3 80.9 + - - +
448A ILE* 1.3 67.0 + - + +
450A ALA* 4.1 8.1 + - - +
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Residues in contact with ILE 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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294A LEU* 3.9 7.0 - - + -
297A TYR* 3.4 42.6 - - + +
385A TYR* 3.5 17.9 - - - +
389A ALA* 4.7 4.9 - - + +
392A PHE* 3.8 20.9 - - + -
393A ILE* 3.6 31.4 - - + -
428A LEU* 5.4 3.8 - - + -
431A MET* 4.7 12.1 - - + -
444A ASP 4.1 5.6 - - - +
445A ILE* 3.1 10.4 + - - +
447A LEU* 1.3 82.1 - - + +
449A ILE* 1.4 64.9 + - - +
450A ALA 3.0 4.6 + - - -
451A VAL* 3.2 9.0 + - - +
452A ASP* 3.1 20.4 + - + -
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Residues in contact with ILE 449 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428A LEU* 3.8 37.9 - - + +
445A ILE* 3.1 26.0 + - + +
446A THR* 3.6 27.1 - - + +
447A LEU 3.5 0.4 - - - -
448A ILE* 1.4 73.6 - - - +
450A ALA* 1.4 63.0 + - - +
452A ASP* 3.4 19.2 - - - +
453A TRP* 4.4 3.1 + - - +
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Residues in contact with ALA 450 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LEU* 5.2 6.3 - - + -
446A THR 4.5 2.5 + - - +
447A LEU 4.1 11.6 + - - +
448A ILE 3.0 1.6 + - - -
449A ILE* 1.4 82.1 - - - +
451A VAL* 1.3 57.0 + - + +
453A TRP* 3.1 25.1 + - - -
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Residues in contact with VAL 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A LEU* 3.8 33.6 - - + +
297A TYR* 3.9 19.1 - - + -
298A MET* 3.7 35.4 - - + -
447A LEU 5.2 0.2 + - - -
448A ILE 3.2 6.5 + - - +
450A ALA* 1.3 74.9 - - + +
452A ASP* 1.4 66.5 + - - +
453A TRP* 3.3 7.8 + - - +
454A LEU* 3.5 16.0 + - + +
455A LEU* 3.7 14.8 + - + +
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Residues in contact with ASP 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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385A TYR* 2.7 27.1 + - - +
425A GLN* 3.7 17.8 - - - +
428A LEU* 3.4 31.2 + - - +
448A ILE* 3.1 12.7 + - + +
449A ILE* 3.4 19.5 - - - +
450A ALA 3.4 0.8 - - - -
451A VAL* 1.4 76.3 - - - +
453A TRP* 1.4 56.3 + - - +
455A LEU* 3.2 10.3 + - - +
456A ASP* 2.8 32.9 + - - +
459A ARG* 2.8 17.6 + - - +
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Residues in contact with TRP 453 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 6.0 2.0 - - - -
280A LYS* 3.9 63.0 - - + +
281A ILE* 3.5 31.9 - - + -
283A GLU 5.7 2.5 + - - -
425A GLN* 5.7 5.6 - - + +
449A ILE 4.4 2.9 + - - +
450A ALA 3.1 28.0 + - - -
451A VAL* 4.3 5.3 - - - +
452A ASP* 1.4 82.5 + - - +
454A LEU* 1.4 104.0 + - + +
456A ASP* 3.4 6.4 + - - +
457A ARG* 3.2 39.6 + - + +
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Residues in contact with LEU 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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281A ILE* 5.5 2.2 - - + -
298A MET* 4.5 22.4 - - + -
302A ILE* 4.7 3.6 - - + -
340A LEU* 6.2 1.1 - - + -
451A VAL* 3.5 11.1 + - + +
452A ASP 3.4 0.4 - - - -
453A TRP* 1.4 115.3 - - + +
455A LEU* 1.4 63.6 + - + +
457A ARG* 3.4 17.6 + - + +
458A PHE* 3.1 48.6 + - + -
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Residues in contact with LEU 455 (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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297A TYR* 3.7 39.0 - - + +
298A MET* 3.6 36.1 - - + +
301A VAL* 3.8 18.2 - - + -
302A ILE* 3.8 18.4 - - + -
305A LEU* 4.5 1.8 - - + +
385A TYR* 4.1 13.2 - - + -
451A VAL* 3.7 22.4 + - + +
452A ASP* 3.2 7.7 + - - +
454A LEU* 1.4 73.2 - - - +
456A ASP* 1.3 54.8 + - - +
458A PHE* 3.3 6.2 + - - +
459A ARG* 2.8 44.8 + - - +
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Residues in contact with ASP 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A SER* 2.7 23.7 + - - +
424A PRO* 3.4 8.3 - - - +
425A GLN* 3.0 28.5 + - + +
452A ASP* 2.8 18.7 + - - +
453A TRP* 3.4 8.5 - - - +
455A LEU* 1.3 76.7 - - - +
457A ARG* 1.4 52.4 + - - +
459A ARG* 3.1 22.2 + - - +
460A THR* 2.7 38.6 + - - -
602A ASP* 2.8 34.3 + - - +
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Residues in contact with ARG 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A LEU* 3.4 24.2 + - - +
277A ILE* 4.2 8.5 - - - +
280A LYS* 3.4 35.4 - - - +
339A ALA 4.5 0.9 - - - -
340A LEU* 3.0 43.1 + - + +
341A GLY 2.8 27.4 + - - -
342A THR 4.1 3.4 + - - -
343A SER* 3.2 28.2 + - - -
424A PRO* 5.8 0.8 - - - +
453A TRP* 3.2 29.6 + - + +
454A LEU* 3.6 20.2 - - + +
455A LEU 3.3 0.4 - - - -
456A ASP* 1.4 74.9 - - - +
458A PHE* 1.3 62.0 + - + +
460A THR* 3.8 1.9 + - - -
461A MET* 3.3 26.0 + - - +
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Residues in contact with PHE 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A ILE* 3.7 35.7 - - + -
305A LEU* 3.8 19.7 - - + -
340A LEU* 3.8 25.1 - - + -
454A LEU* 3.1 49.5 + - + -
455A LEU* 3.3 4.4 + - - +
457A ARG* 1.3 75.3 - - - +
459A ARG* 1.4 62.9 + - - +
460A THR 3.2 0.2 - - - -
461A MET* 3.2 24.1 + - - +
462A VAL* 3.2 17.0 + - - +
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Residues in contact with ARG 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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301A VAL* 5.7 0.7 - - + -
305A LEU* 3.7 12.9 - - + +
381A GLY* 3.4 23.2 - - - +
382A THR* 3.9 11.9 - - - +
385A TYR* 3.3 42.7 - - + -
425A GLN 5.1 0.4 - - - -
426A ALA 5.1 0.2 - - - +
427A GLY* 3.4 17.2 - - - +
452A ASP* 2.8 46.9 + - - -
455A LEU 2.8 15.1 + - - +
456A ASP* 3.1 37.1 + - - +
458A PHE* 1.4 71.9 - - - +
460A THR* 1.4 57.5 + - - +
462A VAL 3.4 0.7 + - - -
463A ASN* 3.0 34.1 + - - +
602A ASP* 3.0 29.7 + - - +
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Residues in contact with THR 460 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ALA* 3.6 32.3 - - + +
343A SER 3.2 5.1 + - - -
344A SER 3.6 7.4 - - - +
345A SER* 3.5 32.3 - - - +
456A ASP 2.7 21.8 + - - -
457A ARG 3.9 1.1 - - - -
459A ARG* 1.4 72.6 - - - +
461A MET* 1.4 59.3 + - - +
463A ASN* 3.2 9.5 + - - +
464A VAL* 2.9 34.5 + - - +
602A ASP* 2.8 22.6 + - - +
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Residues in contact with MET 461 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 3.3 56.5 - - + +
337A ILE* 4.3 6.1 - - + +
339A ALA* 4.0 5.6 - - + -
340A LEU* 3.5 40.2 - - + +
457A ARG 3.3 11.4 + - - +
458A PHE* 3.2 20.8 + - - +
460A THR* 1.4 77.3 - - - +
462A VAL* 1.3 57.2 + - + +
464A VAL* 3.7 0.6 + - - -
465A LEU* 3.1 28.0 + - - +
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Residues in contact with VAL 462 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LEU* 3.8 35.0 - - + +
308A HIS* 3.9 28.0 - - + -
309A GLY* 4.5 9.6 - - - +
313A LEU* 4.3 7.2 - - + +
380A ASP* 4.4 4.5 - - + +
381A GLY* 4.0 19.3 - - - +
458A PHE* 3.2 14.2 + - + +
459A ARG 3.8 5.6 - - - +
460A THR 3.3 0.2 - - - -
461A MET* 1.3 76.4 - - + +
463A ASN* 1.4 59.0 + - - +
465A LEU* 3.6 7.6 - - + +
466A GLY* 3.1 25.8 + - - -
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Residues in contact with ASN 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345A SER* 4.6 5.2 - - - -
378A ASN* 3.7 7.2 - - - +
379A MET* 3.3 22.8 - - + +
380A ASP* 4.6 2.5 - - - +
381A GLY 2.8 32.0 + - - +
382A THR* 2.9 28.2 + - - -
459A ARG 3.0 16.3 + - - +
460A THR 3.2 8.3 + - - +
462A VAL* 1.4 76.4 - - - +
464A VAL* 1.4 58.6 + - - +
466A GLY* 3.8 2.1 + - - -
467A ASP* 3.0 28.3 + - - +
602A ASP* 2.8 32.2 + - - +
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Residues in contact with VAL 464 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ILE* 5.4 0.4 - - + -
335A ALA* 4.3 11.9 - - + +
336A LEU* 4.2 13.5 - - + -
339A ALA* 3.9 10.3 - - + -
345A SER* 3.8 23.3 - - - +
348A THR* 3.8 16.8 - - - +
352A THR* 3.8 30.8 - - + +
460A THR 2.9 19.6 + - - +
461A MET 3.9 4.7 - - - +
463A ASN* 1.4 72.1 - - - +
465A LEU* 1.4 58.2 + - - +
467A ASP* 3.0 15.3 + - - +
468A ALA* 2.9 26.3 + - + +
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Residues in contact with LEU 465 (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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309A GLY* 3.3 39.7 - - - +
310A LEU* 6.2 0.4 - - + -
313A LEU* 4.1 9.2 - - + -
329A ILE* 3.8 30.5 - - + -
332A ILE* 3.9 8.3 - - + -
336A LEU* 3.8 24.2 - - + -
461A MET 3.1 19.1 + - - +
462A VAL* 3.6 10.1 - - + +
464A VAL* 1.4 74.7 - - - +
466A GLY* 1.3 55.7 + - - +
468A ALA* 3.7 5.6 - - - +
469A LEU* 2.9 45.5 + - + +
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Residues in contact with GLY 466 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 2.7 33.3 + - - -
313A LEU* 4.4 8.5 - - - +
378A ASN* 3.5 7.9 - - - -
380A ASP* 3.6 23.6 - - - -
462A VAL 3.1 11.7 + - - -
463A ASN 3.8 1.8 + - - -
464A VAL 3.2 0.4 - - - -
465A LEU* 1.3 75.1 - - - +
467A ASP* 1.4 57.1 + - - +
470A GLY 3.0 9.2 + - - -
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Residues in contact with ASP 467 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 5.4 0.2 - - - -
127A TYR* 5.4 1.3 - - - -
345A SER* 5.5 2.4 - - - -
349A LEU* 5.4 1.0 - - - +
352A THR* 5.9 0.2 - - + -
356A LEU* 4.6 0.3 - - - +
370A VAL* 3.7 11.0 - - - +
371A LEU* 4.1 23.0 - - + +
374A GLY* 3.1 41.8 - - - +
375A ALA* 3.3 10.2 + - - +
378A ASN* 3.2 14.9 - - - +
463A ASN 3.0 20.3 - - - +
464A VAL* 3.0 11.9 + - - +
466A GLY* 1.4 74.7 - - - +
468A ALA* 1.4 55.3 + - - +
470A GLY* 3.2 1.8 + - - -
471A ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 468 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.2 20.6 - - + -
332A ILE* 3.7 44.6 - - + -
352A THR* 4.4 6.5 - - + -
356A LEU* 3.6 18.0 - - + +
371A LEU* 4.7 1.2 - - - +
464A VAL 2.9 14.5 + - - +
465A LEU 3.5 3.3 + - - +
467A ASP* 1.4 77.6 - - - +
469A LEU* 1.4 61.0 + - - +
470A GLY 3.3 0.5 + - - -
471A ALA* 3.4 6.8 + - - +
472A GLY 3.5 1.7 + - - -
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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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126A TYR* 3.9 9.0 - - - +
313A LEU* 4.1 28.7 - - + +
314A PRO 4.6 1.1 - - - -
317A TYR* 3.7 34.1 - - + -
325A PRO* 4.3 12.8 - - + +
328A PHE* 3.6 26.9 - - + -
329A ILE* 4.3 15.9 - - + -
332A ILE* 6.0 0.2 - - + -
465A LEU* 2.9 41.1 + - + +
466A GLY* 5.1 0.2 - - - -
468A ALA* 1.4 71.7 - - + +
470A GLY* 1.3 58.2 - - - +
471A ALA 3.5 0.2 - - - -
472A GLY* 3.5 1.9 + - - -
473A ILE* 3.0 37.6 + - + +
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Residues in contact with GLY 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.4 24.0 + - - -
370A VAL* 4.0 7.4 - - - -
466A GLY 3.0 21.9 + - - -
467A ASP 3.4 2.5 - - - -
468A ALA 3.1 0.4 - - - -
469A LEU* 1.3 74.8 - - - +
471A ALA* 1.4 58.6 + - - +
473A ILE* 3.1 3.3 + - - +
474A VAL* 2.9 35.4 + - - +
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Residues in contact with ALA 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU* 3.9 18.6 - - + -
362A VAL* 4.0 7.6 - - + -
366A ILE* 3.2 26.3 - - + +
367A THR* 4.2 5.4 - - + -
370A VAL* 3.5 17.8 - - + +
371A LEU* 5.3 0.9 - - + -
467A ASP 2.9 11.8 + - - +
468A ALA 3.4 9.4 + - - +
470A GLY* 1.4 73.3 - - - +
472A GLY* 1.3 52.9 + - - +
474A VAL 3.3 0.7 + - - -
475A GLU* 2.8 32.1 + - - +
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Residues in contact with GLY 472 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A TYR* 4.2 6.7 - - - -
321A THR* 3.6 9.9 - - - +
323A LYS* 5.2 1.4 + - - -
328A PHE* 4.0 21.0 - - - -
362A VAL* 4.4 2.4 - - - +
468A ALA 3.5 7.5 + - - -
469A LEU 3.5 4.0 + - - -
470A GLY 3.3 0.4 - - - -
471A ALA* 1.3 77.1 - - - +
473A ILE* 1.4 59.6 + - - +
475A GLU* 3.9 12.2 - - - +
476A HIS* 3.4 24.1 + - - +
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Residues in contact with ILE 473 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.7 36.8 - - + +
313A LEU 5.2 1.1 - - - +
316A ILE* 3.8 20.0 - - + -
317A TYR* 3.8 32.3 - - + +
320A ILE* 3.7 25.5 - - + +
321A THR* 4.2 8.1 - - + -
469A LEU* 3.0 25.0 + - + +
470A GLY* 3.1 3.8 + - - +
472A GLY* 1.4 74.6 - - - +
474A VAL* 1.4 65.9 + - + +
476A HIS* 3.5 4.3 + - - +
477A LEU* 3.2 36.8 + - + +
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Residues in contact with VAL 474 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.8 32.8 - - + +
122A ARG* 3.9 24.7 - - + +
123A ALA* 4.2 22.7 - - - +
126A TYR* 4.7 7.4 - - + -
127A TYR* 6.4 0.2 - - + -
366A ILE* 5.2 0.9 - - + -
370A VAL* 4.1 18.6 - - + -
470A GLY 2.9 25.1 + - - +
471A ALA 4.1 2.2 - - - +
473A ILE* 1.4 74.9 - - + +
475A GLU* 1.4 54.0 + - - +
477A LEU* 3.3 8.3 + - + +
478A SER* 2.8 33.5 + - - -
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Residues in contact with GLU 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 4.8 10.6 + - - -
361A GLY 3.1 23.8 - - - +
362A VAL* 3.9 10.9 - - - +
363A ASP* 3.1 19.2 + - - +
366A ILE* 3.6 27.9 - - + +
471A ALA 2.8 23.2 + - - +
472A GLY* 3.9 8.9 - - - +
474A VAL* 1.4 70.7 - - - +
476A HIS* 1.3 63.4 + - - +
478A SER 3.3 21.1 + - - +
479A ARG* 3.6 2.8 + - - -
482A LEU* 4.1 15.2 - - + +
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Residues in contact with HIS 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A ILE* 3.6 28.5 + - + +
321A THR* 3.6 27.5 + - + -
323A LYS* 3.4 31.9 - - - +
472A GLY 3.4 15.9 + - - +
473A ILE 3.8 3.1 - - - +
474A VAL 3.4 0.2 - - - -
475A GLU* 1.3 78.5 + - - +
477A LEU* 1.4 55.7 + - - +
479A ARG* 2.8 54.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 3.4 48.6 + - + +
126A TYR* 6.5 0.4 - - + -
320A ILE* 3.9 22.9 - - + -
473A ILE* 3.2 40.6 + - + +
474A VAL* 3.7 9.0 - - + +
476A HIS* 1.4 77.7 - - - +
478A SER* 1.4 55.9 + - - +
479A ARG* 3.2 32.4 + - - +
481A GLU* 4.7 0.9 - - - +
----------------------------------------------------------
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Residues in contact with SER 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.3 33.4 - - - +
122A ARG* 2.8 25.6 + - - -
366A ILE* 5.2 2.0 - - - -
474A VAL 2.8 20.1 + - - -
475A GLU* 3.3 6.7 + - - -
477A LEU* 1.4 69.1 - - - +
479A ARG* 1.3 61.0 + - - +
480A LYS 3.7 1.3 - - - -
481A GLU* 3.1 19.5 + - - -
482A LEU* 3.4 27.6 + - - +
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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