Contacts of the helix formed by residues 447 - 479 (chain A) in PDB entry 5W97
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 TYR 447 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A LEU* 3.6 17.9 - - + +
434A SER* 2.5 51.5 + - - -
435A GLY* 3.4 9.9 + - - -
436A MET* 3.7 23.1 - - + -
443A TYR* 3.9 9.9 - - + -
444A PRO* 3.1 50.9 + - + +
445A ASP 3.0 0.6 + - - -
446A ALA* 1.3 77.6 - - + +
448A THR* 1.3 61.8 + - - +
449A MET 3.4 2.1 + - - -
450A TRP* 3.6 5.0 + + - -
451A ASN* 2.9 41.9 + - - +
2B ALA* 3.2 22.2 - - + +
3B TYR 6.0 0.7 - - - -
6B GLN* 6.4 0.2 - - + -
10B GLN* 3.9 4.3 + - - -
195B GLN* 4.5 5.2 + - - -
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Residues in contact with THR 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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44A PRO* 3.7 24.2 - - + -
443A TYR* 3.7 17.8 - - - +
445A ASP* 2.5 24.8 + - - -
446A ALA 3.3 1.4 - - - -
447A TYR* 1.3 75.1 - - - +
449A MET* 1.3 67.2 + - - +
451A ASN* 3.2 2.3 + - - +
452A THR* 2.8 30.9 + - - +
111D PHE* 3.6 20.8 - - + -
39K GLU* 3.7 22.4 - - + +
40K TRP 4.2 7.9 - - - +
42K PRO* 4.6 4.3 - - - -
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Residues in contact with MET 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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446A ALA 4.6 3.0 + - - +
447A TYR 3.4 0.6 - - - -
448A THR* 1.3 79.2 - - - +
450A TRP* 1.3 80.1 - - + +
452A THR* 3.1 5.5 + - - -
453A ILE* 3.0 36.9 + - + +
5B MET* 3.3 55.0 - - + +
40K TRP* 3.5 36.2 + - + +
41K ASN 3.8 20.2 - - - +
42K PRO* 3.8 4.6 - - + +
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Residues in contact with TRP 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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427A PRO* 4.1 25.4 - - + +
430A PHE* 3.7 22.8 - + + +
431A LEU* 3.6 35.0 - - + -
434A SER* 5.6 1.3 - - - -
446A ALA 5.8 1.3 - - - -
447A TYR* 3.6 5.2 + + - -
448A THR 3.3 0.2 - - - -
449A MET* 1.3 85.0 - - + +
451A ASN* 1.3 64.9 + - - +
453A ILE* 3.4 26.2 + - + +
454A SER* 3.0 25.3 + - - -
608A TGL 4.2 34.5 - - + -
5B MET* 3.9 29.5 - - + +
6B GLN 2.9 25.1 + - - -
7B LEU* 3.6 22.7 - - + -
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Residues in contact with ASN 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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38A ARG* 3.0 24.6 + - - +
41A LEU* 3.4 19.8 - - - +
371A TYR* 5.3 0.7 - - - -
431A LEU* 3.5 17.6 - - - +
436A MET* 3.4 32.6 - - - +
443A TYR* 3.7 27.4 - - - +
447A TYR* 2.9 26.5 + - - +
448A THR 3.2 2.5 + - - +
450A TRP* 1.3 75.7 - - - +
452A THR* 1.3 58.5 + - - +
454A SER 3.3 0.2 + - - -
455A SER* 2.9 33.4 + - - -
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Residues in contact with THR 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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42A GLY 3.5 24.0 + - - +
43A GLN* 4.9 1.4 - - - +
44A PRO* 5.2 0.2 - - - +
443A TYR* 5.0 0.5 + - - -
448A THR* 2.8 35.8 + - - +
449A MET* 3.4 5.6 - - - -
451A ASN* 1.3 75.0 - - - +
453A ILE* 1.3 66.0 + - - +
455A SER* 3.5 2.4 + - - -
456A MET* 3.2 44.7 + - + +
38K ILE* 4.2 13.2 - - + -
39K GLU 4.3 4.0 + - - -
40K TRP* 3.8 19.5 - - + -
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Residues in contact with ILE 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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423A MET* 3.8 30.2 - - + +
427A PRO* 4.1 11.2 - - + -
449A MET* 3.0 27.9 + - + +
450A TRP* 3.8 34.5 - - + +
452A THR* 1.3 74.6 - - - +
454A SER* 1.3 63.0 + - - +
456A MET* 3.0 11.7 + - - +
457A GLY* 3.0 20.1 + - - -
608A TGL 5.8 4.5 - - + -
40K TRP* 3.8 19.7 - - + -
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Residues in contact with SER 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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38A ARG* 3.4 24.1 + - - -
423A MET 3.7 11.9 - - - -
424A THR* 2.6 31.1 + - - +
427A PRO* 4.8 3.8 - - - -
428A GLN* 3.4 14.0 + - - -
431A LEU* 5.5 0.7 - - - -
450A TRP 3.0 18.5 + - - -
451A ASN* 3.6 5.6 - - - -
452A THR 3.3 0.2 - - - -
453A ILE* 1.3 77.1 - - - +
455A SER* 1.3 61.4 + - - +
457A GLY* 3.2 10.2 + - - -
458A SER 3.2 9.7 + - - -
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Residues in contact with SER 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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38A ARG* 2.5 52.6 + - - +
42A GLY* 3.2 24.3 + - - -
451A ASN 2.9 11.2 + - - -
452A THR 4.0 3.1 - - - -
454A SER* 1.3 78.1 - - - +
456A MET* 1.3 59.8 + - - +
458A SER* 2.6 23.0 + - - -
459A PHE* 3.5 10.6 + - - -
96D LEU* 5.2 1.1 - - - -
99D GLU* 6.1 0.4 - - - -
104D TYR* 5.1 1.1 - - - -
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Residues in contact with MET 456 (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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423A MET* 4.5 5.2 - - - -
452A THR* 3.2 27.1 + - + +
453A ILE* 3.0 11.9 + - - +
455A SER* 1.3 75.9 - - - +
457A GLY* 1.3 63.0 + - - +
459A PHE* 3.1 15.4 + - - +
460A ILE* 3.5 13.5 + - - +
96D LEU* 3.7 34.6 - - + +
29K TRP* 4.2 16.2 - - + -
32K MET* 3.7 30.7 - - + -
38K ILE* 3.8 17.7 - - + -
40K TRP* 3.6 31.0 - - + -
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Residues in contact with GLY 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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420A GLY 3.2 14.2 - - - +
423A MET* 3.9 22.9 - - - -
424A THR* 2.9 18.2 + - - -
453A ILE 3.0 11.4 + - - -
454A SER 3.2 2.9 + - - -
456A MET* 1.3 74.4 - - - +
458A SER* 1.3 63.4 + - - +
460A ILE* 3.3 7.1 + - - +
461A SER* 3.3 15.6 + - - -
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Residues in contact with SER 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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35A LEU* 3.4 27.4 - - - +
38A ARG* 3.7 19.5 - - - +
424A THR* 3.0 9.4 + - - -
454A SER 3.2 5.2 + - - -
455A SER 2.6 20.1 + - - -
457A GLY* 1.3 77.3 - - - +
459A PHE* 1.3 60.5 + - - +
461A SER* 3.5 7.2 + - - -
462A LEU 3.1 20.8 + - - -
601A HEA 4.0 24.4 + - - -
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Residues in contact with PHE 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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35A LEU* 4.3 9.0 - - + -
38A ARG 6.2 0.7 - - - -
39A ALA* 5.7 2.9 - - - -
455A SER* 3.8 8.7 - - - -
456A MET 3.1 9.3 + - - +
458A SER* 1.3 90.8 + - - +
460A ILE* 1.3 63.5 + - - +
462A LEU* 3.2 12.4 + - + +
463A THR* 3.2 24.6 + - - -
92D THR* 3.4 16.0 - - + +
95D LEU* 3.8 39.7 - - + -
96D LEU* 3.8 16.6 - - + -
99D GLU* 3.7 34.5 - - + -
34M LEU* 5.9 0.2 - - + -
101M DMU 3.3 50.0 - - + -
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Residues in contact with ILE 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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416A ILE* 3.5 34.3 - - + +
419A VAL* 4.2 9.0 - - + -
420A GLY* 3.6 9.4 - - - +
423A MET* 3.8 33.7 - - + -
456A MET 3.8 6.7 - - - +
457A GLY* 3.3 9.1 + - - +
459A PHE* 1.3 76.3 - - - +
461A SER* 1.3 61.5 + - - +
463A THR* 3.0 15.2 + - - -
464A ALA 3.3 8.1 + - - -
89D ILE* 4.2 22.7 - - + -
92D THR* 3.8 24.7 - - + +
29K TRP* 3.9 18.6 - - + -
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Residues in contact with SER 461 (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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417A MET* 4.4 8.1 + - - +
420A GLY* 3.2 29.6 + - - -
421A VAL* 3.3 11.4 + - - +
424A THR* 4.5 1.4 + - - -
457A GLY 3.3 4.1 + - - -
458A SER* 3.7 11.0 - - - -
460A ILE* 1.3 80.0 - - - +
462A LEU* 1.3 60.7 + - - +
464A ALA* 3.3 11.2 + - - +
465A VAL* 3.1 25.3 + - - +
601A HEA 4.2 25.9 - - - +
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Residues in contact with LEU 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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31A THR* 4.9 7.0 - - + -
35A LEU* 3.8 22.2 - - + -
458A SER 3.1 14.4 + - - +
459A PHE* 3.3 15.9 - - + +
460A ILE 3.2 0.6 - - - -
461A SER* 1.3 75.4 - - - +
463A THR* 1.3 64.0 + - - +
465A VAL* 3.0 9.4 + - + +
466A MET* 3.0 38.2 + - + +
95D LEU* 4.6 10.1 - - + -
33L PHE* 3.7 29.2 - - + -
26M PHE* 4.6 3.4 - - + -
27M LEU* 4.4 17.5 - - + -
101M DMU 4.4 23.3 - - + -
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Residues in contact with THR 463 (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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416A ILE* 4.7 6.1 - - + -
459A PHE 3.2 7.8 + - - -
460A ILE 3.0 10.8 + - - -
462A LEU* 1.3 77.7 - - - +
464A ALA* 1.3 58.4 + - - +
466A MET* 3.4 9.9 + - - +
467A LEU* 2.9 28.5 + - - +
88D PHE* 3.7 44.2 - - + +
91D PHE* 4.3 8.6 - - + -
92D THR* 2.8 23.1 + - - +
95D LEU* 4.4 8.7 - - - +
23M PHE* 4.3 9.0 - - + -
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Residues in contact with ALA 464 (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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413A HIS* 3.0 30.1 + - + +
416A ILE* 4.0 11.7 - - + +
417A MET* 3.9 37.9 - - - +
460A ILE 3.3 4.2 + - - -
461A SER 3.3 10.3 + - - +
463A THR* 1.3 74.7 - - - +
465A VAL* 1.3 64.7 + - - +
467A LEU* 3.3 4.2 + - - +
468A MET 2.9 19.1 + - - -
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Residues in contact with VAL 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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28A MET* 3.8 36.6 - - + -
31A THR* 4.4 12.6 - - + -
413A HIS* 5.0 0.4 - - - -
417A MET* 5.2 3.6 - - - -
461A SER 3.1 14.6 + - - +
462A LEU* 3.0 11.4 + - + +
464A ALA* 1.3 76.4 - - + +
466A MET* 1.3 64.6 + - - +
468A MET* 3.2 18.7 + - + +
469A VAL* 3.3 13.0 + - - +
601A HEA 3.7 42.4 - - + -
26M PHE* 4.3 8.1 - - + -
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Residues in contact with MET 466 (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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462A LEU* 3.0 27.0 + - + +
463A THR* 3.6 11.0 - - - +
465A VAL* 1.3 77.5 - - - +
467A LEU* 1.3 61.2 + - - +
469A VAL* 3.2 14.6 + - - +
470A PHE* 3.3 9.7 + - - +
91D PHE* 4.4 5.8 - - + -
95D LEU* 5.1 1.3 - - + -
22M THR* 3.6 7.2 - - + +
23M PHE* 3.0 60.8 - - + -
26M PHE* 3.4 50.7 - - + -
27M LEU* 3.9 25.1 - - + -
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Residues in contact with LEU 467 (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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409A TRP* 3.9 20.6 - - + -
412A ILE* 3.8 29.4 - - + -
413A HIS* 4.3 13.7 - - + +
416A ILE* 3.8 15.7 - - + -
463A THR 2.9 17.7 + - - +
464A ALA* 3.6 6.3 - - - +
466A MET* 1.3 75.1 - - - +
468A MET* 1.3 58.1 + - - +
470A PHE* 3.3 6.4 + - + +
471A ILE* 2.9 40.9 + - + +
88D PHE* 4.1 13.7 - - + -
19M LEU* 3.4 30.1 - - + -
23M PHE* 4.0 4.9 - - + -
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Residues in contact with MET 468 (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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28A MET* 4.1 21.5 - - + -
390A MET* 3.7 34.1 - - - +
393A PHE* 5.6 5.6 - - + -
413A HIS* 3.7 21.3 - - + +
464A ALA 2.9 13.4 + - - +
465A VAL* 3.4 14.6 - - + +
466A MET 3.2 0.2 - - - -
467A LEU* 1.3 73.1 - - - +
469A VAL* 1.3 69.3 + - + +
471A ILE* 3.1 10.0 + - + +
472A ILE* 3.0 35.5 + - + +
601A HEA 3.6 40.2 - - + -
29L PHE* 5.7 1.3 - - + -
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Residues in contact with VAL 469 (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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28A MET* 4.4 7.0 - - + -
465A VAL 3.5 14.1 - - - +
466A MET 3.2 7.8 + - - +
468A MET* 1.3 81.1 - - + +
470A PHE* 1.3 62.7 - - - +
472A ILE* 3.3 8.1 + - - -
473A TRP* 3.0 19.3 + - + +
25L MET* 3.5 16.2 - - + +
26L THR* 5.7 1.3 - - - +
29L PHE* 3.6 42.4 - - + -
22M THR* 3.8 18.2 - - + +
26M PHE* 3.8 22.7 - - + -
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Residues in contact with PHE 470 (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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409A TRP* 3.6 32.8 - + - -
466A MET 3.3 8.2 + - - +
467A LEU* 3.3 13.6 + - + +
468A MET 3.3 0.6 - - - -
469A VAL* 1.3 79.9 - - - +
471A ILE* 1.3 62.1 + - + +
473A TRP* 3.2 31.2 + + - +
474A GLU* 2.8 35.6 + - + +
15M GLN* 3.5 45.8 - - + -
18M GLY 3.9 1.8 - - - -
19M LEU* 3.4 45.1 - - + -
22M THR* 4.1 14.6 - - - +
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Residues in contact with ILE 471 (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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405A LEU* 4.0 27.7 - - + -
406A ASN* 4.9 3.4 - - + +
409A TRP* 3.3 48.2 - - + +
410A ALA* 3.9 10.1 - - + +
413A HIS* 3.7 22.7 - - + +
467A LEU* 2.9 25.5 + - + +
468A MET* 3.1 10.3 + - + +
470A PHE* 1.3 83.7 - - + +
472A ILE* 1.3 64.1 + - + +
474A GLU* 3.3 7.2 + - - +
475A ALA* 3.2 22.5 + - - +
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Residues in contact with ILE 472 (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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393A PHE* 3.8 34.3 - - + -
397A PHE* 4.7 6.1 - - + -
405A LEU* 4.8 4.5 - - + -
468A MET* 3.0 26.3 + - + +
469A VAL* 3.7 8.3 - - - +
470A PHE 3.3 0.2 - - - -
471A ILE* 1.3 79.6 - - + +
473A TRP* 1.3 64.1 + - - +
475A ALA* 3.4 5.5 + - - +
476A PHE* 3.4 37.7 + - + -
601A HEA 4.4 12.8 - - + -
25L MET* 3.9 4.5 - - + -
29L PHE* 5.0 4.9 - - + -
101L TGL 3.6 38.6 - - + -
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Residues in contact with TRP 473 (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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469A VAL* 3.0 14.6 + - + +
470A PHE* 3.4 39.7 - + - +
472A ILE* 1.3 75.9 - - - +
474A GLU* 1.3 66.3 + - + +
476A PHE* 3.1 5.5 + - - +
477A ALA* 2.7 47.0 + - + +
18L LYS* 2.9 29.4 + - + +
19L TRP* 3.9 25.6 - + - -
21L LEU* 4.0 7.4 - - + +
22L LEU* 3.5 39.4 - - + +
25L MET* 3.6 23.8 - - + +
10M THR* 3.9 24.9 - - + -
14M GLU 3.8 18.2 - - - -
15M GLN* 4.3 0.7 - - - -
18M GLY* 4.0 9.6 - - - -
22M THR* 5.6 0.2 - - - +
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Residues in contact with GLU 474 (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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406A ASN* 3.8 19.9 + - - +
409A TRP* 5.0 3.8 - - + -
470A PHE* 2.8 29.4 + - + +
471A ILE* 3.7 7.6 - - - +
472A ILE 3.3 0.2 - - - -
473A TRP* 1.3 84.7 - - + +
475A ALA* 1.3 63.3 + - - +
477A ALA* 3.3 3.2 + - - +
478A SER* 2.9 41.1 + - - +
480A ARG* 3.0 34.5 + - - -
606A PGV 6.1 1.0 - - - +
10M THR* 4.4 6.5 - - - +
15M GLN* 4.3 32.0 + - + +
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Residues in contact with ALA 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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397A PHE* 3.9 24.7 - - + -
403A TYR* 4.3 10.0 - - + +
404A THR 3.5 23.2 - - - +
405A LEU* 4.0 9.6 - - + -
471A ILE 3.2 12.0 + - - +
472A ILE 3.6 9.2 - - - +
473A TRP 3.2 0.2 - - - -
474A GLU* 1.3 80.9 + - - +
476A PHE* 1.3 58.9 + - - +
478A SER* 4.0 0.7 - - - -
479A LYS* 3.0 26.9 + - - -
480A ARG* 3.9 2.7 + - - +
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Residues in contact with PHE 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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397A PHE* 4.1 22.2 - + - -
401A SER* 4.3 7.2 - - - -
403A TYR* 3.8 30.3 - + - -
472A ILE* 3.4 37.6 + - + +
473A TRP* 3.1 5.2 + - - +
475A ALA* 1.3 79.9 - - - +
477A ALA* 1.3 61.6 + - - +
479A LYS* 3.5 24.1 - - - +
8L GLY* 5.7 0.4 - - - -
11L ILE* 4.3 16.8 - - + -
13L PHE* 4.0 25.6 - + - -
15L VAL* 3.9 21.2 - - + +
18L LYS* 5.8 0.3 - - - -
21L LEU* 3.5 23.2 - - + +
25L MET* 5.4 2.9 - - - -
101L TGL 4.3 21.8 - - + -
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Residues in contact with ALA 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 2.7 37.3 + - + +
474A GLU* 3.7 4.3 - - - +
476A PHE* 1.3 78.6 - - - +
478A SER* 1.3 51.7 + - - +
479A LYS* 4.6 1.1 - - - +
18L LYS* 3.3 36.6 - - + +
21L LEU* 4.4 1.3 - - - +
8M THR* 2.6 30.0 + - - +
10M THR* 3.6 13.5 - - - +
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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
----------------------------------------------------------
474A GLU* 2.9 25.7 + - - -
475A ALA 4.1 0.2 - - - -
477A ALA* 1.3 76.5 - - - +
479A LYS* 1.3 71.7 + - - +
480A ARG* 3.4 25.9 + - - -
6M ALA* 3.3 12.6 - - - +
7M LYS 3.2 14.0 + - - -
8M THR 3.2 13.1 + - - -
10M THR* 2.6 28.6 + - - -
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Residues in contact with LYS 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 3.6 37.4 + - + +
475A ALA 3.0 10.8 + - - -
476A PHE 3.5 18.2 - - - +
477A ALA 5.2 0.7 - - - -
478A SER* 1.3 77.5 - - - +
480A ARG* 1.3 62.3 + - - +
481A GLU* 3.6 4.2 + - - +
15L VAL* 3.0 42.8 + - - +
16L GLU* 4.1 20.2 + - - +
5M PRO 4.2 0.7 - - - +
7M LYS* 3.0 44.4 + - + +
8M THR* 4.2 17.3 - - + +
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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