Contacts of the helix formed by residues 448 - 480 (chain E) in PDB entry 6N0M
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 ARG 448 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375E TYR* 4.8 15.8 - - - +
377E THR* 3.1 35.3 + - - +
379E ALA* 2.7 40.4 + - - +
380E MET* 4.9 4.2 + - - +
446E HIS 4.0 0.8 + - - +
447E PHE* 1.3 77.5 - - - +
449E HIS* 1.3 65.2 + - - +
450E SER* 3.8 23.5 + - - +
451E GLU* 2.7 37.6 + - - +
452E LYS* 3.4 7.0 + - - +
900E K94 4.7 1.0 + - - -
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Residues in contact with HIS 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 6.3 0.2 - - - -
237E GLN 3.8 13.0 - - - -
238E SER* 3.6 25.4 - - - -
239E SER* 3.7 19.4 + - - -
440E TYR* 3.5 22.8 + + - +
441E ASN* 5.6 3.9 + - - -
447E PHE 4.6 6.1 - - - -
448E ARG* 1.3 71.7 - - - +
450E SER* 1.3 67.0 + - - +
452E LYS* 3.0 22.2 + - + +
453E VAL* 3.0 16.1 + - - +
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Residues in contact with SER 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU* 4.6 23.5 - - - +
86E HIS* 2.8 35.0 + - - -
375E TYR* 6.1 1.3 - - - -
448E ARG* 3.8 29.5 + - - +
449E HIS* 1.3 76.8 - - - +
451E GLU* 1.3 59.4 + - - +
453E VAL* 3.4 6.8 + - - +
454E HIS* 2.8 13.9 + - - +
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Residues in contact with GLU 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E THR* 3.9 1.7 + - - -
378E ILE* 3.7 2.4 - - - -
379E ALA* 2.7 38.8 + - - +
444E TRP* 4.9 0.4 - - + -
447E PHE* 3.3 14.5 - - + +
448E ARG* 2.7 52.0 + - + +
449E HIS 3.1 1.2 - - - -
450E SER* 1.3 76.9 + - - +
452E LYS* 1.3 60.1 + - - +
454E HIS* 3.2 9.8 - - + +
455E VAL* 2.9 31.8 + - - +
900E K94 2.9 43.3 + - + +
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Residues in contact with LYS 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424E TYR* 4.9 0.8 - - - +
440E TYR* 3.2 64.6 - - + +
441E ASN* 4.1 4.6 + - - +
443E PHE* 2.4 50.6 + - + -
444E TRP* 3.1 23.3 + - + +
445E ARG 5.2 1.0 + - - -
447E PHE* 4.8 4.0 + - + +
448E ARG 3.4 13.2 + - - +
449E HIS* 3.0 14.6 + - + +
451E GLU* 1.3 73.8 - - - +
453E VAL* 1.3 60.3 + - - +
454E HIS 3.1 0.2 - - - -
455E VAL* 3.3 8.4 + - - +
456E ASN* 2.9 36.0 + - - -
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Residues in contact with VAL 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E VAL* 3.9 31.9 - - + +
85E LEU* 4.2 9.6 - - + -
86E HIS* 3.8 19.7 - - + +
210E PHE* 4.1 17.4 - - + -
214E CYS* 4.1 8.5 - - - -
238E SER* 3.8 21.3 - - - +
440E TYR* 5.3 1.8 - - + +
449E HIS 3.0 14.0 + - - +
450E SER* 3.6 8.3 - - - +
452E LYS* 1.3 72.6 - - - +
454E HIS* 1.3 69.9 + - - +
456E ASN* 3.2 9.4 + - - +
457E LEU* 3.2 21.0 + - + +
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Residues in contact with HIS 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E HIS* 3.8 22.4 + + + -
370E ALA 4.5 7.4 - - - -
373E LEU* 2.9 52.3 + - + +
374E THR* 4.2 1.4 - - - -
375E TYR* 5.3 4.5 - + - -
390E ARG* 4.3 3.6 - - - -
450E SER 2.8 14.9 + - - +
451E GLU* 3.2 15.3 - - + +
453E VAL* 1.3 75.9 - - - +
455E VAL* 1.3 64.1 + - - +
457E LEU* 2.8 21.8 + - + +
458E LEU* 2.9 17.3 + - + +
900E K94 3.5 47.3 + - + +
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Residues in contact with VAL 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393E ILE* 4.0 9.2 - - + +
421E LEU* 4.2 10.5 - - + -
424E TYR* 4.5 12.1 - - + -
425E ILE* 4.1 28.3 - - + -
443E PHE* 4.8 0.9 - - + -
444E TRP* 3.2 24.9 - - + -
451E GLU 2.9 11.4 + - - +
452E LYS* 3.4 11.0 - - - +
454E HIS* 1.3 73.3 - - - +
456E ASN* 1.3 60.8 + - - +
457E LEU 3.1 0.2 + - - -
458E LEU* 3.3 9.0 + - - +
459E LEU* 2.8 34.4 + - + +
900E K94 3.2 27.8 - - - -
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Residues in contact with ASN 456 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E SER 3.8 2.8 - - - +
210E PHE* 4.1 8.5 - - + -
213E GLY* 3.5 12.2 - - - -
214E CYS* 3.7 23.6 - - - +
424E TYR* 2.5 37.0 + - - -
428E VAL* 3.4 28.0 - - - +
440E TYR* 5.3 0.6 - - - -
452E LYS 2.9 19.6 + - - +
453E VAL 3.3 9.9 - - - +
455E VAL* 1.3 78.7 - - - +
457E LEU* 1.3 56.1 + - - +
459E LEU* 3.5 7.7 - - - +
460E LEU* 2.8 28.1 + - - +
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Residues in contact with LEU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E MET* 4.3 4.9 - - - +
86E HIS* 4.4 10.8 - - + -
89E TYR* 3.4 51.1 - - + -
210E PHE* 4.3 9.2 - - + -
370E ALA* 4.7 5.4 - - + -
373E LEU* 3.7 27.6 - - + -
453E VAL* 3.2 26.1 + - + +
454E HIS* 2.8 19.8 + - + +
456E ASN* 1.3 70.3 - - - +
458E LEU* 1.3 78.9 + - - +
459E LEU 3.0 0.9 - - - -
460E LEU* 3.9 13.0 - - + -
461E GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E ALA* 3.4 27.6 - - - +
371E TYR* 4.2 9.9 - - + +
390E ARG* 3.9 31.6 - - + +
393E ILE* 3.8 29.2 - - + -
394E TRP* 3.5 31.1 - - + +
397E ILE* 5.2 0.4 - - - -
454E HIS* 2.9 17.8 + - + +
455E VAL* 3.4 10.1 - - - +
457E LEU* 1.3 82.8 - - - +
459E LEU* 1.3 56.1 + - - +
462E ALA* 3.1 25.7 + - - +
900E K94 3.9 18.4 - - - -
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Residues in contact with LEU 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E SER* 4.8 3.4 - - - -
393E ILE* 5.1 1.3 - - + +
397E ILE* 3.4 25.4 - - + -
424E TYR* 5.7 0.9 - - + -
425E ILE* 3.6 36.1 - - + +
428E VAL* 3.7 25.1 - - + -
429E ALA* 3.6 28.3 - - + +
455E VAL* 2.8 21.5 + - + +
456E ASN* 3.5 11.4 - - - +
457E LEU 3.0 0.6 - - - -
458E LEU* 1.3 73.1 - - - +
460E LEU* 1.3 71.9 + - - +
461E GLU 3.1 1.6 - - - -
462E ALA* 2.8 13.5 + - - +
463E ARG* 2.8 19.8 + - + -
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Residues in contact with LEU 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E MET* 4.2 9.0 - - + -
89E TYR* 3.6 23.1 - - - +
203E HIS* 6.1 0.9 - - - +
206E SER* 3.4 44.7 - - - +
207E LEU* 4.6 6.7 - - + -
209E SER* 4.8 4.5 - - - -
210E PHE* 3.8 38.1 - - + +
366E LYS* 5.9 0.4 - - - -
456E ASN 2.8 14.6 + - - +
457E LEU* 3.4 17.4 + - + +
459E LEU* 1.3 79.4 - - - +
461E GLU* 1.3 71.7 + - - +
463E ARG* 3.7 3.2 + - - +
464E MET* 3.1 26.7 + - - +
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Residues in contact with GLU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E TYR* 2.4 30.0 + - - +
366E LYS* 2.8 45.4 + - - +
367E PHE* 3.2 28.6 + - + -
370E ALA* 3.6 17.9 - - + -
394E TRP* 3.9 16.8 - - + -
457E LEU 3.0 19.8 + - - +
458E LEU 3.9 2.9 - - - +
460E LEU* 1.3 81.6 - - + +
462E ALA* 1.3 60.1 + - - +
464E MET* 3.3 2.7 + - - +
465E GLN* 2.8 31.7 + - - +
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Residues in contact with ALA 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394E TRP* 3.7 33.8 - - + +
397E ILE* 3.7 22.2 - - + -
398E HIS* 2.7 29.7 + - + -
458E LEU 3.1 13.3 + - - +
459E LEU 2.8 9.0 + - - +
461E GLU* 1.3 80.3 - - - +
463E ARG* 1.3 61.8 + - - +
465E GLN 3.3 0.2 + - - -
466E ALA 3.1 8.0 + - - -
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Residues in contact with ARG 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E HIS* 3.3 31.8 + - - -
166E LEU 4.8 1.2 + - - -
167E ALA* 2.6 34.1 + - - +
202E THR* 6.4 0.2 - - + -
205E HIS* 2.9 36.7 + - + +
206E SER* 4.5 10.3 - - - +
209E SER* 3.0 23.1 + - - +
397E ILE* 3.6 12.8 - - + +
401E PHE* 3.8 20.5 - - + -
429E ALA* 3.2 22.6 + - - +
430E CYS* 5.3 1.6 + - - +
432E PRO* 4.7 0.2 - - - +
459E LEU* 2.8 26.5 + - + +
460E LEU 3.8 3.6 - - - +
462E ALA* 1.3 72.7 - - - +
464E MET* 1.3 65.8 + - + +
466E ALA* 3.4 7.0 - - - +
467E ALA* 3.1 23.4 + - + +
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Residues in contact with MET 464 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 5.1 0.4 - - + -
199E VAL* 4.0 10.1 - - + +
202E THR* 3.7 34.8 - - - +
203E HIS* 3.7 22.7 - - + +
206E SER* 4.1 15.3 - - - -
363E LEU* 3.8 23.6 - - + -
366E LYS* 4.0 21.1 - - - +
367E PHE* 4.2 9.4 - - + -
460E LEU* 3.1 17.9 + - - +
461E GLU* 3.6 7.4 - - - +
463E ARG* 1.3 79.3 - - - +
465E GLN* 1.3 61.4 + - - +
467E ALA* 3.7 4.7 - - - +
468E LEU* 2.7 36.6 + - + +
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Residues in contact with GLN 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344E TRP* 3.4 35.8 - - + +
367E PHE* 3.5 38.4 - - + +
394E TRP* 3.4 25.0 + - + -
398E HIS* 3.8 16.7 - - + +
405E TYR* 4.4 3.8 + - - -
461E GLU 2.8 20.2 + - - +
462E ALA 3.6 4.7 - - - +
464E MET* 1.3 72.7 - - - +
466E ALA* 1.3 66.1 + - - +
468E LEU* 3.6 1.2 - - - +
469E LEU* 2.8 41.0 + - + +
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Residues in contact with ALA 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398E HIS* 3.6 9.1 + - + +
401E PHE* 3.8 30.7 - - + -
403E ILE* 3.8 23.2 - - + +
462E ALA 3.1 10.1 + - - +
463E ARG* 3.4 10.5 - - - +
465E GLN* 1.3 81.2 - - - +
467E ALA* 1.3 62.5 + - - +
469E LEU* 3.3 3.4 + - - +
470E TYR* 3.1 29.8 + - + -
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Residues in contact with ALA 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 3.4 32.1 - - + +
170E PRO* 3.7 17.9 - - + -
202E THR* 3.5 24.9 - - + -
401E PHE* 5.3 2.2 - - + -
463E ARG* 3.1 15.3 + - + +
464E MET* 3.8 1.1 - - - +
465E GLN 3.2 0.2 - - - -
466E ALA* 1.3 76.9 - - - +
468E LEU* 1.3 66.0 + - - +
470E TYR* 3.4 2.9 + - - +
471E ALA 3.0 18.0 + - - -
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Residues in contact with LEU 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 5.0 0.7 - - + -
198E LEU* 3.9 22.9 - - + +
199E VAL* 4.4 8.7 - - + +
202E THR* 3.3 25.7 - - + +
344E TRP* 3.9 26.5 - - + -
352E ILE* 4.5 6.5 - - + -
363E LEU* 4.1 29.2 - - + -
367E PHE* 4.3 7.0 - - + -
464E MET* 2.7 25.3 + - + +
465E GLN* 3.7 2.9 - - - +
467E ALA* 1.3 74.5 - - - +
469E LEU* 1.3 56.2 + - - +
471E ALA* 3.3 6.6 + - + +
472E LEU* 2.9 40.9 + - + +
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Residues in contact with LEU 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E PHE* 6.1 3.6 - - + -
342E TYR* 3.8 36.6 - - + +
343E THR* 3.8 5.8 - - - +
344E TRP* 3.5 45.8 - - + +
348E GLY* 4.5 2.2 - - - -
398E HIS* 5.0 2.5 - - + -
403E ILE* 4.7 17.5 - - + -
405E TYR* 5.4 3.6 - - - +
465E GLN* 2.8 42.9 + - + +
466E ALA 3.5 4.5 - - - +
468E LEU* 1.3 69.7 - - - +
470E TYR* 1.3 62.1 + - + +
472E LEU* 3.3 2.7 + - + -
473E ARG* 2.9 33.1 + - - +
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Residues in contact with TYR 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E PRO* 3.2 32.1 - - + +
171E TRP* 3.4 34.5 - - + +
173E ILE* 4.3 5.0 - - + +
335E PRO* 4.8 1.2 + - - +
337E PHE* 4.0 26.5 - + + +
401E PHE* 2.6 31.1 + - + -
402E GLY* 3.4 19.8 + - - -
403E ILE* 3.5 13.5 - - + +
466E ALA 3.1 21.9 + - - -
467E ALA 3.7 5.2 - - - +
469E LEU* 1.3 79.0 - - + +
471E ALA* 1.3 62.4 + - - +
473E ARG* 3.5 35.5 + - - +
474E ALA* 3.2 22.2 + - - +
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Residues in contact with ALA 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E LEU* 3.9 13.5 - - + -
173E ILE* 4.1 14.5 - - + +
178E ILE* 4.3 1.9 - - - +
198E LEU* 3.5 29.2 - - + -
467E ALA 3.0 14.5 + - - +
468E LEU* 3.5 11.7 - - + +
469E LEU 3.1 0.2 - - - -
470E TYR* 1.3 76.7 - - - +
472E LEU* 1.3 63.7 + - + +
474E ALA* 3.3 7.4 + - - +
475E ILE* 3.1 24.0 + - - +
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Residues in contact with LEU 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ILE* 4.4 14.1 - - + -
198E LEU* 6.3 0.9 - - + -
342E TYR* 3.5 14.3 + - + +
344E TRP* 4.1 12.1 - - + -
348E GLY* 3.7 21.1 - - - +
351E LEU* 3.3 28.7 - - + +
352E ILE* 3.3 44.9 - - + +
468E LEU* 2.9 27.8 + - + +
469E LEU* 3.8 6.1 - - - +
471E ALA* 1.3 76.2 - - + +
473E ARG* 1.3 52.7 + - - +
475E ILE* 3.0 9.9 + - + +
476E THR 2.8 29.8 + - - -
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Residues in contact with ARG 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TRP 4.0 15.2 + - - -
173E ILE 4.1 11.5 + - - -
337E PHE* 3.4 44.0 - - - -
342E TYR* 3.8 34.5 - - + -
469E LEU 2.9 18.6 + - - +
470E TYR* 3.7 34.0 + - - +
471E ALA 3.2 0.2 - - - -
472E LEU* 1.3 75.0 - - - +
474E ALA* 1.3 60.2 + - - +
476E THR* 3.1 5.2 + - + +
477E ARG* 2.9 70.0 + - - +
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Residues in contact with ALA 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E ILE* 3.6 26.7 - - + +
174E THR* 3.6 4.9 - - - +
175E LYS* 3.3 33.6 - - - +
178E ILE* 3.7 6.9 - - + +
470E TYR 3.2 7.0 + - - +
471E ALA 3.5 9.0 - - - +
473E ARG* 1.3 80.5 - - - +
475E ILE* 1.3 56.0 + - - +
477E ARG* 3.3 7.0 + - - +
478E TYR* 3.0 24.6 + - - +
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Residues in contact with ILE 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E ILE* 3.6 28.9 - - + -
191E LEU* 3.8 24.5 - - + -
194E LEU* 4.6 8.1 - - + -
195E ILE* 3.5 25.8 - - + -
198E LEU* 4.1 20.0 - - + -
351E LEU* 3.8 22.2 - - + -
355E LEU* 4.5 1.8 - - + -
471E ALA 3.1 14.7 + - - +
472E LEU* 3.0 18.6 + - + +
474E ALA* 1.3 74.7 - - - +
476E THR* 1.3 56.3 + - - +
478E TYR* 3.5 1.4 + - - +
479E MET* 2.9 31.3 + - + +
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Residues in contact with THR 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342E TYR* 2.9 34.0 + - + -
347E HIS* 5.3 8.2 - - + +
351E LEU* 3.4 11.6 - - - +
472E LEU 2.8 11.1 + - - -
473E ARG* 3.4 9.0 - - + +
475E ILE* 1.3 71.3 - - - +
477E ARG* 1.3 67.2 + - + +
479E MET* 3.4 4.2 + - - -
480E THR* 3.1 45.8 + - + +
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Residues in contact with ARG 477 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E LYS* 3.6 43.1 - - + +
337E PHE* 5.0 5.3 - - - -
341E ASP* 5.8 3.0 - - - +
473E ARG* 2.9 68.6 + - - +
474E ALA* 3.3 6.0 + - - +
476E THR* 1.3 78.8 - - + +
478E TYR* 1.3 63.8 + - - +
480E THR* 3.6 14.2 - - - +
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Residues in contact with TYR 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E LYS* 3.7 12.9 - - + +
178E ILE* 4.1 12.8 - - + -
179E GLN* 3.8 49.4 - - + -
182E LEU* 3.6 26.0 - - + +
183E LYS* 3.1 37.4 - - + +
191E LEU* 5.3 7.0 - - + -
474E ALA 3.0 16.7 + - - +
475E ILE 3.7 3.4 - - - +
477E ARG* 1.3 79.6 - - - +
479E MET* 1.3 80.9 + - + +
480E THR* 3.4 4.3 - - - +
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Residues in contact with MET 479 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E LEU* 4.6 19.3 - - + -
351E LEU* 4.0 26.9 - - - -
354E ARG* 4.2 24.0 - - - +
355E LEU* 4.6 11.0 - - + -
475E ILE* 2.9 31.2 + - + +
476E THR* 3.4 4.2 + - - +
478E TYR* 1.3 88.6 - - + +
480E THR* 1.3 67.7 + - + +
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Residues in contact with THR 480 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476E THR* 3.1 31.4 + - + +
477E ARG* 3.6 13.4 - - - +
478E TYR 3.4 7.8 - - - +
479E MET* 1.3 88.1 - - + +
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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
------------------------------------------------------------
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