Contacts of the helix formed by residues 432 - 463 (chain F) in PDB entry 5JLH
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 432 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A SER 6.0 2.2 - - - +
382F ARG* 5.1 3.6 - - - +
387F ASP* 3.3 34.5 - - - +
388F GLN 4.1 2.1 - - - +
431F GLN* 1.3 77.8 - - - +
433F LYS* 1.3 63.8 + - - +
434F GLU* 3.2 11.4 + - - +
435F GLN* 2.6 49.7 + - + +
436F ALA* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 433 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F LEU* 3.3 30.1 - - + +
381F LYS 4.2 0.2 - - - -
382F ARG* 3.7 45.3 - - + +
387F ASP 4.1 3.0 + - - -
389F ALA* 3.9 19.9 - - + +
432F THR* 1.3 72.0 - - - +
434F GLU* 1.3 71.0 + - + +
436F ALA* 3.5 3.6 + - - +
437F ASP* 2.9 54.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F ARG* 6.3 0.9 - - - +
432F THR* 3.2 7.6 + - - +
433F LYS* 1.3 87.3 + - + +
435F GLN* 1.3 58.9 + - + +
437F ASP* 3.2 12.3 + - - +
438F PHE* 2.9 55.5 + - + -
612F MET* 5.1 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 435 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY* 6.2 2.0 - - - -
429F LYS* 5.1 9.9 + - - +
430F ALA 4.1 4.3 - - - +
431F GLN* 3.5 23.0 + - + +
432F THR* 2.6 45.1 + - + +
434F GLU* 1.3 74.4 - - + +
436F ALA* 1.3 56.8 + - - +
438F PHE* 3.2 15.4 + - + +
439F ALA* 2.9 26.9 + - - +
615F MET* 6.0 3.8 - - + -
617F PRO* 4.6 6.5 - - + +
666F MET* 5.3 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F LEU* 3.2 26.0 - - + -
389F ALA* 6.1 0.2 - - + -
415F LEU* 4.2 11.2 - - + +
416F LEU* 5.0 9.2 - - + -
431F GLN* 3.8 21.5 + - + +
432F THR 3.1 15.2 + - - +
433F LYS* 4.0 0.9 - - - +
435F GLN* 1.3 79.7 - - - +
437F ASP* 1.3 61.5 + - - +
439F ALA* 3.0 7.6 + - - +
440F LEU* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328F ARG* 5.5 9.3 + - - +
380F LEU* 3.2 26.5 + - - +
433F LYS* 2.9 45.3 + - - +
434F GLU* 3.2 16.3 + - - +
436F ALA* 1.3 74.1 - - - +
438F PHE* 1.3 65.9 + - + +
440F LEU* 3.2 11.9 + - + +
441F GLU* 3.0 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F ARG* 5.9 0.4 - - - -
434F GLU* 2.9 53.7 + - + -
435F GLN* 3.2 9.8 + - + +
437F ASP* 1.3 76.9 - - + +
439F ALA* 1.3 52.9 + - - +
441F GLU* 3.2 18.1 + - - +
442F ALA* 2.7 35.5 + - - +
612F MET* 4.0 38.6 - - + -
615F MET* 3.7 46.9 - - + +
616F ASP* 5.1 0.9 - - - -
617F PRO* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F LEU* 4.1 8.1 - - + -
431F GLN* 4.9 2.0 - - - +
435F GLN 2.9 13.1 + - - +
436F ALA* 3.0 11.6 + - - +
438F PHE* 1.3 76.5 - - - +
440F LEU* 1.3 57.7 - - - +
442F ALA* 3.2 1.9 + - - +
443F LEU* 2.9 36.7 + - + +
617F PRO* 3.6 17.9 + - + +
618F LEU* 5.5 0.2 - - - +
619F ASN* 4.1 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329F PHE* 4.6 3.1 - - + -
375F PHE* 3.8 27.3 - - + +
378F ILE* 3.9 36.6 - - + +
380F LEU* 3.5 32.5 - - + +
411F PHE* 4.6 7.9 - - + -
415F LEU* 3.3 30.5 - - + -
436F ALA 2.9 15.3 + - - +
437F ASP* 3.4 13.7 - - - +
439F ALA* 1.3 74.7 - - - +
441F GLU* 1.3 60.8 + - + +
443F LEU* 3.8 3.8 - - + +
444F ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 441 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F ILE* 3.8 32.4 - - + +
293F ARG* 4.6 17.1 + - - +
328F ARG* 3.0 32.8 + - - +
329F PHE* 3.9 14.8 - - + -
437F ASP* 3.0 20.1 + - - +
438F PHE* 3.6 22.9 - - - +
440F LEU* 1.3 76.5 - - + +
442F ALA* 1.3 58.1 + - - +
444F ALA* 3.2 5.0 - - - +
445F LYS* 2.9 37.1 + - + +
612F MET 5.1 3.8 - - - +
615F MET 5.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438F PHE 2.7 16.7 + - - +
439F ALA 3.2 4.2 + - - +
441F GLU* 1.3 72.4 - - - +
443F LEU* 1.3 52.7 + - - +
445F LYS* 2.7 9.6 + - - +
446F ALA* 2.6 38.3 + - - +
615F MET 5.7 0.6 + - - -
616F ASP* 2.9 30.1 - - - +
617F PRO 3.1 29.2 - - - +
618F LEU* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375F PHE* 3.7 25.6 - - + -
411F PHE* 5.0 5.6 - - + -
415F LEU* 5.1 5.8 - - + -
439F ALA* 2.9 26.6 + - + +
440F LEU* 3.8 4.5 - - + +
442F ALA* 1.3 72.7 - - - +
444F ALA* 1.3 56.7 + - - +
446F ALA* 4.5 2.0 - - - -
447F THR* 2.5 36.6 + - - +
618F LEU* 3.4 26.2 - - + -
619F ASN* 5.6 2.9 - - + +
622F VAL* 3.4 37.5 - - + -
623F ALA* 4.9 4.9 - - - +
626F LEU* 4.2 22.4 - - + -
638F TRP* 4.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 444 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ALA* 6.5 0.7 - - + -
292F ILE* 5.2 1.6 - - + +
329F PHE* 3.3 33.0 - - + -
372F VAL* 3.2 24.8 - - + +
375F PHE* 3.8 13.3 - - + -
440F LEU 2.9 11.1 + - - +
441F GLU 3.2 10.5 - - - +
443F LEU* 1.3 77.5 - - - +
445F LYS* 1.3 59.5 + - + +
447F THR* 3.2 2.9 - - - -
448F TYR* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 445 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LYS* 3.7 44.0 - - + +
289F SER* 4.1 13.0 - - - +
291F ALA* 5.4 2.5 - - + -
292F ILE* 3.5 34.7 - - + +
441F GLU* 2.9 27.7 + - + +
442F ALA* 2.7 13.7 + - - +
444F ALA* 1.3 75.5 - - + +
446F ALA* 1.3 56.4 + - - +
448F TYR* 3.2 8.7 + - - +
449F GLU* 2.9 27.4 + - - +
612F MET 5.3 0.6 + - - -
613F LYS* 3.7 13.1 + - - +
615F MET 3.7 13.1 + - - +
616F ASP* 4.5 3.8 - - - +
670F VAL* 3.3 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 446 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LYS* 4.4 7.3 - - - +
442F ALA 2.6 20.9 + - - +
443F LEU* 4.4 0.9 - - - +
445F LYS* 1.3 74.7 - - - +
447F THR* 1.3 55.3 + - - +
449F GLU* 3.2 7.7 + - - +
450F ARG* 2.9 39.8 + - + +
616F ASP* 5.2 1.1 - - - +
618F LEU* 4.4 11.0 - - + -
638F TRP* 4.0 18.2 - - + -
668F ARG* 4.1 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 447 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F MET* 3.3 31.1 - - + +
371F ALA* 5.5 2.0 - - + -
372F VAL* 4.5 14.4 - - + -
375F PHE* 4.1 16.2 - - + -
443F LEU* 2.5 26.9 + - - +
444F ALA* 3.2 6.1 - - - +
446F ALA* 1.3 75.1 - - - +
448F TYR* 1.3 61.5 + - - +
450F ARG* 3.3 3.7 + - - +
451F LEU* 2.9 28.6 + - + +
626F LEU* 4.7 2.3 - - - +
638F TRP* 3.4 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 448 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F PHE* 2.6 46.2 + + + +
286F LEU* 4.1 21.3 - - + -
288F LYS* 5.2 3.6 - - + -
291F ALA* 4.8 9.4 - - + -
301F PHE* 3.6 30.2 - + - -
303F ILE* 4.1 6.0 - - + +
304F PHE* 3.8 27.4 - + - -
369F VAL* 5.2 2.9 - - + -
372F VAL* 4.3 15.0 - - + -
444F ALA 2.9 12.9 + - - +
445F LYS* 3.5 9.4 - - - +
447F THR* 1.3 77.7 - - - +
449F GLU* 1.3 59.7 - - - +
451F LEU* 3.2 26.7 + - + +
452F PHE* 2.9 35.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 449 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286F LEU* 4.2 26.9 - - + -
288F LYS* 3.9 29.1 + - + +
445F LYS 2.9 12.9 + - - +
446F ALA* 3.5 9.0 - - - +
448F TYR* 1.3 77.1 - - - +
450F ARG* 1.3 64.4 + - - +
452F PHE* 3.2 4.9 + - + +
453F ARG* 2.9 61.0 + - + +
668F ARG* 4.1 10.4 + - - -
673F LEU* 5.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446F ALA* 2.9 26.7 + - - +
447F THR* 3.6 4.9 - - - +
449F GLU* 1.3 82.1 + - - +
451F LEU* 1.3 58.2 - - - +
453F ARG* 3.2 26.0 + - - +
454F TRP* 2.9 29.8 + - - +
618F LEU* 5.2 0.2 - - - +
637F ILE* 3.2 30.3 + - + +
638F TRP* 3.1 60.3 - - + +
640F ASP* 3.0 36.5 + - - +
664F ARG* 3.5 16.2 - - - +
668F ARG* 5.0 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F PHE* 3.9 25.1 - - + -
365F MET* 4.9 12.6 - - + -
368F MET* 3.6 40.2 - - + +
369F VAL* 3.6 23.8 - - + +
372F VAL* 6.1 0.4 - - + -
447F THR* 2.9 13.2 + - + +
448F TYR* 3.2 28.9 + - + +
450F ARG* 1.3 76.7 - - - +
452F PHE* 1.3 57.3 + - - +
454F TRP* 3.2 16.1 + - + +
455F LEU* 2.9 25.7 + - + +
633F LEU* 5.8 0.4 - - + -
637F ILE* 4.2 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 452 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F LEU* 4.4 14.5 - - + +
248F PHE* 4.1 32.5 - + + -
249F GLY* 4.3 12.1 - - - -
262F PHE* 3.7 37.2 - + + -
283F THR* 3.3 37.2 - - + -
286F LEU* 4.4 22.2 - - + -
448F TYR* 2.9 23.3 + + + +
449F GLU* 3.4 11.9 - - + +
451F LEU* 1.3 77.5 - - + +
453F ARG* 1.3 66.5 + - + +
455F LEU* 3.2 9.6 + - + +
456F VAL* 3.0 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 453 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F THR* 5.3 4.9 - - - +
449F GLU* 2.9 44.6 + - + +
450F ARG* 3.2 24.7 + - - +
452F PHE* 1.3 81.9 - - + +
454F TRP* 1.3 60.6 + - - +
456F VAL* 2.7 32.4 - - + +
457F LEU* 3.0 22.5 + - + +
640F ASP* 5.6 4.6 + - - -
680F ARG* 5.2 12.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 454 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357F PHE* 5.8 2.7 - + - -
361F GLU* 5.1 15.7 - - + -
365F MET* 4.0 36.6 - - + -
450F ARG 2.9 13.4 + - - +
451F LEU* 3.2 16.4 + - + +
453F ARG* 1.3 75.8 - - - +
455F LEU* 1.3 80.6 + - + +
457F LEU* 3.2 9.8 + - + +
458F ARG* 2.8 60.9 + - + +
633F LEU* 3.7 27.1 - - + +
636F GLU* 2.8 44.5 + - - -
637F ILE* 4.0 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 455 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F ILE* 3.5 33.4 - - + -
245F LEU* 4.0 19.5 - - + -
248F PHE* 3.5 35.7 - - + -
352F LEU* 5.1 1.3 - - + -
357F PHE* 4.8 15.3 - - + -
365F MET* 4.3 15.5 - - + -
451F LEU 2.9 13.5 + - - +
452F PHE* 3.4 11.2 - - + +
454F TRP* 1.3 90.8 - - + +
456F VAL* 1.3 56.6 + - - +
458F ARG* 3.7 0.8 - - + -
459F LEU* 2.8 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 456 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245F LEU* 5.4 8.3 - - + -
281F ILE* 3.7 35.7 - - + +
282F GLU* 4.6 1.3 - - - -
283F THR* 4.0 35.9 - - + +
452F PHE* 3.0 10.2 + - + +
453F ARG* 2.7 32.0 + - + +
455F LEU* 1.3 77.1 - - - +
457F LEU* 1.3 65.2 + - + +
459F LEU* 3.3 7.0 + - + +
460F ASN* 2.9 35.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 457 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453F ARG* 3.0 25.1 + - + +
454F TRP* 3.8 10.5 - - + +
456F VAL* 1.3 79.3 - - + +
458F ARG* 1.3 62.0 + - - +
460F ASN* 3.1 17.7 + - + +
461F ARG* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 458 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F GLY 4.7 5.9 + - - -
357F PHE* 3.1 38.9 - - + -
361F GLU* 3.5 28.9 + - - -
454F TRP* 2.8 55.2 + - + +
455F LEU* 4.0 2.9 - - - +
457F LEU* 1.3 75.1 - - - +
459F LEU* 1.3 61.1 + - - +
461F ARG* 3.2 34.5 + - - +
462F ALA 3.1 16.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 459 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F ALA* 4.2 26.0 - - + +
244F ILE* 5.1 5.2 - - + -
245F LEU* 4.6 25.4 - - + -
281F ILE* 5.2 8.1 - - + -
355F LEU* 4.0 31.4 - - + -
357F PHE* 3.9 8.5 - - + -
455F LEU* 2.8 28.5 + - + +
456F VAL* 3.5 7.6 - - + +
458F ARG* 1.3 75.2 - - - +
460F ASN* 1.4 63.8 + - - +
462F ALA* 2.9 16.7 + - + +
463F LEU* 2.8 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 460 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ALA 5.4 0.2 - - - +
280F ASN* 3.8 16.2 - - + +
281F ILE* 2.9 51.5 + - - +
282F GLU* 5.4 0.8 - - - +
456F VAL* 2.9 23.3 + - - +
457F LEU* 3.1 19.1 + - + +
459F LEU* 1.4 76.0 - - - +
461F ARG* 1.3 52.9 + - - +
463F LEU* 2.7 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 461 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457F LEU 2.9 11.9 + - - +
458F ARG* 3.2 38.9 - - - +
459F LEU 3.0 0.2 - - - -
460F ASN* 1.3 76.0 - - - +
462F ALA* 1.3 59.5 + - - +
463F LEU 3.0 11.4 + - - +
464F ASP* 3.5 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 462 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237F GLN* 3.1 17.3 + - - +
355F LEU* 3.5 28.0 - - + +
357F PHE* 3.8 24.6 - - + -
458F ARG* 3.1 5.5 + - - -
459F LEU* 2.9 20.3 + - + +
461F ARG* 1.3 73.6 - - - +
463F LEU* 1.3 59.1 + - - +
464F ASP* 3.8 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 463 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F GLU* 5.0 10.5 - - + +
237F GLN* 3.3 31.4 - - + +
238F LEU* 4.5 18.4 - - + -
241F ALA* 6.5 1.1 - - + -
279F ALA* 3.6 28.9 - - + +
280F ASN* 4.1 5.2 - - - -
281F ILE* 4.4 13.5 - - + -
459F LEU* 2.8 21.9 + - + +
460F ASN* 2.7 51.2 - - - +
461F ARG* 3.0 8.7 + - - +
462F ALA* 1.3 76.2 - - - +
464F ASP* 1.3 62.1 + - - +
465F ARG 4.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
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