Contacts of the helix formed by residues 443 - 474 (chain T) in PDB entry 4BOG
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 GLY 443 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309T ARG* 5.2 5.6 - - - -
441T LEU 2.9 12.4 + - - -
442T ILE* 1.3 64.4 - - - +
444T LYS* 1.3 65.2 + - - -
445T VAL 3.3 2.9 - - - -
446T ILE* 4.0 13.0 - - - -
447T ASP* 2.7 39.7 + - - +
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Residues in contact with LYS 444 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442T ILE* 2.6 33.4 + - + +
443T GLY* 1.3 71.4 - - - +
445T VAL* 1.3 60.3 + - + +
447T ASP* 4.0 16.8 + - - +
448T LYS* 2.6 47.7 + - + +
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Residues in contact with VAL 445 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306T VAL* 4.4 20.0 - - + -
309T ARG* 4.2 26.2 - - + +
310T THR* 6.4 0.4 - - + -
443T GLY 3.3 0.4 - - - -
444T LYS* 1.3 82.1 - - + +
446T ILE* 1.3 52.5 + - - +
448T LYS* 3.6 3.4 - - - +
449T ALA* 2.7 36.1 + - + +
452T TRP* 4.2 9.6 + - + +
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Residues in contact with ILE 446 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240T TYR 4.7 1.4 - - - +
243T PRO* 4.5 31.6 - - + -
244T ALA* 4.8 8.7 - - + +
306T VAL* 4.4 11.9 - - + -
307T SER* 5.1 10.8 - - - -
309T ARG* 2.9 33.1 - - - +
443T GLY* 3.6 11.0 + - - +
444T LYS 3.5 0.4 - - - -
445T VAL* 1.3 75.7 - - - +
447T ASP* 1.3 82.5 + - - +
449T ALA* 2.7 19.0 + - - +
450T CYS* 3.1 11.1 + - - +
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Residues in contact with ASP 447 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244T ALA* 3.7 23.2 - - - +
443T GLY* 2.7 26.2 + - - +
444T LYS* 4.0 13.6 + - - +
446T ILE* 1.3 81.9 - - - +
448T LYS* 1.3 68.6 + - + +
450T CYS* 2.9 33.6 + - - +
451T PHE* 3.5 3.8 + - - +
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Residues in contact with LYS 448 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444T LYS* 2.6 38.1 - - + +
445T VAL* 3.8 4.0 - - - +
447T ASP* 1.3 83.7 - - + +
449T ALA* 1.3 51.4 + - - +
451T PHE* 3.2 21.3 + - - +
452T TRP* 2.6 69.3 + - + +
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Residues in contact with ALA 449 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240T TYR* 5.1 3.8 - - + +
299T ASN* 6.0 0.9 - - - +
303T VAL* 5.6 7.0 - - + -
306T VAL* 4.2 20.2 - - + -
445T VAL* 2.7 22.5 + - + +
446T ILE* 2.7 16.5 + - + +
448T LYS* 1.3 71.7 - - - +
450T CYS* 1.3 56.3 + - - +
452T TRP* 3.0 18.9 - - + +
453T ILE* 3.0 36.0 + - + +
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Residues in contact with CYS 450 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240T TYR* 2.5 34.9 + - - -
241T PHE* 2.7 54.5 - - + -
243T PRO* 4.7 1.3 - - - -
244T ALA* 5.1 5.6 - - - -
446T ILE 3.1 7.8 + - - -
447T ASP* 2.9 17.4 + - - +
449T ALA* 1.3 77.1 - - - +
451T PHE* 1.3 59.2 + - - +
453T ILE* 2.9 11.5 - - - +
454T ALA* 2.8 27.5 + - - +
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Residues in contact with PHE 451 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241T PHE* 4.0 8.5 - + + -
447T ASP 3.5 3.4 + - - +
448T LYS* 3.2 26.7 + - - +
450T CYS* 1.3 77.2 - - - +
452T TRP* 1.4 79.7 + + - +
454T ALA* 3.4 12.1 - - + -
455T LEU* 3.1 44.8 + - + +
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Residues in contact with TRP 452 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299T ASN* 5.1 4.5 - - - +
445T VAL* 4.2 12.3 + - + +
448T LYS* 2.6 44.9 + - + +
449T ALA* 3.0 31.3 - - + +
451T PHE* 1.4 86.8 - + - +
453T ILE* 1.3 61.3 + - + +
455T LEU* 4.3 0.9 - - - +
456T LEU* 2.9 30.8 + - - +
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Residues in contact with ILE 453 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237T VAL* 3.2 32.1 - - + -
240T TYR* 2.7 51.4 - - + -
299T ASN* 3.1 32.1 - - - +
303T VAL* 5.5 0.9 - - + -
449T ALA* 3.3 13.7 - - + +
450T CYS 2.9 16.4 - - - +
452T TRP* 1.3 72.4 - - + +
454T ALA* 1.3 74.3 + - - +
456T LEU* 3.4 13.0 - - + +
457T LEU* 2.3 43.9 + - + +
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Residues in contact with ALA 454 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237T VAL* 5.2 0.9 - - + -
241T PHE* 4.2 10.8 - - + -
450T CYS 2.8 15.6 + - - +
451T PHE* 3.3 21.5 - - + +
453T ILE* 1.3 87.6 - - + +
455T LEU* 1.3 52.6 + - - +
457T LEU* 2.7 29.3 - - - +
458T PHE* 2.7 16.6 + - - +
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Residues in contact with LEU 455 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451T PHE* 3.1 39.5 + - + +
452T TRP 4.5 0.7 - - - +
454T ALA* 1.3 79.4 - - - +
456T LEU* 1.3 52.5 + - - +
458T PHE* 3.9 26.9 - - + -
459T SER* 2.7 36.7 + - - +
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Residues in contact with LEU 456 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240T TYR* 5.7 0.7 - - + -
295T VAL* 4.5 7.4 - - + +
299T ASN* 3.8 25.1 - - + +
452T TRP 2.9 21.8 + - - +
453T ILE* 3.4 17.7 - - + +
455T LEU* 1.3 77.3 - - - +
457T LEU* 1.3 60.6 + - + +
459T SER* 2.5 23.8 + - - +
460T LEU* 2.7 55.6 + - + +
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Residues in contact with LEU 457 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233T SER* 3.7 30.1 - - - +
236T VAL* 5.6 2.9 - - + -
237T VAL* 3.6 30.3 - - + -
240T TYR* 5.9 2.9 - - + -
453T ILE* 2.3 36.2 + - + +
454T ALA* 2.7 11.0 - - - +
456T LEU* 1.3 73.5 - - + +
458T PHE* 1.3 58.0 + - - +
460T LEU* 3.3 8.8 + - + +
461T GLY* 2.8 28.9 + - - -
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Residues in contact with PHE 458 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454T ALA 2.7 14.3 + - - +
455T LEU* 3.4 27.8 - - + +
457T LEU* 1.3 74.6 - - - +
459T SER* 1.3 52.4 + - - +
461T GLY* 3.7 0.6 - - - -
462T THR* 2.6 64.0 + - + -
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Residues in contact with SER 459 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455T LEU* 2.7 19.3 + - - -
456T LEU* 2.5 36.6 + - - +
458T PHE* 1.3 73.5 - - - +
460T LEU* 1.3 57.7 + - - +
461T GLY 3.1 1.1 - - - -
462T THR* 3.9 4.7 - - - -
463T LEU* 2.5 39.1 + - - +
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Residues in contact with LEU 460 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291T PHE* 5.5 3.4 - - + -
292T VAL* 4.4 28.8 - - + +
295T VAL* 3.4 46.7 - - + -
296T ILE* 4.8 4.0 - - + +
456T LEU* 2.7 53.3 + - + +
457T LEU* 3.8 10.3 - - + +
459T SER* 1.3 73.6 + - - +
461T GLY* 1.3 59.0 + - - +
463T LEU* 3.6 13.6 - - + +
464T ALA* 2.9 31.0 + - - +
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Residues in contact with GLY 461 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292T VAL* 6.1 1.3 - - - -
457T LEU 2.8 18.5 + - - -
458T PHE* 3.8 0.9 - - - -
460T LEU* 1.3 74.4 - - - +
462T THR* 1.3 57.8 + - - +
464T ALA* 3.0 4.6 + - - -
465T ILE* 2.6 46.8 + - - +
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Residues in contact with THR 462 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458T PHE* 2.6 57.5 + - + -
459T SER* 3.9 4.5 - - - -
461T GLY* 1.3 71.0 - - - +
463T LEU* 1.3 64.3 + - - +
465T ILE* 4.9 6.8 - - + +
466T PHE* 2.7 46.7 + - + +
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Residues in contact with LEU 463 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T PHE* 5.8 2.5 - - + -
291T PHE* 3.6 35.9 - - + -
292T VAL* 5.3 2.7 - - + -
459T SER 2.5 31.9 + - - +
460T LEU* 3.6 12.6 - - + +
462T THR* 1.3 68.8 - - - +
464T ALA* 1.3 60.8 + - - +
466T PHE* 4.2 5.6 - - + +
467T LEU* 3.1 43.0 + - + +
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Residues in contact with ALA 464 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T PHE* 4.6 16.4 - - + -
292T VAL* 4.0 23.6 - - + -
460T LEU 2.9 19.0 + - - +
461T GLY* 3.0 3.7 + - - +
463T LEU* 1.3 76.9 - - + +
465T ILE* 1.3 56.6 + - + +
466T PHE 3.1 0.9 - - - -
467T LEU* 2.9 6.5 + - - +
468T THR* 2.6 40.3 + - - +
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Residues in contact with ILE 465 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461T GLY* 2.6 32.0 + - - +
462T THR* 4.8 4.5 - - + +
464T ALA* 1.3 74.2 - - + +
466T PHE* 1.3 55.6 + - - +
468T THR* 3.5 10.2 - - - +
469T GLY* 2.7 30.7 + - - -
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Residues in contact with PHE 466 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462T THR* 2.7 44.6 + - + +
463T LEU* 4.8 4.5 - - + -
465T ILE* 1.3 77.1 - - + +
467T LEU* 1.3 69.6 + - + +
469T GLY* 2.9 17.4 + - - -
470T HIS* 3.0 13.0 + - + +
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Residues in contact with LEU 467 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288T PHE* 3.8 33.4 - - + -
463T LEU* 3.1 36.0 + - + +
464T ALA* 2.9 5.6 + - - +
466T PHE* 1.3 88.3 - - + +
468T THR* 1.3 62.3 + - - +
469T GLY 2.9 1.6 - - - -
470T HIS* 2.7 32.1 + - + +
471T LEU* 2.8 16.6 + - - +
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Residues in contact with THR 468 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136T PHE* 5.7 4.3 - - + -
219T LEU* 6.5 0.4 - - + -
285T TYR* 4.8 19.7 - - + -
288T PHE* 4.9 14.1 - - - +
464T ALA* 2.6 30.3 + - - +
465T ILE* 3.7 10.1 - - - -
467T LEU* 1.3 73.6 - - - +
469T GLY* 1.3 65.0 + - - +
470T HIS 3.3 0.2 + - - -
471T LEU* 3.5 5.4 + - - +
472T ASN* 3.5 21.5 + - + +
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Residues in contact with GLY 469 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465T ILE 2.7 14.8 + - - -
466T PHE* 2.9 7.7 + - - -
468T THR* 1.3 79.3 - - - +
470T HIS* 1.3 55.9 + - - +
472T ASN* 3.8 7.1 - - - +
473T GLN* 2.9 31.7 + - - +
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Residues in contact with HIS 470 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466T PHE* 3.0 9.5 + - + +
467T LEU* 2.7 28.1 + - + +
469T GLY* 1.3 73.8 - - - +
471T LEU* 1.3 61.4 + - + +
472T ASN 2.9 4.7 - - - -
473T GLN* 2.9 7.5 + - + +
474T VAL* 2.2 68.1 + - + +
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Residues in contact with LEU 471 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135T PRO* 5.3 2.5 - - + -
136T PHE* 3.2 23.6 - - + +
137T ASP* 5.0 4.0 - - - +
282T ILE* 6.3 0.2 - - + -
284T LYS* 4.2 23.3 - - + -
285T TYR* 3.2 40.2 - - + +
288T PHE* 4.5 15.5 - - + -
467T LEU 2.8 17.3 + - - +
468T THR* 3.5 5.1 + - - +
470T HIS* 1.3 76.2 - - + +
472T ASN* 1.3 55.8 + - - +
475T PRO* 3.8 22.1 - - + +
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Residues in contact with ASN 472 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136T PHE* 3.3 27.8 - - + +
215T GLN* 5.9 2.4 - - - +
217T LYS* 6.2 0.4 - - - +
468T THR* 3.5 16.8 + - + +
469T GLY* 3.8 6.1 - - - +
470T HIS 2.9 0.4 - - - -
471T LEU* 1.3 77.7 - - - +
473T GLN* 1.3 55.1 + - - +
474T VAL 3.6 0.7 - - - -
475T PRO* 4.1 0.8 - - - -
476T GLU* 2.4 74.8 + - - +
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Residues in contact with GLN 473 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469T GLY 2.9 19.9 + - - +
470T HIS* 2.9 9.7 + - + +
472T ASN* 1.3 78.7 - - - +
474T VAL* 1.3 64.0 + - - +
476T GLU* 3.4 29.8 - - - +
477T PHE 4.3 0.9 + - - -
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Residues in contact with VAL 474 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470T HIS* 2.2 59.5 + - + +
473T GLN* 1.3 74.0 - - - +
475T PRO* 1.3 74.0 - - + +
476T GLU 3.0 0.2 - - - -
477T PHE 2.8 17.0 + - - -
----------------------------------------------------------
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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