Contacts of the helix formed by residues 444 - 472 (chain D) in PDB entry 5MG3
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 444 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D GLY* 3.4 4.2 + - - -
263D ILE 2.9 17.6 + - - -
264D GLN* 5.2 1.1 - - - +
265D ASP* 4.7 9.0 + - - -
443D PRO* 1.3 76.2 - - - +
445D LEU* 1.3 54.5 + - - +
446D GLY 4.4 1.3 - - - +
447D MET* 3.5 28.9 - - + +
448D GLN* 2.7 34.0 + - - +
129F LYS 4.9 1.1 - - - -
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Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D GLY* 3.0 19.4 + - - +
444D THR* 1.3 71.0 - - - +
446D GLY* 1.3 59.0 + - - +
448D GLN* 3.0 29.0 + - - +
449D ASN* 2.9 49.1 + - - +
59F GLU* 3.7 32.5 - - + +
95F MET* 5.6 0.2 - - - -
129F LYS* 3.6 42.6 + - + +
130F ARG* 3.8 17.6 - - + +
269F VAL* 3.5 22.2 - - + -
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Residues in contact with GLY 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D THR* 4.4 2.4 - - - +
445D LEU* 1.3 78.2 - - - +
447D MET* 1.3 60.7 + - - +
449D ASN* 3.5 17.8 - - - +
450D ILE* 3.7 12.8 + - - +
504D MET* 5.6 0.3 - - - +
130F ARG* 3.5 27.6 - - - +
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Residues in contact with MET 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D PRO 5.2 0.2 - - - +
444D THR* 3.5 26.6 + - + +
445D LEU 3.3 0.2 - - - -
446D GLY* 1.3 75.4 - - - +
448D GLN* 1.4 64.0 + - - +
450D ILE* 3.2 39.9 + - + +
451D GLU* 3.4 40.4 + - + +
502D LEU* 5.5 5.8 - - + -
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Residues in contact with GLN 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D PRO* 3.4 7.2 - - - +
262D GLY 3.0 14.3 + - - +
440D THR 4.4 4.9 - - - +
441D ILE* 3.3 21.9 - - - +
442D GLY 2.8 40.6 + - - +
443D PRO 4.2 3.0 + - - +
444D THR 2.7 23.8 + - - +
445D LEU* 3.0 28.7 + - - +
447D MET* 1.4 70.2 - - - +
449D ASN* 1.3 55.6 + - - +
451D GLU* 3.1 10.4 + - - +
452D GLN* 2.8 48.6 + - + +
129F LYS* 5.2 0.4 - - - +
269F VAL* 4.3 4.4 - - - +
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Residues in contact with ASN 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU* 2.9 40.2 + - - +
446D GLY* 3.5 17.6 - - - +
448D GLN* 1.3 68.3 - - - +
450D ILE* 1.4 63.2 + - - +
452D GLN* 3.0 29.4 + - - +
453D GLY* 2.9 24.3 + - - -
504D MET* 3.7 24.0 - - + +
130F ARG* 3.7 15.5 + - - +
269F VAL* 3.7 11.6 - - - +
270F LEU* 4.6 12.6 - - + +
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Residues in contact with ILE 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D GLY 3.7 14.6 + - - +
447D MET* 3.2 32.5 + - + +
449D ASN* 1.4 74.1 - - - +
451D GLU* 1.4 58.5 + - + +
453D GLY* 3.7 0.9 - - - -
454D LEU* 2.9 29.3 + - + +
502D LEU* 3.7 36.3 - - + +
503D SER* 3.9 20.9 - - - +
504D MET* 3.8 20.6 - - + +
507D ILE* 3.9 20.3 - - + +
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Residues in contact with GLU 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D GLU* 4.3 21.8 - - - +
440D THR* 4.3 15.0 + - + +
447D MET* 3.4 37.6 + - + +
448D GLN* 3.1 9.0 + - - +
450D ILE* 1.4 76.5 - - + +
452D GLN* 1.3 55.7 + - - +
454D LEU* 3.6 10.8 - - + +
455D GLU* 2.9 29.6 + - - +
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Residues in contact with GLN 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D THR* 3.9 21.7 - - + +
441D ILE* 4.4 9.3 - - + +
448D GLN* 2.8 35.3 + - + +
449D ASN* 3.0 40.9 + - - +
451D GLU* 1.3 71.0 - - - +
453D GLY* 1.3 57.2 + - - +
455D GLU* 3.8 2.8 - - - +
456D ALA* 3.4 20.1 + - - +
262F LEU* 5.0 0.2 - - - +
265F PHE* 2.9 40.0 + - - +
266F GLY 3.4 17.9 + - - -
268F PRO* 6.1 0.2 - - - +
269F VAL* 3.4 12.7 - - - +
270F LEU* 3.8 12.3 - - + -
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Residues in contact with GLY 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D ASN 2.9 16.8 + - - -
450D ILE 3.8 0.7 - - - -
452D GLN* 1.3 74.2 - - - +
454D LEU* 1.4 56.8 + - - -
455D GLU 3.4 0.2 - - - -
456D ALA* 3.2 9.1 - - - +
457D CYS* 3.0 32.7 + - - -
504D MET* 4.1 7.6 - - - -
507D ILE* 3.7 16.6 - - - -
262F LEU* 4.2 9.4 - - - +
270F LEU* 5.2 0.2 - - - -
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Residues in contact with LEU 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D ILE* 2.9 22.4 + - + +
451D GLU* 3.3 11.9 + - + +
453D GLY* 1.4 68.9 - - - +
455D GLU* 1.3 66.6 + - - +
457D CYS* 3.3 15.6 + - + +
458D LEU* 3.3 30.5 + - + +
502D LEU* 5.9 7.0 - - + -
507D ILE* 4.1 19.7 - - + +
510D ILE* 5.9 4.0 - - + -
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Residues in contact with GLU 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D THR* 2.7 42.5 + - + +
451D GLU 2.9 18.3 + - - +
452D GLN 3.8 3.6 - - - +
454D LEU* 1.3 77.7 - - - +
456D ALA* 1.4 54.8 + - - +
458D LEU* 3.3 15.2 + - - +
459D ALA* 2.9 31.2 + - + +
265F PHE* 4.3 24.6 - - + -
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Residues in contact with ALA 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452D GLN 3.4 11.1 + - - +
453D GLY 3.2 11.3 + - - +
455D GLU* 1.4 79.5 - - - +
457D CYS* 1.3 57.8 + - - +
459D ALA* 4.6 2.5 - - - +
460D GLY* 2.7 28.8 + - - -
511D VAL* 5.9 0.4 - - + -
258F VAL* 4.6 3.3 - - - +
261F MET* 3.9 13.1 - - - +
262F LEU* 3.5 45.3 - - + -
265F PHE* 5.0 1.3 - - + -
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Residues in contact with CYS 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D GLY 3.0 26.9 + - - +
454D LEU* 3.3 10.2 + - + +
456D ALA* 1.3 75.6 - - - +
458D LEU* 1.3 60.2 + - + +
461D LEU* 3.1 27.7 + - - +
507D ILE* 3.6 20.2 - - - -
510D ILE* 4.2 20.2 - - + -
511D VAL* 3.5 30.7 - - - -
514D LEU* 3.3 20.3 - - + +
258F VAL* 5.6 0.4 - - - -
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Residues in contact with LEU 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 4.2 26.9 - - + -
454D LEU* 3.3 33.4 + - + +
455D GLU* 3.5 15.3 - - - +
457D CYS* 1.3 77.4 - - + +
459D ALA* 1.3 63.7 + - - +
461D LEU* 3.5 21.2 - - + +
462D LEU* 3.2 22.5 + - - +
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Residues in contact with ALA 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D GLU* 2.9 22.9 + - + +
456D ALA* 4.1 0.4 - - - +
458D LEU* 1.3 72.9 - - - +
460D GLY* 1.4 56.7 + - - +
462D LEU* 3.0 9.6 + - - +
463D VAL* 2.9 34.9 + - + +
261F MET* 3.6 25.8 - - + -
265F PHE* 4.6 14.1 - - + -
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Residues in contact with GLY 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D ALA 2.7 22.8 + - - -
457D CYS 4.1 0.7 - - - -
459D ALA* 1.4 69.8 - - - +
461D LEU* 1.4 54.9 + - - +
463D VAL* 3.7 1.2 + - - +
464D SER* 2.7 37.7 + - - -
258F VAL* 3.6 25.1 + - - +
261F MET* 3.5 16.0 - - - +
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Residues in contact with LEU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 6.4 1.6 - - + -
457D CYS 3.1 18.5 + - - +
458D LEU* 3.5 24.7 - - + +
460D GLY* 1.4 70.8 - - - +
462D LEU* 1.3 65.2 + - + +
464D SER* 3.3 6.2 + - - -
465D ILE* 3.2 32.4 + - + +
483D LEU* 4.2 22.7 - - + -
484D ILE* 6.3 1.6 - - + -
487D LEU* 3.7 34.3 - - + -
514D LEU* 4.0 22.1 - - + +
518D VAL* 5.3 0.7 - - + -
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Residues in contact with LEU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D LEU 3.2 11.6 + - - +
459D ALA* 3.0 12.6 + - - +
461D LEU* 1.3 81.7 - - + +
463D VAL* 1.4 59.7 + - + +
465D ILE* 3.3 21.7 + - + +
466D LEU* 3.2 34.1 + - + +
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Residues in contact with VAL 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459D ALA* 2.9 16.5 + - + +
460D GLY 4.2 3.1 - - - +
462D LEU* 1.4 73.4 - - + +
464D SER* 1.3 58.6 + - - +
465D ILE 3.1 0.9 - - - -
466D LEU* 3.1 24.3 + - + +
467D PHE* 2.8 27.5 + - - +
257F MET* 3.6 35.7 - - + +
261F MET* 3.6 33.4 - - + -
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Residues in contact with SER 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D GLY 2.7 23.5 + - - -
461D LEU 3.3 6.5 + - - -
463D VAL* 1.3 74.8 - - - +
465D ILE* 1.4 58.7 + - - +
467D PHE* 3.4 19.2 - - - +
468D MET* 3.5 13.3 + - - +
483D LEU* 6.4 0.4 - - - -
518D VAL* 3.5 28.0 - - - +
254F THR* 3.1 18.2 + - - +
257F MET* 4.3 3.7 - - - +
258F VAL* 3.0 23.6 + - - +
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Residues in contact with ILE 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461D LEU* 3.2 27.1 + - + +
462D LEU* 3.5 22.7 - - + +
463D VAL 3.1 0.6 - - - -
464D SER* 1.4 74.4 - - - +
466D LEU* 1.4 65.1 + - + +
467D PHE 3.2 0.2 - - - -
468D MET* 3.0 20.5 + - + +
469D ILE* 3.0 33.8 + - + +
480D THR* 4.0 33.7 - - + +
483D LEU* 4.8 11.2 - - + -
484D ILE* 5.9 3.8 - - + -
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Residues in contact with LEU 466 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462D LEU* 3.2 23.5 + - + +
463D VAL* 3.3 30.7 - - + +
465D ILE* 1.4 75.7 - - + +
467D PHE* 1.3 56.9 + - - +
469D ILE* 3.8 19.8 - - + +
470D ILE* 2.9 50.2 + - + +
520G THR* 6.0 6.1 - - + -
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Residues in contact with PHE 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D VAL* 2.8 13.0 + - - +
464D SER* 3.4 13.5 - - - +
466D LEU* 1.3 75.6 - - - +
468D MET* 1.4 59.3 + - - +
470D ILE* 3.3 5.3 + - - -
471D PHE* 2.9 73.0 + + + +
472D TYR* 5.3 4.0 - + - -
522D VAL* 4.5 9.0 - - + -
250F ILE* 3.5 38.6 - - + -
253F GLY* 3.6 32.5 - - - -
254F THR* 3.7 20.0 - - + -
257F MET* 4.2 19.2 - - + +
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Residues in contact with MET 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D SER 3.6 13.7 - - - +
465D ILE* 3.0 14.4 + - + +
467D PHE* 1.4 76.0 - - + +
469D ILE* 1.4 62.5 + - + +
472D TYR* 3.2 57.2 + - + +
479D ALA* 3.9 22.0 - - + +
480D THR* 5.2 9.0 - - - +
518D VAL 5.7 0.2 - - - +
521D ASN* 3.4 31.0 - - - +
522D VAL* 4.1 19.3 - - - -
525D ASN* 3.8 20.2 - - - +
254F THR* 5.0 1.8 - - + -
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Residues in contact with ILE 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465D ILE* 3.0 36.4 + - + +
466D LEU* 3.8 20.2 - - + +
468D MET* 1.4 74.4 - - + +
470D ILE* 1.3 63.1 + - + +
472D TYR 3.0 20.2 - - - +
474D LYS* 5.9 10.2 - - + +
480D THR* 6.2 0.2 - - - +
515G PHE* 3.8 12.5 - - + +
517G THR* 4.7 24.5 - - + +
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466D LEU* 2.9 41.7 + - + +
467D PHE* 3.3 3.3 + - - +
469D ILE* 1.3 78.7 - - + +
471D PHE* 1.4 80.1 + - + +
257F MET* 6.1 5.6 - - + -
514G ASN* 3.4 18.6 - - + +
515G PHE* 2.8 50.4 + - - +
516G MET* 4.6 17.9 - - + -
517G THR 5.9 0.4 - - - +
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Residues in contact with PHE 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C MET* 3.4 21.5 - - + +
467D PHE* 2.9 71.6 + + + +
470D ILE* 1.4 84.8 - - + +
472D TYR* 1.3 75.2 + - + +
250F ILE* 4.4 23.8 - - + -
257F MET* 5.1 7.9 - - + -
513G GLY 4.1 15.3 - - - -
514G ASN* 4.1 15.9 - - + -
5Y PRO* 5.6 8.5 - - + -
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Residues in contact with TYR 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409C MET* 5.0 0.2 - - - -
467D PHE* 5.3 4.3 - + - -
468D MET* 3.2 50.2 + - + +
469D ILE* 3.0 19.8 - - - +
470D ILE 3.5 0.6 - - - -
471D PHE* 1.3 95.7 - - + +
473D LYS* 1.3 68.3 + - - +
474D LYS 3.5 2.6 + - - -
522D VAL* 4.1 11.3 + - + +
525D ASN* 3.7 25.2 - - + +
526D GLU* 2.7 44.6 + - - +
529D LYS* 4.1 23.1 - - + -
604D LEU* 6.3 4.0 - - + -
250F ILE* 4.0 13.5 - - + +
515G PHE* 3.7 10.3 - - - -
----------------------------------------------------------
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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