Contacts of the helix formed by residues 459 - 491 (chain A) in PDB entry 1UCU
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 ALA 459 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 1.4 91.5 - - + +
460A THR* 1.4 59.8 + - - +
462A VAL* 3.7 8.0 - - - +
463A SER* 2.6 39.1 + - - -
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Residues in contact with THR 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TYR* 4.0 2.4 - - - -
459A ALA* 1.4 79.4 - - - +
461A GLU* 1.3 65.6 + - + +
463A SER* 3.1 6.1 + - - -
464A ASN* 3.0 33.5 + - - +
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Residues in contact with GLU 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ASP* 6.0 0.9 - - - +
456A SER 3.7 11.7 + - - +
457A ASP* 3.1 35.6 - - + +
458A TYR 3.7 2.8 + - - +
459A ALA 3.4 0.2 - - - -
460A THR* 1.3 79.7 - - + +
462A VAL* 1.3 60.3 + - - +
464A ASN* 3.3 17.9 + - + +
465A MET* 3.0 23.1 + - + +
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.5 24.5 - - + -
457A ASP* 4.1 7.6 - - - +
458A TYR* 2.4 58.6 + - - +
459A ALA* 3.3 9.0 - - - +
461A GLU* 1.3 66.9 - - - +
463A SER* 1.3 60.3 + - - +
465A MET 3.2 0.3 + - - -
466A SER* 2.4 49.5 + - - -
469A GLN* 5.5 0.9 - - - +
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ALA 2.6 23.0 + - - -
460A THR* 3.4 5.6 - - - -
462A VAL* 1.3 79.0 - - - +
464A ASN* 1.3 56.4 + - - +
466A SER* 4.1 5.4 - - - -
467A ARG* 2.7 41.4 + - - +
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Residues in contact with ASN 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A THR* 3.0 31.6 + - - +
461A GLU* 3.4 25.1 - - + +
462A VAL 3.1 0.2 - - - -
463A SER* 1.3 78.6 - - - +
465A MET* 1.3 64.9 + - + +
467A ARG* 2.9 42.2 + - - +
468A ALA* 3.1 21.9 + - - +
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Residues in contact with MET 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 4.8 19.2 - - + +
30A ARG* 4.9 24.9 - - + +
31A LEU* 3.8 17.1 - - + +
457A ASP* 3.3 26.5 - - - +
461A GLU* 3.0 9.4 + - + +
464A ASN* 1.3 81.1 - - + +
466A SER* 1.3 58.9 - - - +
468A ALA* 3.4 12.6 - - + +
469A GLN* 2.9 30.4 + - - +
472A GLN* 5.8 3.1 - - - +
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Residues in contact with SER 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 2.4 43.6 + - - -
463A SER* 4.1 4.5 - - - -
465A MET* 1.3 65.8 - - - +
467A ARG* 1.3 62.5 + - - +
468A ALA 3.0 1.3 - - - -
469A GLN* 2.9 37.6 + - - +
470A ILE* 3.0 20.5 + - - +
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Residues in contact with ARG 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A SER* 2.7 22.8 + - - +
464A ASN* 2.9 49.7 + - - +
466A SER* 1.3 76.0 - - - +
468A ALA* 1.3 57.6 + - - +
470A ILE* 3.3 6.5 + - - +
471A LEU* 2.6 58.9 + - + +
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Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ASN 3.1 20.5 + - - +
465A MET* 3.4 20.4 - - + +
466A SER 3.0 0.4 - - - -
467A ARG* 1.3 83.5 - - - +
469A GLN* 1.3 56.1 + - - +
471A LEU* 3.8 10.5 - - + -
472A GLN* 2.8 55.2 + - + +
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Residues in contact with GLN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.3 13.4 - - + +
27A ALA* 4.7 10.8 - - + -
28A ILE* 3.9 26.1 - - + +
31A LEU* 3.1 36.7 - - + +
462A VAL* 5.5 0.8 - - - +
465A MET 2.9 17.1 + - - +
466A SER* 2.9 31.5 + - - +
468A ALA* 1.3 77.5 - - - +
470A ILE* 1.3 53.9 + - + +
472A GLN* 5.0 1.1 - - - +
473A GLN* 2.7 53.6 + - - +
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Residues in contact with ILE 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A SER* 3.0 17.2 + - - +
467A ARG* 4.0 7.2 - - - +
469A GLN* 1.3 75.6 - - + +
471A LEU* 1.3 57.0 + - - +
473A GLN* 3.5 19.5 - - + +
474A ALA* 2.7 33.7 + - + +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG* 2.6 48.4 + - + +
468A ALA* 3.7 8.5 - - + +
469A GLN 3.3 0.2 - - - -
470A ILE* 1.3 72.7 - - - +
472A GLN* 1.3 66.1 + - + +
474A ALA* 3.2 11.0 - - + +
475A GLY* 3.1 15.6 + - - -
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Residues in contact with GLN 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.4 4.7 - - + +
20A SER* 4.2 18.8 - - - +
23A ALA* 4.2 13.5 - - - +
24A LEU* 3.4 21.2 - - + +
27A ALA* 5.0 12.3 - - - +
465A MET* 5.8 3.8 - - - +
468A ALA* 2.8 41.5 + - + +
469A GLN 4.7 0.4 - - - +
471A LEU* 1.3 76.0 - - + +
473A GLN* 1.3 54.7 + - - +
475A GLY* 2.9 5.9 + - - +
476A THR* 2.7 31.5 + - - -
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Residues in contact with GLN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 19.2 - - + +
469A GLN* 2.7 46.2 + - - +
470A ILE* 3.2 21.2 + - + +
472A GLN* 1.3 69.3 - - - +
474A ALA* 1.3 56.5 + - - +
476A THR* 3.1 14.5 - - + +
477A SER* 2.7 34.0 + - - -
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 2.7 15.9 + - + +
471A LEU* 3.2 17.3 - - + +
473A GLN* 1.3 75.8 - - - +
475A GLY* 1.3 50.7 + - - +
477A SER* 3.2 9.1 + - - -
478A VAL* 2.7 40.6 + - + +
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Residues in contact with GLY 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.8 10.6 - - - +
471A LEU 3.1 8.9 + - - -
472A GLN* 2.9 10.1 + - - -
474A ALA* 1.3 78.4 - - - +
476A THR* 1.3 56.0 + - - +
478A VAL* 3.1 11.0 + - - +
479A LEU* 2.9 30.8 + - - +
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.5 25.4 + - - +
18A ASN* 5.2 0.5 + - - -
21A GLN* 3.8 23.0 + - + +
24A LEU* 4.0 15.3 - - + -
472A GLN 2.7 14.3 + - - -
473A GLN* 3.1 28.5 + - + +
475A GLY* 1.3 69.8 - - - +
477A SER* 1.3 58.0 + - - +
479A LEU* 3.4 2.6 + - - +
480A ALA* 2.7 35.9 + - + +
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Residues in contact with SER 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A GLN 2.7 17.7 + - - -
474A ALA* 3.3 10.3 - - - -
476A THR* 1.3 78.0 - - - +
478A VAL* 1.3 65.2 + - - +
480A ALA* 3.3 7.8 - - - +
481A GLN* 3.0 44.3 + - - +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ALA* 2.7 28.8 + - + +
475A GLY* 3.3 10.8 - - - +
477A SER* 1.3 78.1 - - - +
479A LEU* 1.3 69.6 + - + +
481A GLN* 3.4 12.6 + - - +
482A ALA* 2.8 29.7 + - + +
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 4.2 2.9 - - - +
14A GLN* 3.4 40.1 - - + +
17A LEU* 3.4 41.5 - - + -
475A GLY 2.9 17.4 + - - +
476A THR* 3.4 4.0 - - - +
478A VAL* 1.3 84.4 - - + +
480A ALA* 1.3 59.6 + - - +
482A ALA* 3.4 23.0 - - + -
483A ASN* 3.0 24.8 + - - +
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Residues in contact with ALA 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A THR* 2.7 20.8 + - + +
477A SER* 3.0 12.5 + - - +
479A LEU* 1.3 72.6 - - - +
481A GLN* 1.3 67.3 + - + +
483A ASN* 3.2 25.7 - - - +
484A GLN* 3.8 9.0 + - - -
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Residues in contact with GLN 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A SER* 3.0 35.6 + - - +
478A VAL* 3.6 12.1 - - - +
480A ALA* 1.3 73.9 - - + +
482A ALA* 1.3 57.8 + - - +
483A ASN 3.0 9.4 + - - -
484A GLN* 3.1 19.2 + - - +
485A VAL* 3.3 18.4 + - + +
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Residues in contact with ALA 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 2.9 21.2 + - - +
478A VAL* 2.8 22.2 + - + +
479A LEU* 3.4 26.0 - - + -
480A ALA 3.3 0.2 - - - -
481A GLN* 1.3 75.8 - - - +
483A ASN* 1.3 55.2 + - - +
484A GLN 3.5 0.4 - - - -
485A VAL* 3.9 13.2 - - + -
486A PRO* 2.8 20.8 - - + +
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Residues in contact with ASN 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.5 0.3 - - - +
14A GLN* 4.1 8.7 - - + -
15A ASN* 5.8 2.2 + - - -
18A ASN* 6.2 0.2 - - - +
479A LEU 3.0 18.0 + - - +
480A ALA* 3.2 16.3 - - - +
481A GLN 3.0 0.6 - - - -
482A ALA* 1.3 79.0 - - - +
484A GLN* 1.3 77.6 + - - +
486A PRO* 3.4 14.3 - - - +
487A GLN* 3.9 24.5 + - - +
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Residues in contact with GLN 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ALA 4.0 12.1 + - - -
481A GLN* 3.1 10.2 + - - +
483A ASN* 1.3 90.4 + - - +
485A VAL* 1.3 64.1 + - + +
486A PRO 3.5 0.6 - - - -
487A GLN* 3.8 6.7 + - - +
488A ASN* 3.1 34.5 + - - +
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A GLN* 3.3 19.7 - - + +
482A ALA* 3.9 10.3 - - + -
484A GLN* 1.3 79.4 - - + +
486A PRO* 1.3 66.0 - - + +
488A ASN* 3.4 4.5 + - - +
489A VAL* 3.0 44.6 + - + +
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Residues in contact with PRO 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 3.4 11.7 - - - +
11A LEU* 3.1 40.6 - - + -
14A GLN* 3.6 4.7 - - - +
482A ALA 2.8 28.9 - - - +
483A ASN 3.4 13.7 - - - +
484A GLN 3.6 0.2 - - - -
485A VAL* 1.3 88.7 - - + +
487A GLN* 1.3 61.6 + - - +
489A VAL* 2.8 9.2 + - + +
490A LEU* 2.7 39.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.6 13.5 - - + +
483A ASN* 3.9 28.9 + - - +
484A GLN* 3.8 8.9 + - - +
485A VAL 3.6 0.4 - - - -
486A PRO* 1.3 78.4 - - - +
488A ASN* 1.3 62.9 + - - +
490A LEU* 3.6 14.7 + - + +
491A SER* 3.5 18.5 + - - -
----------------------------------------------------------
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Residues in contact with ASN 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A GLN* 3.1 25.7 + - - +
485A VAL* 3.4 7.3 + - - +
486A PRO 3.0 0.8 - - - -
487A GLN* 1.3 76.3 - - - +
489A VAL* 1.3 66.0 + - + +
490A LEU 3.1 2.0 - - - -
491A SER* 2.9 22.0 + - - -
492A LEU* 3.5 5.9 + - - +
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASN* 5.4 5.8 - - - +
485A VAL* 3.0 39.5 + - + +
486A PRO* 2.8 11.1 + - + +
488A ASN* 1.3 75.1 - - + +
490A LEU* 1.3 63.9 + - + +
492A LEU* 2.9 41.8 - - + +
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Residues in contact with LEU 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.2 13.9 - - + +
4A ILE* 4.2 37.7 - - + +
7A ASN* 3.4 41.3 - - + +
8A SER* 6.2 0.2 - - - -
11A LEU* 4.5 9.9 - - + -
486A PRO 2.7 23.4 + - - +
487A GLN* 3.7 13.0 - - + +
489A VAL* 1.3 83.2 - - + +
491A SER* 1.3 55.8 + - - +
492A LEU* 3.3 1.1 - - - -
493A LEU* 2.9 26.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A GLN 3.5 10.7 + - - -
488A ASN* 2.9 15.2 + - - -
490A LEU* 1.3 77.5 - - - +
492A LEU* 1.3 60.5 + - - +
493A LEU* 3.5 9.8 + - - +
494A ARG* 5.5 0.9 + - - -
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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