Contacts of the helix formed by residues 60 - 88 (chain O) in PDB entry 2DYS
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 GLU 60 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O ASP* 2.9 36.9 - - - +
58O ALA 2.6 8.3 + - - -
59O GLN* 1.3 78.1 + - - +
61O VAL* 1.3 83.8 + - - +
62O GLU* 3.2 2.5 - - - +
63O THR* 3.1 30.7 + - - +
64O ILE* 3.8 8.6 + - - +
304O PSC 3.7 38.9 - - - +
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Residues in contact with VAL 61 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N PHE* 3.5 29.2 - - + -
58O ALA 3.6 3.6 - - - +
60O GLU* 1.3 93.0 - - - +
62O GLU* 1.3 59.6 + - + +
63O THR 3.1 5.4 - - - -
64O ILE* 3.1 16.3 + - + +
65O TRP* 2.9 59.5 + - + -
304O PSC 3.6 40.8 - - + -
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Residues in contact with GLU 62 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N PHE* 4.4 1.6 - - - -
269N GLY* 4.2 4.9 - - - -
272N GLY* 4.0 14.0 - - - -
318N VAL* 3.6 26.8 - - - +
322N SER* 4.0 10.2 + - - -
58O ALA* 3.2 35.2 - - + +
59O GLN* 5.0 3.1 - - - +
60O GLU 3.2 2.2 - - - +
61O VAL* 1.3 76.1 - - + +
63O THR* 1.3 60.1 + - - +
65O TRP* 3.5 17.4 + - + +
66O THR* 2.9 33.1 + - - -
302O CHD 2.6 47.7 + - + +
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Residues in contact with THR 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O GLN* 4.8 3.1 + - - -
60O GLU* 3.1 24.6 + - - -
62O GLU* 1.3 76.9 - - - +
64O ILE* 1.3 66.2 + - - +
66O THR* 3.3 0.6 + - - -
67O ILE* 3.0 43.1 + - + +
302O CHD 3.2 22.0 + - + +
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Residues in contact with ILE 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60O GLU 4.0 7.9 - - - +
61O VAL* 3.2 18.6 - - + +
63O THR* 1.3 82.6 - - - +
65O TRP* 1.3 61.2 + - - +
66O THR 2.9 6.9 + - - -
67O ILE* 4.0 1.7 - - - +
68O LEU* 3.0 44.8 + - + +
304O PSC 4.0 51.6 - - + -
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Residues in contact with TRP 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268N PHE* 3.6 31.9 - + - -
314N ILE* 4.8 1.9 - - - +
318N VAL* 3.9 33.1 + - + +
321N PHE* 3.3 51.2 - + + -
322N SER* 4.0 9.9 - - - -
325N ALA* 4.0 6.7 - - + -
61O VAL* 2.9 39.8 + - + -
62O GLU* 3.5 32.0 - - + +
64O ILE* 1.3 76.9 - - + +
66O THR* 1.3 56.1 + - - +
69O PRO* 3.6 18.2 - - - +
304O PSC 3.3 51.4 - - + -
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Residues in contact with THR 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PEK 3.7 38.1 - - + -
275N TRP* 5.1 0.2 - - - -
314N ILE* 4.3 17.3 - - + +
318N VAL* 3.8 13.2 - - - +
62O GLU 2.9 19.9 + - - -
63O THR 3.7 1.8 - - - +
64O ILE 3.1 0.2 - - - -
65O TRP* 1.3 76.4 + - - +
67O ILE* 1.3 77.1 + - + +
68O LEU 3.4 0.7 - - - -
69O PRO* 3.4 3.5 - - - +
70O ALA* 3.2 23.9 + - - +
302O CHD 3.7 23.9 - - - +
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Residues in contact with ILE 67 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PEK 4.8 11.9 - - + -
101G CDL 6.6 0.2 - - + -
63O THR* 3.0 32.4 + - + +
64O ILE* 4.2 1.8 - - - +
66O THR* 1.3 87.9 - - + +
68O LEU* 1.3 66.8 + - + +
70O ALA* 3.4 7.6 + - + +
71O ILE* 3.0 40.6 + - + +
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Residues in contact with LEU 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O ILE* 3.0 36.9 + - + +
67O ILE* 1.3 78.1 - - + +
69O PRO* 1.3 71.5 - - + +
71O ILE* 3.1 10.7 + - + +
72O ILE* 3.0 36.1 + - + +
304O PSC 3.7 29.4 - - + -
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Residues in contact with PRO 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313N ALA 5.2 0.2 - - - +
314N ILE* 4.6 17.7 - - + +
317N GLY* 5.6 1.6 - - - -
321N PHE* 4.7 4.0 - - + -
605N HEA 3.5 35.3 - - + +
65O TRP* 3.6 23.1 - - - +
66O THR 3.4 15.9 - - - +
68O LEU* 1.3 96.2 - - + +
70O ALA* 1.3 54.7 + - - +
72O ILE* 3.2 4.3 + - + +
73O LEU* 2.9 36.3 + - - +
304O PSC 4.0 15.3 - - + -
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Residues in contact with ALA 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PEK 6.1 0.7 - - + -
101G CDL 3.8 28.5 - - + +
314N ILE* 3.9 17.1 - - + +
66O THR* 3.2 18.3 + - + +
67O ILE* 3.5 11.4 - - + +
68O LEU 3.2 0.2 - - - -
69O PRO* 1.3 78.3 - - - +
71O ILE* 1.3 62.4 + - + +
73O LEU* 3.4 5.4 + - - +
74O ILE* 3.0 31.1 + - + +
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Residues in contact with ILE 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67O ILE* 3.0 33.2 + - + +
68O LEU* 3.4 10.8 - - + +
70O ALA* 1.3 77.5 - - + +
72O ILE* 1.3 60.3 + - + +
74O ILE* 2.9 30.2 + - + +
75O LEU* 3.0 32.5 + - + +
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Residues in contact with ILE 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605N HEA 3.5 23.3 - - + -
30O ILE* 3.5 35.0 - - + -
34O ILE* 4.6 11.2 - - + -
68O LEU* 3.0 29.8 + - + +
69O PRO* 3.2 7.6 + - + +
71O ILE* 1.3 78.0 - - + +
73O LEU* 1.3 61.8 + - - +
75O LEU* 3.2 21.0 + - + +
76O ILE* 3.2 18.6 + - + +
304O PSC 4.6 14.1 - - + -
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Residues in contact with LEU 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 4.3 15.7 - - + -
310N MET* 3.3 55.5 - - + +
311N ILE* 4.3 2.2 - - - -
313N ALA* 4.1 7.6 - - + -
314N ILE* 3.8 32.1 - - + -
356N ILE* 4.6 2.2 - - + -
605N HEA 3.6 29.6 - - + -
69O PRO 2.9 19.2 + - - +
70O ALA* 3.7 5.2 - - - +
71O ILE 3.2 0.2 - - - -
72O ILE* 1.3 75.4 - - - +
74O ILE* 1.3 58.2 + - - +
76O ILE* 3.0 6.9 + - + +
77O ALA* 2.8 30.6 + - - +
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Residues in contact with ILE 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G LEU* 5.4 13.0 - - + -
101G CDL 3.8 42.0 - - + -
70O ALA* 3.0 24.0 + - + +
71O ILE* 2.9 13.5 + - + +
73O LEU* 1.3 75.7 - - - +
75O LEU* 1.3 65.8 + - + +
77O ALA* 4.4 6.1 - - - +
78O LEU* 3.1 49.8 + - + +
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Residues in contact with LEU 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26O HIS* 2.8 31.8 + - + +
30O ILE* 5.0 5.4 - - + -
71O ILE* 3.0 32.4 + - + +
72O ILE* 3.4 16.8 - - + +
73O LEU 3.1 0.2 - - - -
74O ILE* 1.3 86.3 - - + +
76O ILE* 1.3 58.4 + - - +
78O LEU* 4.7 8.5 - - + -
79O PRO* 3.4 14.3 - - - +
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Residues in contact with ILE 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310N MET* 3.4 28.9 - - + -
356N ILE* 4.2 12.1 - - + -
360N ASN* 3.7 14.4 - - - +
605N HEA 4.7 2.2 - - + -
23O PHE* 3.3 3.8 - - + -
26O HIS* 4.3 3.8 - - - +
27O THR* 3.7 27.6 - - + +
30O ILE* 3.6 31.6 - - + -
31O VAL* 6.5 1.1 - - + -
72O ILE* 3.2 24.2 - - + +
73O LEU* 3.0 8.4 + - + +
75O LEU* 1.3 78.9 - - - +
77O ALA* 1.3 65.0 + - - +
78O LEU 3.4 0.2 - - - -
79O PRO* 3.3 12.3 - - - +
80O SER* 3.2 13.7 - - - -
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Residues in contact with ALA 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.8 36.1 - - + -
306N THR* 5.7 3.4 - - + -
307N SER* 5.3 2.7 - - - +
310N MET* 4.6 11.9 - - - -
360N ASN* 4.8 0.2 - - - -
73O LEU 2.8 15.0 + - - +
74O ILE 4.1 2.9 - - - +
76O ILE* 1.3 76.0 - - - +
78O LEU* 1.3 56.6 + - - +
80O SER* 3.2 5.3 + - - -
81O LEU* 2.8 46.9 + - + +
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Residues in contact with LEU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G LEU* 5.5 4.7 - - + -
101G CDL 3.5 41.4 - - + +
74O ILE* 3.1 43.9 + - + +
75O LEU* 4.7 9.9 - - + -
77O ALA* 1.3 76.0 - - - +
79O PRO* 1.4 66.2 - - + +
81O LEU* 3.2 2.3 + - - +
82O ARG* 2.9 29.5 + - - +
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Residues in contact with PRO 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O PHE* 3.8 20.4 - - + -
26O HIS* 4.3 8.1 - - + +
75O LEU 3.4 17.5 - - - +
76O ILE 3.3 12.3 - - - +
78O LEU* 1.4 96.7 - - + +
80O SER* 1.3 61.3 + - - +
82O ARG* 3.6 28.7 - - - +
83O ILE* 3.1 32.0 + - - +
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Residues in contact with SER 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306N THR* 4.3 6.4 - - - +
360N ASN* 2.8 42.5 + - - +
361N SER* 4.8 0.9 + - - -
362N SER* 3.0 17.8 + - - -
23O PHE* 3.5 14.9 - - - -
76O ILE 3.2 12.8 - - - -
77O ALA* 3.4 6.3 - - - -
78O LEU 3.1 0.6 - - - -
79O PRO* 1.3 83.7 - - - +
81O LEU* 1.3 60.1 + - - +
83O ILE* 3.5 2.3 + - - +
84O LEU* 2.9 22.2 + - - +
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Residues in contact with LEU 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.7 68.2 - - + +
303N ALA* 3.9 30.5 - - + +
306N THR* 4.6 16.2 - - + -
307N SER* 4.3 10.3 - - - +
361N SER* 5.5 0.4 - - - +
77O ALA* 2.8 26.2 + - + +
78O LEU 3.9 2.5 - - - +
80O SER* 1.3 72.8 - - - +
82O ARG* 1.3 66.1 + - - +
84O LEU* 4.0 11.7 - - + -
85O TYR* 3.0 34.0 + - + -
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Residues in contact with ARG 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 4.3 15.0 - - + +
19O GLU* 3.7 25.2 + - - -
23O PHE* 5.5 1.6 - - - +
78O LEU 2.9 16.6 + - - +
79O PRO* 3.6 31.8 + - - +
81O LEU* 1.3 75.5 - - - +
83O ILE* 1.3 76.9 + - - +
85O TYR* 3.5 4.0 + - - +
86O MET* 3.1 55.5 + - + +
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Residues in contact with ILE 83 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362N SER* 3.9 6.5 - - - +
16O ILE* 4.6 7.4 - - + -
19O GLU* 3.5 50.3 - - + +
20O LEU* 3.7 24.9 - - + -
23O PHE* 3.6 23.8 - - + -
79O PRO 3.1 17.2 + - - +
80O SER* 3.7 4.5 - - - +
82O ARG* 1.3 86.7 - - - +
84O LEU* 1.3 64.0 + - - +
86O MET* 3.2 8.5 - - - +
87O MET* 3.0 31.3 + - + +
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Residues in contact with LEU 84 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299N VAL* 3.6 36.3 - - + +
302N ARG* 3.3 28.6 + - - +
303N ALA* 3.8 24.0 - - + +
361N SER* 3.1 30.1 - - - +
362N SER* 3.2 11.4 + - - +
80O SER 2.9 11.5 + - - +
81O LEU* 3.2 16.6 + - + +
83O ILE* 1.3 77.4 - - - +
85O TYR* 1.3 64.2 + - + +
87O MET* 3.3 32.2 + - + +
88O ASP 3.4 4.5 + - - -
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Residues in contact with TYR 85 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G CDL 3.8 59.5 + - - +
299N VAL* 3.6 27.6 - - + -
300N ASP* 2.8 24.4 + - - -
303N ALA* 3.4 32.3 - - + +
81O LEU* 3.0 31.9 + - + +
82O ARG* 4.0 3.8 - - - +
84O LEU* 1.3 80.3 - - + +
86O MET* 1.3 60.3 + - - +
88O ASP* 3.1 20.2 + - + +
89O GLU* 3.2 15.2 + - - +
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Residues in contact with MET 86 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16O ILE* 4.1 18.6 - - + +
19O GLU* 4.1 26.9 - - - +
82O ARG* 3.1 58.8 + - + +
83O ILE* 3.2 12.3 - - - +
85O TYR* 1.3 76.4 - - - +
87O MET* 1.3 62.8 + - - +
88O ASP 3.3 0.5 + - - -
89O GLU* 3.3 43.5 + - - +
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Residues in contact with MET 87 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302N ARG* 4.3 8.1 - - - +
362N SER* 3.7 30.1 - - - +
365N ILE* 4.4 15.0 - - + -
16O ILE* 4.3 34.8 - - + -
20O LEU* 5.4 3.4 - - - -
83O ILE* 3.0 18.3 + - + +
84O LEU* 3.4 35.9 - - + +
85O TYR 3.2 0.2 - - - -
86O MET* 1.3 76.8 - - - +
88O ASP* 1.3 57.0 + - - +
89O GLU 3.4 2.5 - - - +
91O ASN* 5.3 1.7 - - - +
169O GLY 5.7 2.7 - - - +
183O THR* 5.2 7.1 + - - +
23U GLN* 5.9 0.5 + - - -
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Residues in contact with ASP 88 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299N VAL* 3.7 45.6 + - + +
302N ARG* 3.9 10.9 + - - +
84O LEU 3.4 1.0 + - - +
85O TYR* 3.1 12.9 + - + +
87O MET* 1.3 78.7 - - - +
89O GLU* 1.3 66.1 + - - +
90O ILE* 3.5 4.7 + - - +
21U PRO 4.5 11.5 - - - +
22U ASN* 4.4 13.7 - - - +
23U GLN* 5.0 9.2 + - - +
----------------------------------------------------------
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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