Contacts of the helix formed by residues 48 - 82 (chain D) in PDB entry 5T0H
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 GLN 48 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.4 19.8 - - + +
44D TYR* 2.8 22.7 - - - +
45D LYS* 2.5 41.4 + - - +
47D LEU* 1.3 72.8 - - - +
49D GLN* 1.3 69.4 + - - +
51D LEU* 3.7 13.5 - - + -
52D GLU* 2.9 50.9 + - + +
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS 2.7 30.7 + - - +
46D LYS* 3.0 21.2 - - - +
47D LEU 3.4 0.6 - - - -
48D GLN* 1.3 84.9 - - - +
50D GLU* 1.3 65.1 + - - +
52D GLU* 3.1 4.2 + - - +
53D PHE* 2.8 57.4 + - + -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS 3.1 18.3 - - - +
47D LEU* 2.9 41.9 - - - +
49D GLN* 1.3 76.3 - - - +
51D LEU* 1.3 57.1 + - + +
53D PHE* 3.6 15.5 - - + +
54D LEU* 2.8 42.1 + - + +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 4.3 13.7 - - + +
28C ILE* 3.6 51.8 - - + +
29C GLU* 3.9 10.5 - - + +
32C GLN* 3.9 19.4 - - + +
47D LEU 3.6 17.9 - - - +
48D GLN* 3.4 10.0 + - + +
49D GLN 3.1 0.6 - - - -
50D GLU* 1.3 82.5 - - + +
52D GLU* 1.3 70.3 + - + +
54D LEU* 3.3 7.3 + - - +
55D GLU* 2.9 33.6 + - - +
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLN* 2.9 35.3 + - + +
49D GLN* 3.8 4.7 - - - +
51D LEU* 1.3 79.0 - - + +
53D PHE* 1.3 67.0 + - + +
55D GLU* 3.5 18.7 - - - +
56D VAL* 2.9 29.6 + - - +
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Residues in contact with PHE 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLN* 2.8 51.3 + - + +
50D GLU* 3.6 12.1 - - + +
52D GLU* 1.3 85.7 - - + +
54D LEU* 1.3 57.3 + - + +
56D VAL* 3.1 12.5 - - + +
57D GLN* 3.0 33.8 + - + +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 3.5 20.0 - - + +
36C ASN* 3.5 30.5 - - - +
43C ARG* 5.8 5.4 - - - +
50D GLU* 2.8 32.0 + - + +
51D LEU* 3.7 5.2 - - - +
53D PHE* 1.3 74.9 - - + +
55D GLU* 1.3 58.7 + - - +
57D GLN* 3.3 14.4 + - + +
58D GLU* 2.9 32.9 + - - +
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Residues in contact with GLU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 3.6 19.9 - - - +
51D LEU* 2.9 20.3 + - - +
52D GLU* 3.2 24.3 + - - +
54D LEU* 1.3 74.3 - - - +
56D VAL* 1.3 64.0 + - - +
58D GLU* 3.1 20.3 + - + +
59D GLU* 3.2 25.1 + - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU 2.9 14.8 + - - +
53D PHE* 3.1 26.5 - - + +
55D GLU* 1.3 76.7 - - - +
57D GLN* 1.3 63.8 + - - +
59D GLU* 3.9 12.9 + - + +
60D TYR* 3.0 28.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 5.3 14.1 + - - +
53D PHE* 3.0 27.0 + - + +
54D LEU* 3.5 18.8 - - + +
55D GLU 3.1 0.2 - - - -
56D VAL* 1.3 83.4 - - - +
58D GLU* 1.3 59.3 + - - +
60D TYR* 3.3 35.6 - - - +
61D ILE* 2.8 34.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C GLN* 3.3 16.9 + - - +
35C VAL* 2.9 41.4 - - + +
36C ASN* 3.2 12.3 - - - +
38C LYS* 4.6 0.9 - - - +
39C SER* 2.9 34.8 + - - -
54D LEU* 2.9 21.1 + - - +
55D GLU* 3.1 10.3 + - + +
57D GLN* 1.3 77.4 - - - +
59D GLU* 1.3 61.8 + - + +
61D ILE* 3.2 4.0 + - - +
62D LYS* 2.8 41.2 + - + +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLU* 3.2 28.9 + - + +
56D VAL* 4.4 11.5 - - + +
58D GLU* 1.3 80.1 - - + +
60D TYR* 1.3 64.0 + - - +
62D LYS* 3.7 8.0 - - - +
63D ASP* 3.0 24.8 + - - +
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Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 3.0 22.3 + - + +
57D GLN* 3.3 41.3 - - - +
58D GLU 3.1 0.2 - - - -
59D GLU* 1.3 75.2 - - - +
61D ILE* 1.3 63.9 + - + +
63D ASP* 3.0 7.5 + - - +
64D GLU* 2.6 72.1 + - + -
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Residues in contact with ILE 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 3.8 24.5 - - - +
43C ARG* 3.4 47.3 - - + +
46C GLN* 3.6 15.5 - - - +
57D GLN 2.8 18.4 + - - +
58D GLU* 3.3 9.6 - - - +
60D TYR* 1.3 82.3 - - + +
62D LYS* 1.3 60.0 + - + +
64D GLU* 3.4 22.9 - - - +
65D GLN* 2.8 44.7 + - - +
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 5.5 4.9 + - + +
39C SER* 5.9 1.6 - - - -
42C LEU* 3.4 23.1 - - + +
58D GLU* 2.8 28.8 + - + +
59D GLU* 3.7 8.5 - - - +
61D ILE* 1.3 79.8 - - + +
63D ASP* 1.3 59.0 + - - +
65D GLN* 3.4 18.3 - - - +
66D LYS* 2.9 45.0 + - + +
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Residues in contact with ASP 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU 3.0 16.4 + - - +
60D TYR* 3.0 5.6 + - - +
62D LYS* 1.3 73.0 - - - +
64D GLU* 1.3 65.4 + - - +
66D LYS* 4.0 16.2 - - + +
67D ASN* 3.0 43.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLN* 3.3 24.2 + - - +
60D TYR* 2.6 61.2 + - + +
61D ILE* 3.4 20.7 - - - +
63D ASP* 1.3 71.2 - - - +
65D GLN* 1.3 58.3 + - - +
67D ASN* 3.1 9.1 + - - +
68D LEU* 2.9 29.6 + - + +
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 5.3 1.0 - - - +
42C LEU* 3.1 54.9 - - + +
43C ARG 4.2 0.2 + - - -
46C GLN* 3.0 38.3 - - + +
61D ILE* 2.8 41.1 + - - +
62D LYS* 3.4 27.1 - - + +
64D GLU* 1.3 73.8 - - - +
66D LYS* 1.3 57.7 + - + +
68D LEU* 4.3 4.7 - - - -
69D LYS* 3.0 38.0 + - - +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LYS* 2.9 38.1 + - + +
63D ASP* 3.5 16.6 - - + +
64D GLU 3.0 0.2 - - - -
65D GLN* 1.3 77.0 - - + +
67D ASN* 1.3 61.8 + - - +
69D LYS* 3.4 12.9 + - + +
70D LYS* 2.7 42.5 + - - +
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Residues in contact with ASN 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ASP* 3.0 39.3 + - - +
64D GLU* 3.8 3.9 - - - +
66D LYS* 1.3 73.3 - - - +
68D LEU* 1.3 60.8 + - - +
70D LYS* 3.2 27.4 + - - +
71D GLU* 2.9 38.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLN* 3.6 35.2 - - + +
49C ARG 6.5 0.2 - - - -
50C ASN* 4.0 27.6 - - + +
53C ASN* 5.0 13.5 - - + +
64D GLU* 2.9 18.1 + - + +
65D GLN* 4.3 4.3 - - - -
67D ASN* 1.3 76.9 - - - +
69D LYS* 1.3 56.2 + - - +
71D GLU* 3.2 28.2 + - + +
72D PHE* 2.8 28.6 + - + +
----------------------------------------------------------
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Residues in contact with LYS 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 5.4 11.4 - - - +
45C LEU* 6.2 1.8 - - - +
49C ARG* 3.0 44.6 + - - +
65D GLN* 3.0 30.0 + - - +
66D LYS* 3.5 12.8 - - - +
67D ASN 3.2 0.4 - - - -
68D LEU* 1.3 77.2 - - - +
70D LYS* 1.3 58.3 + - + +
72D PHE* 3.0 5.9 + - - +
73D LEU* 2.8 40.3 + - + +
----------------------------------------------------------
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Residues in contact with LYS 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LYS* 2.7 45.0 + - - +
67D ASN* 3.2 25.7 + - - +
69D LYS* 1.3 78.0 - - + +
71D GLU* 1.3 56.9 + - + +
73D LEU* 3.4 20.3 + - + +
74D HIS* 2.8 26.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN* 6.1 1.3 - - - +
67D ASN* 2.9 25.8 + - - +
68D LEU* 3.3 31.8 - - + +
69D LYS 3.2 0.2 - - - -
70D LYS* 1.3 77.9 - - + +
72D PHE* 1.3 57.1 + - - +
74D HIS* 3.3 12.4 + - - +
75D ALA* 2.8 25.6 + - - +
----------------------------------------------------------
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Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 3.1 69.1 - - + +
52C LEU* 3.6 35.2 - - + -
53C ASN* 3.8 17.7 - - + -
56C VAL* 5.1 4.5 - - + -
68D LEU* 2.8 15.3 + - + +
69D LYS* 3.0 8.5 + - - +
71D GLU* 1.3 74.6 - - - +
73D LEU* 1.3 59.3 + - + +
75D ALA* 3.1 7.9 + - + +
76D GLN* 2.8 61.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 3.8 16.6 - - - +
69D LYS* 2.8 30.1 + - + +
70D LYS* 3.6 22.9 - - + +
72D PHE* 1.3 72.6 - - + +
74D HIS* 1.3 58.4 + - - +
76D GLN* 3.1 12.8 + - + +
77D GLU* 3.0 34.4 + - + +
----------------------------------------------------------
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Residues in contact with HIS 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ARG* 6.1 3.6 - - - -
70D LYS 2.8 15.5 + - - +
71D GLU* 3.3 13.7 + - - +
73D LEU* 1.3 76.0 - - - +
75D ALA* 1.3 57.9 + - - +
77D GLU* 3.1 14.8 + - + +
78D GLU* 2.9 63.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASN* 4.3 9.2 - - - +
56C VAL* 4.1 26.2 - - + +
71D GLU 2.8 14.4 + - - +
72D PHE* 3.1 19.0 + - + +
74D HIS* 1.3 78.3 + - - +
76D GLN* 1.3 59.2 + - - +
78D GLU* 3.1 12.8 + - - +
79D VAL* 3.0 32.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 5.0 7.5 - - - +
72D PHE* 2.8 53.8 + - + +
73D LEU* 3.1 18.4 + - + +
75D ALA* 1.3 75.2 - - - +
77D GLU* 1.3 63.6 + - - +
79D VAL* 3.3 16.8 - - - +
80D LYS* 3.0 43.7 + - + +
118D THR* 5.5 8.1 - - - +
----------------------------------------------------------
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 3.0 23.3 + - - +
74D HIS* 3.1 15.7 + - + +
76D GLN* 1.3 78.3 - - - +
78D GLU* 1.3 61.7 + - - +
80D LYS* 4.3 5.8 - - - +
81D ARG* 3.0 29.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG* 6.2 2.0 - - + -
74D HIS* 2.9 49.2 + - + +
75D ALA* 3.1 13.6 + - - +
77D GLU* 1.3 77.9 - - - +
79D VAL* 1.3 58.0 + - + +
81D ARG* 3.0 31.3 + - - +
82D ILE* 2.7 47.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C VAL* 3.8 32.1 - - + +
59C LEU* 4.5 23.3 - - + -
60C ARG* 5.9 2.2 - - + -
75D ALA 3.0 13.6 + - - +
76D GLN* 3.3 33.0 - - - +
78D GLU* 1.3 78.1 - - + +
80D LYS* 1.3 66.7 + - + +
82D ILE* 2.9 31.2 + - + +
116D LEU* 5.6 4.9 - - - +
118D THR* 5.8 7.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN* 3.0 29.6 + - + +
77D GLU* 4.3 6.7 - - - +
79D VAL* 1.3 83.8 - - + +
81D ARG* 1.3 64.3 + - - +
82D ILE 3.6 4.0 - - - +
118D THR* 6.0 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ARG* 4.7 9.3 - - - +
77D GLU 3.0 20.0 + - - +
78D GLU* 3.3 25.4 + - - +
80D LYS* 1.3 75.2 - - - +
82D ILE* 1.3 98.3 + - - +
83D GLN* 3.2 18.3 + - - +
85D ILE* 4.8 5.5 - - - +
----------------------------------------------------------
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 4.6 12.6 - - + -
60C ARG* 3.3 41.3 - - + +
63C LEU* 3.7 21.1 - - + -
78D GLU* 2.7 38.5 + - + +
79D VAL* 2.9 26.7 - - + +
80D LYS 3.6 4.9 - - - +
81D ARG* 1.3 102.0 - - - +
83D GLN* 1.3 75.1 + - + +
116D LEU* 5.8 5.4 - - + +
140D VAL* 5.9 1.0 - - - +
----------------------------------------------------------
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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