Contacts of the helix formed by residues 54 - 84 (chain D) in PDB entry 2WP9
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 SER 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 4.9 0.9 + - - -
50D GLY 3.4 7.8 + - - -
51D PHE* 3.2 18.3 + - - -
53D ALA* 1.3 80.0 - - - +
55D ALA* 1.3 65.5 + - - +
56D PHE* 3.3 22.5 + - - +
57D THR* 3.0 8.4 + - - -
58D LYS* 2.9 21.7 + - - +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA 3.4 4.3 + - - -
54D SER* 1.3 71.5 + - - +
56D PHE* 1.3 64.3 + - - +
58D LYS* 4.5 8.5 - - - -
59D VAL* 3.0 33.0 + - + +
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Residues in contact with PHE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 3.4 41.5 - + - +
54D SER* 3.1 11.2 + - - +
55D ALA* 1.3 80.6 - - - +
57D THR* 1.3 62.8 + - - +
59D VAL* 3.9 3.6 - - - +
60D PHE* 3.0 51.6 + + + +
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Residues in contact with THR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D TYR* 2.5 32.0 + - + +
33D MET* 5.0 0.9 - - - -
51D PHE* 3.0 50.2 + - + +
52D PHE* 3.8 29.8 - - + -
54D SER* 3.0 8.3 + - - -
56D PHE* 1.3 78.8 - - - +
58D LYS* 1.3 60.9 + - - +
60D PHE* 4.0 0.3 - - - +
61D THR* 2.8 36.9 + - - +
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Residues in contact with LYS 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D PHE* 3.7 20.9 - - - +
53D ALA 3.7 20.2 + - - +
54D SER 2.9 12.5 + - - +
55D ALA* 3.8 7.4 - - - +
57D THR* 1.3 78.4 - - - +
59D VAL* 1.3 66.4 + - + +
61D THR* 3.7 3.8 - - - -
62D LEU* 3.0 31.7 + - + +
112D VAL* 3.4 45.3 + - + +
113D TRP* 5.1 6.7 + - - +
115D VAL* 3.9 18.5 + - - +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ALA* 3.0 21.3 + - + +
56D PHE* 3.9 2.9 - - - +
58D LYS* 1.3 78.0 - - + +
60D PHE* 1.3 67.4 + - - +
62D LEU* 3.0 8.9 + - - +
63D LEU* 2.9 31.5 + - + +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.3 15.3 - - + -
28D LEU* 3.8 14.6 - - + -
29D TYR* 3.5 44.2 - + + -
32D TYR* 3.8 29.2 - + + -
56D PHE* 3.0 48.8 + + + +
57D THR* 4.0 4.9 - - - +
59D VAL* 1.3 78.6 - - - +
61D THR* 1.3 56.9 + - - +
63D LEU* 3.3 16.2 + - + +
64D ALA* 2.9 27.9 + - + +
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Residues in contact with THR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU* 6.4 1.3 - - + -
48C LEU* 5.5 6.5 - - + -
29D TYR* 2.8 32.7 + - - +
52D PHE* 4.3 9.4 - - + -
57D THR* 2.8 32.2 + - - +
58D LYS* 3.7 4.9 - - - -
60D PHE* 1.3 77.4 - - - +
62D LEU* 1.3 58.1 + - + +
64D ALA* 3.2 3.5 + - - +
65D LEU* 3.0 40.7 + - + +
112D VAL* 4.6 19.1 - - + -
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LYS* 3.0 19.4 + - + +
59D VAL* 3.0 7.6 + - - +
61D THR* 1.3 72.6 - - + +
63D LEU* 1.3 67.4 + - - +
65D LEU* 3.1 12.4 + - + +
66D PHE* 3.1 32.0 + - + -
105D VAL* 4.4 4.9 - - + +
108D GLY 4.3 3.4 - - - -
109D PHE* 3.5 66.0 - - + +
112D VAL* 3.7 26.5 - - + -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 4.1 21.5 - - + -
59D VAL* 2.9 20.5 + - + +
60D PHE* 3.3 24.7 - - + +
62D LEU* 1.3 75.5 - - - +
64D ALA* 1.3 58.7 + - - +
66D PHE* 3.2 14.1 + - + +
67D SER* 2.9 38.1 + - - +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D VAL* 5.1 3.4 - - - -
26D LEU* 3.4 18.2 - - + +
29D TYR* 3.6 37.2 - - + -
60D PHE* 2.9 14.4 + - - +
61D THR 3.4 9.0 - - - +
63D LEU* 1.3 76.2 - - - +
65D LEU* 1.3 58.9 + - + +
67D SER* 3.2 2.4 + - - -
68D ILE* 2.8 36.4 + - + +
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Residues in contact with LEU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 5.0 4.3 - - + -
45C LEU* 3.8 32.1 - - + -
61D THR* 3.0 32.2 + - + +
62D LEU* 3.1 15.7 + - + +
64D ALA* 1.3 75.8 - - + +
66D PHE* 1.3 59.1 + - - +
68D ILE* 3.2 20.0 + - + +
69D LEU 2.9 22.5 + - - -
104D TYR* 4.2 14.1 - - + +
105D VAL* 3.6 25.4 - - + +
108D GLY* 3.6 32.8 - - - -
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Residues in contact with PHE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 3.1 28.8 + - + -
63D LEU* 3.6 14.1 - - + +
65D LEU* 1.3 75.4 - - - +
67D SER* 1.3 64.5 + - - +
69D LEU* 2.9 31.4 + - + +
70D ILE* 3.1 25.3 + - + +
105D VAL* 4.4 19.5 - - + -
109D PHE* 4.2 24.9 - + - -
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D THR* 3.7 23.2 - - - +
25D VAL* 3.3 24.0 - - - +
26D LEU* 3.7 23.6 - - - -
63D LEU* 2.9 20.0 + - - +
64D ALA 3.4 7.9 - - - -
66D PHE* 1.3 76.9 - - - +
68D ILE* 1.3 57.0 + - - +
70D ILE* 3.4 1.1 + - - -
71D HIS* 2.8 33.3 + - - +
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 6.1 1.1 - - + -
41C VAL* 4.7 33.4 - - + -
26D LEU* 3.7 26.9 - - + -
29D TYR* 6.2 1.8 - - + -
64D ALA* 2.8 29.4 + - + +
65D LEU* 3.7 20.0 - - + +
67D SER* 1.3 74.3 - - - +
69D LEU* 1.3 67.5 + - - +
71D HIS* 4.5 2.2 - - - +
72D ALA* 2.9 30.3 + - + +
101D LEU* 4.0 16.2 - - + -
104D TYR* 4.9 3.4 - - + -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU 2.9 13.1 + - - +
66D PHE* 2.9 25.7 + - + +
68D ILE* 1.3 76.6 - - - +
70D ILE* 1.3 67.9 + - + +
73D TRP* 3.1 29.8 + - + +
98D VAL* 4.8 3.4 - - + +
101D LEU* 3.4 43.3 - - + +
102D VAL* 4.1 18.6 - - + +
105D VAL* 4.0 16.2 - - + -
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Residues in contact with ILE 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 4.2 27.1 - - + -
22D THR* 4.1 16.8 - - + -
66D PHE* 3.1 24.0 + - + +
67D SER* 4.0 2.9 - - - +
69D LEU* 1.3 83.0 - - + +
71D HIS* 1.3 64.9 + - - +
73D TRP* 3.3 5.7 + - + +
74D ILE* 3.1 41.0 + - + +
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C HIS* 4.0 23.3 + + - -
19D VAL* 3.0 44.8 + - + +
22D THR* 3.0 19.2 + - - +
23D ALA* 3.8 20.9 + - + -
26D LEU* 4.5 12.8 - - + -
67D SER 2.8 21.2 + - - +
68D ILE* 4.4 0.9 - - - +
70D ILE* 1.3 73.6 - - - +
72D ALA* 1.3 63.4 + - + +
74D ILE* 3.4 3.3 + - - +
75D GLY* 3.0 24.0 + - - -
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Residues in contact with ALA 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C PHE* 4.4 16.6 - - + -
68D ILE* 2.9 25.7 + - + +
71D HIS* 1.3 81.7 - - + +
73D TRP* 1.3 60.2 + - - +
75D GLY* 4.2 1.6 - - - +
76D MET* 2.9 39.1 + - + +
101D LEU* 3.8 19.5 - - + -
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Residues in contact with TRP 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 3.1 25.2 + - + +
70D ILE* 3.7 4.5 - - + +
72D ALA* 1.3 74.9 - - - +
74D ILE* 1.3 73.8 + - + +
76D MET* 5.3 0.4 - - + -
77D TRP* 3.0 48.2 + + + +
80D LEU* 5.3 1.3 - - + -
94D GLN* 3.3 46.2 - - + -
97D ILE* 4.2 16.6 - - + -
98D VAL* 3.5 33.0 - - + -
101D LEU* 3.7 9.5 - - + +
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP* 3.9 36.6 - - + +
18D LEU* 3.7 19.1 - - + -
19D VAL* 3.3 47.3 - - + +
70D ILE* 3.1 21.8 + - + +
71D HIS 3.7 1.1 - - - +
73D TRP* 1.3 85.6 - - + +
75D GLY* 1.3 63.6 + - - +
77D TRP* 3.2 7.8 + - + +
78D GLN* 3.1 40.0 + - + +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 5.1 3.1 - - - -
71D HIS* 3.0 17.4 + - - -
72D ALA* 3.9 2.2 - - - -
73D TRP 3.2 0.2 - - - -
74D ILE* 1.3 81.6 - - - +
76D MET* 1.3 62.3 + - - +
78D GLN* 3.2 14.7 + - - +
79D VAL* 3.2 26.9 + - - +
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Residues in contact with MET 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLY 5.1 1.3 - - - +
35C VAL* 4.3 33.2 - - + -
38C PHE* 4.0 42.2 - - + -
72D ALA* 2.9 23.8 + - + +
73D TRP* 4.2 2.9 - - + +
75D GLY* 1.3 75.7 - - - +
77D TRP* 1.3 58.1 + - - +
79D VAL* 3.3 9.0 + - + +
80D LEU* 2.9 41.9 + - + +
97D ILE* 3.7 43.3 - - + -
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Residues in contact with TRP 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 3.6 30.3 - - + -
201B PHE* 3.8 21.1 - + - -
205B ARG* 3.5 17.3 - - - -
15D ASP* 4.2 14.8 - - - -
73D TRP* 3.0 47.2 + + + +
74D ILE* 3.4 7.6 - - + +
76D MET* 1.3 75.3 - - - +
78D GLN* 1.3 75.0 + - + +
80D LEU* 3.5 5.0 + - - +
81D THR* 2.8 47.4 + - + +
90D ARG* 5.5 2.0 - - - +
94D GLN* 3.4 25.5 - - - +
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Residues in contact with GLN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B PHE 6.1 0.9 - - - -
205B ARG* 3.3 31.4 + - - +
207B THR* 5.4 10.0 - - - +
31C ARG* 4.2 12.0 - - - +
15D ASP* 4.9 6.9 - - - +
19D VAL* 5.2 4.8 - - - +
74D ILE* 3.1 34.7 + - - +
75D GLY* 3.2 14.2 + - - +
77D TRP* 1.3 88.4 - - + +
79D VAL* 1.3 65.8 + - + +
81D THR* 3.2 11.6 + - - -
82D ASP* 3.3 5.0 + - - -
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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
----------------------------------------------------------
31C ARG* 3.8 37.2 - - + +
35C VAL* 4.3 23.3 - - + -
75D GLY 3.2 14.7 + - - +
76D MET* 3.3 13.2 + - + +
78D GLN* 1.3 77.0 - - + +
80D LEU* 1.3 70.1 + - + +
82D ASP* 2.9 14.4 + - - +
83D TYR* 3.2 34.5 + - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TRP* 5.3 1.1 - - + -
76D MET* 2.9 27.6 + - + +
77D TRP* 3.9 4.0 - - - +
79D VAL* 1.3 81.6 - - + +
81D THR* 1.3 56.8 + - - +
82D ASP 3.0 1.2 + - - -
83D TYR* 5.4 0.4 - - - -
84D VAL* 2.7 55.3 + - + +
90D ARG* 4.1 15.0 - - + +
93D LEU* 4.2 18.4 - - + -
94D GLN* 3.7 37.0 - - + +
97D ILE* 3.8 26.9 - - + -
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Residues in contact with THR 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN* 3.5 20.6 + - - +
168B LYS* 5.5 2.5 + - - -
201B PHE* 4.1 11.6 - - + -
205B ARG* 2.7 31.7 + - - -
77D TRP* 2.8 50.1 + - + +
78D GLN 3.2 1.1 + - - -
80D LEU* 1.3 74.8 - - - +
82D ASP* 1.3 58.6 + - - +
84D VAL 4.8 1.8 - - - -
85D LYS* 3.6 7.4 + - - +
90D ARG* 3.7 31.9 - - - +
94D GLN* 4.6 0.7 - - - +
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B SER* 5.2 6.2 + - - +
164B TRP* 3.5 35.0 - - + +
165B ASN* 2.9 14.4 + - - -
205B ARG* 2.5 33.1 + - - -
31C ARG* 2.9 35.1 + - - +
78D GLN 3.3 2.8 + - - -
79D VAL 2.9 10.3 + - - +
81D THR* 1.3 79.4 - - - +
83D TYR* 1.3 71.5 + - + +
84D VAL 3.7 0.2 - - - -
85D LYS* 3.6 19.8 + - - -
----------------------------------------------------------
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Residues in contact with TYR 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TRP* 3.5 44.5 + + - -
28C ILE* 4.3 11.9 - - + +
31C ARG* 3.0 45.2 + - - -
79D VAL* 3.2 29.7 + - + +
82D ASP* 1.3 83.8 - - + +
84D VAL* 1.3 68.0 + - + +
85D LYS* 3.9 4.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 2.7 41.3 + - + +
81D THR* 5.0 0.7 - - - -
82D ASP 3.7 0.4 - - - -
83D TYR* 1.3 80.7 - - + +
85D LYS* 1.3 63.1 + - - +
86D PRO* 4.2 5.8 - - + +
89D LEU* 4.1 22.7 - - + -
90D ARG* 3.1 56.9 + - + +
93D LEU* 4.2 9.6 - - + -
----------------------------------------------------------
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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