Contacts of the helix formed by residues 58 - 87 (chain D) in PDB entry 1F33
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 ASN 58 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.5 33.1 - - + +
56D GLY 3.4 0.4 + - - -
57D ALA* 1.3 76.2 - - + +
59D PHE* 1.3 64.3 + - - +
60D ILE 3.7 0.7 - - - -
61D ALA* 3.4 21.2 - - - +
62D VAL* 3.2 30.0 + - + +
114D VAL* 4.3 2.3 - - + +
115D GLN* 5.9 3.8 - - - +
118D LEU* 5.8 0.2 - - - +
165D ASN* 3.2 31.7 + - - +
57E ALA* 5.3 0.9 - - - +
58E ASN* 3.6 34.8 - - + +
59E PHE 4.2 0.2 - - - +
60E ILE* 4.5 2.3 - - - +
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 4.1 11.4 - + - -
161A PHE* 3.6 35.7 - + - -
164A SER* 3.0 44.4 - - - +
165A ASN* 3.4 17.9 + - - +
51D HIS 4.6 1.1 - - - -
54D MET* 3.4 40.5 - - + +
56D GLY 3.2 8.8 + - - +
58D ASN* 1.3 75.5 - - - +
60D ILE* 1.3 77.0 + - + +
62D VAL* 3.3 2.8 + - - +
63D HIS* 2.7 68.6 + + + +
114D VAL* 4.2 7.0 - - + -
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 4.8 2.9 - - - +
61A ALA* 3.7 34.1 - - + +
62A VAL 4.7 0.9 - - - +
65A MET* 4.0 17.9 - - + -
161A PHE* 3.4 42.4 - - + -
165A ASN* 3.2 23.5 + - - +
59D PHE* 1.3 88.3 - - + +
61D ALA* 1.3 60.8 + - - +
63D HIS* 3.4 3.2 - - + +
64D GLU* 2.9 59.1 + - + +
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 4.2 10.1 - - + -
602A TRS 5.6 6.1 + - - +
58D ASN* 3.4 20.7 + - - +
59D PHE 3.3 0.8 - - - -
60D ILE* 1.3 81.7 - - - +
62D VAL* 1.3 57.8 + - - +
64D GLU* 4.0 7.1 - - - +
65D MET* 2.9 31.1 + - - +
60E ILE* 3.7 20.0 - - + +
61E ALA* 4.2 16.6 - - + -
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D MET* 3.4 30.7 - - + -
58D ASN* 3.2 38.4 + - - +
59D PHE 3.3 2.1 + - - +
61D ALA* 1.3 73.6 - - - +
63D HIS* 1.3 66.0 + - - +
65D MET* 3.2 9.0 + - + +
66D LEU* 2.9 30.8 + - + +
114D VAL* 4.3 11.4 - - + -
118D LEU* 3.8 23.3 - - + -
165D ASN* 4.2 19.1 - - + +
60E ILE* 4.9 1.6 - - + -
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Residues in contact with HIS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 3.9 21.5 - + - -
161A PHE* 3.9 33.0 - + - -
51D HIS* 2.6 85.6 + + - +
52D TRP* 4.6 2.2 - + - -
54D MET* 4.1 7.6 - - - -
59D PHE* 2.7 39.7 + + + +
60D ILE* 3.4 8.5 - - + +
62D VAL* 1.3 74.6 - - - +
64D GLU* 1.3 67.5 + - + +
66D LEU* 3.6 2.2 + - - +
67D ASP 3.4 5.5 + - - -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 4.8 4.6 - - + -
602A TRS 3.3 43.6 + - - +
51D HIS* 5.0 0.2 - - - -
60D ILE* 2.9 43.1 + - + +
61D ALA* 4.0 5.6 - - - +
63D HIS* 1.3 78.9 - - + +
65D MET* 1.3 67.2 + - - +
67D ASP* 3.1 17.8 + - - +
68D GLY* 3.2 10.4 + - - -
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Residues in contact with MET 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ALA 2.9 19.3 + - - +
62D VAL* 3.5 15.9 - - + +
64D GLU* 1.3 76.7 - - - +
66D LEU* 1.3 76.6 + - + +
68D GLY* 3.0 13.1 + - - -
69D PHE* 3.1 51.3 + - + -
118D LEU* 5.1 2.0 - - + -
161D PHE* 4.0 17.0 - - + +
162D ILE* 4.4 8.5 - - + -
165D ASN* 3.6 29.2 - - - +
60E ILE* 3.9 24.9 - - + -
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Residues in contact with LEU 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 3.3 26.1 - - + +
51D HIS* 4.0 22.0 - - + +
54D MET* 3.4 33.9 - - + -
62D VAL* 2.9 24.6 + - + +
63D HIS 3.8 3.8 - - - +
65D MET* 1.3 83.5 - - + +
67D ASP* 1.3 63.4 + - - +
69D PHE* 3.0 35.3 + - + +
70D ARG 3.0 10.0 + - - -
118D LEU* 5.5 0.4 - - + -
121D LEU* 3.7 27.6 - - + -
125D TYR* 5.1 0.9 - - - +
162D ILE* 4.8 5.6 - - + -
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Residues in contact with ASP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 5.4 0.2 - - - -
48D LYS* 2.8 33.6 + - - +
51D HIS* 3.9 19.7 + - + -
63D HIS 3.4 3.0 + - - +
64D GLU* 3.1 12.4 + - - +
66D LEU* 1.3 78.4 - - - +
68D GLY* 1.3 63.1 + - - +
70D ARG* 3.2 23.7 + - - +
71D THR* 3.3 17.3 + - - -
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Residues in contact with GLY 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU 3.2 5.3 + - - -
65D MET* 3.0 9.7 + - - -
67D ASP* 1.3 81.0 - - - +
69D PHE* 1.3 63.0 + - - +
71D THR* 3.2 17.8 + - - -
72D ALA* 3.2 12.3 + - - +
158D PHE* 5.6 0.4 - - - -
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Residues in contact with PHE 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D THR* 4.5 0.2 - - + -
65D MET* 3.1 41.5 + - + -
66D LEU* 3.0 21.8 + - + +
68D GLY* 1.3 76.3 - - - +
70D ARG* 1.3 53.5 + - - +
72D ALA* 3.0 4.2 + - - +
73D LEU* 2.7 38.6 + - - +
125D TYR* 3.6 26.5 - + - +
158D PHE* 3.3 52.0 - + + -
161D PHE* 3.7 29.6 - + + -
162D ILE* 3.8 24.5 - - + -
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Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D SER* 4.1 24.8 + - - +
47D THR* 4.4 7.3 - - + +
48D LYS* 3.0 46.8 - - + +
52D TRP* 5.5 3.4 - - - -
66D LEU 3.0 11.6 + - - +
67D ASP* 3.3 22.5 + - - +
69D PHE* 1.3 77.1 - - - +
71D THR* 1.3 68.6 + - - +
73D LEU* 3.3 11.0 + - - +
74D ILE* 3.0 46.7 + - - +
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Residues in contact with THR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ASP* 3.3 13.6 + - - -
68D GLY* 3.2 12.1 + - - -
70D ARG* 1.3 86.4 + - - +
72D ALA* 1.3 62.8 + - - +
74D ILE* 3.3 6.3 + - - +
75D ASP* 3.1 35.0 + - - +
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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
----------------------------------------------------------
68D GLY 3.2 6.2 + - - +
69D PHE 3.0 8.1 + - - +
71D THR* 1.3 76.1 - - - +
73D LEU* 1.3 67.0 + - - +
75D ASP* 3.1 17.8 + - - +
76D HIS* 3.1 21.9 + - + -
154D ASP* 4.2 12.6 - - - +
158D PHE* 3.6 27.6 - - + -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 3.9 21.4 - - + +
43D LEU* 4.1 14.6 - - + -
44D SER* 3.8 25.4 - - - +
47D THR* 3.8 10.3 - - - +
69D PHE 2.7 23.3 + - - +
70D ARG* 3.5 5.8 - - - +
72D ALA* 1.3 72.1 - - - +
74D ILE* 1.3 59.6 + - - +
76D HIS* 3.3 4.5 + - + +
77D LEU* 2.9 32.9 + - - +
125D TYR* 3.4 23.8 - - - +
155D LEU* 4.1 27.8 - - + -
158D PHE* 4.1 17.3 - - + -
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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
----------------------------------------------------------
44D SER* 4.6 10.8 - - - +
70D ARG* 3.0 46.7 + - - +
71D THR* 3.6 7.9 - - - +
73D LEU* 1.3 78.1 - - - +
75D ASP* 1.3 64.2 + - - +
77D LEU* 3.4 17.1 - - + +
78D ASP* 2.8 45.2 + - - +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D THR* 3.1 26.8 + - - +
72D ALA* 3.1 11.2 + - - +
74D ILE* 1.3 77.9 - - - +
76D HIS* 1.3 66.0 + - + +
78D ASP* 3.4 8.3 + - - +
79D THR* 2.8 29.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PHE* 4.0 10.5 - + + -
72D ALA* 3.1 28.7 + - + +
73D LEU* 3.8 7.6 - - + +
75D ASP* 1.3 76.1 - - + +
77D LEU* 1.3 65.0 + - - +
79D THR* 2.9 11.2 + - - -
80D MET* 2.9 28.6 + - + +
147D ILE* 4.7 3.4 + - + +
150D ALA* 3.4 32.9 - - + +
151D ALA* 3.4 29.6 + - + +
154D ASP* 2.7 36.1 + - + +
155D LEU* 5.5 1.3 - - + -
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 4.1 12.2 - - + +
40D PHE* 4.1 13.0 - - + +
41D ILE* 3.3 54.1 - - + +
44D SER* 4.7 1.8 - - - +
73D LEU 2.9 16.1 + - - +
74D ILE* 3.4 22.7 - - + +
76D HIS* 1.3 76.8 - - - +
78D ASP* 1.3 82.0 + - - +
80D MET* 3.1 18.4 + - - +
81D ALA* 2.9 23.5 + - + +
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Residues in contact with ASP 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE* 2.8 35.2 + - - +
75D ASP* 3.8 7.3 - - - +
77D LEU* 1.3 91.0 - - - +
79D THR* 1.3 57.7 + - - +
81D ALA* 3.3 6.4 + - - +
82D GLU* 2.9 45.3 + - + +
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASP 2.8 19.2 + - - -
76D HIS* 2.9 13.2 + - - -
78D ASP* 1.3 78.9 - - - +
80D MET* 1.3 61.6 + - - +
82D GLU* 3.3 10.6 + - - +
83D ARG* 3.0 21.5 + - - +
147D ILE* 3.8 32.0 - - + +
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Residues in contact with MET 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 3.6 22.9 - - + +
36D GLN* 3.6 28.9 - - + -
37D VAL* 4.0 11.7 - - + +
40D PHE* 3.6 47.1 - - + -
76D HIS* 2.9 13.0 + - + +
77D LEU* 3.1 20.8 + - - +
79D THR* 1.3 75.0 - - - +
81D ALA* 1.3 64.1 + - - +
83D ARG* 3.1 6.5 + - - +
84D ALA* 3.0 20.6 + - - +
147D ILE* 3.6 20.0 - - + -
148D LEU* 3.8 17.3 - - - -
151D ALA* 5.0 4.3 - - - -
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 3.8 18.3 - - + +
77D LEU* 2.9 15.9 + - + +
78D ASP* 3.6 11.9 - - - +
80D MET* 1.3 76.7 - - - +
82D GLU* 1.3 62.8 + - + +
84D ALA* 3.2 6.7 + - - +
85D VAL* 3.1 26.5 + - - +
91D ALA* 3.8 22.2 - - + +
----------------------------------------------------------
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ASP* 2.9 30.1 + - + +
79D THR* 3.7 8.0 - - - +
81D ALA* 1.3 76.7 - - + +
83D ARG* 1.3 57.9 + - - +
85D VAL* 3.3 8.2 + - - +
86D GLN* 2.9 50.1 + - - +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASN* 4.6 10.5 - - - +
21D VAL* 4.9 4.2 - - - +
33D LEU* 3.5 17.3 - - + -
79D THR 3.0 13.6 + - - +
80D MET* 3.1 9.2 + - - +
82D GLU* 1.3 76.5 - - - +
84D ALA* 1.3 63.6 + - - +
86D GLN* 3.2 29.2 + - - +
87D LEU* 3.2 45.2 + - + +
141D ASP* 2.7 39.4 + - - -
143D ASP* 3.3 31.0 + - - +
144D THR* 3.6 9.3 + - - +
147D ILE* 3.6 25.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.6 26.6 - - + +
33D LEU* 3.4 21.9 - - + +
34D ASN* 4.6 10.1 - - - +
37D VAL* 6.1 0.4 - - + -
80D MET 3.0 12.1 + - - +
81D ALA* 3.4 11.7 - - - +
83D ARG* 1.3 77.3 - - - +
85D VAL* 1.3 62.5 + - - +
87D LEU* 3.1 8.6 + - - -
88D GLY 3.5 0.2 + - - -
89D GLY* 3.0 21.4 + - - -
91D ALA* 4.9 7.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 6.4 1.8 - - + -
81D ALA 3.1 14.0 + - - +
82D GLU* 3.7 9.6 - - - +
83D ARG 3.3 0.2 - - - -
84D ALA* 1.3 76.9 - - - +
86D GLN* 1.3 62.6 + - + +
88D GLY* 3.0 14.2 + - - -
89D GLY 3.7 13.2 - - - +
90D VAL* 4.9 0.7 - - - -
91D ALA* 4.0 26.5 - - + +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 4.0 19.1 + - - +
19D ASN* 4.2 11.7 + - - +
82D GLU* 2.9 48.1 + - - +
83D ARG* 3.4 36.6 + - - +
85D VAL* 1.3 78.0 - - + +
87D LEU* 1.3 59.2 + - - +
88D GLY 3.3 2.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.9 4.0 - - - +
17D THR* 4.5 1.8 - - - -
19D ASN* 4.2 11.0 - - - +
21D VAL* 3.8 34.8 - - + -
26D LYS* 3.1 42.0 - - + +
29D THR* 3.3 42.0 - - + +
30D VAL* 4.2 8.7 - - + +
33D LEU* 4.9 0.7 - - + -
83D ARG* 3.2 39.4 + - + +
84D ALA 3.1 9.4 + - - +
86D GLN* 1.3 75.8 - - - +
88D GLY* 1.3 58.4 + - - +
89D GLY 3.4 1.2 + - - -
141D ASP* 4.2 4.5 - - + +
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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