Contacts of the helix formed by residues 82 - 111 (chain D) in PDB entry 3BVI
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 GLY 82 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TRP* 3.5 21.9 - - - -
80D PHE 3.5 2.2 - - - -
81D GLU* 1.3 80.8 - - - +
83D LEU* 1.3 65.8 + - - -
84D THR* 3.4 2.5 - - - -
85D GLN* 3.3 5.5 + - - +
86D ILE* 3.1 23.6 + - - +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D TRP* 4.2 5.1 - - - -
31D CYS* 4.4 4.9 - - - -
36D LEU* 4.2 21.3 - - + +
39D ALA* 3.8 19.3 - - + -
82D GLY* 1.3 70.5 - - - -
84D THR* 1.3 66.2 + - - +
86D ILE* 3.2 6.1 + - + +
87D PHE* 3.1 56.9 + - + -
141D ILE* 4.1 18.4 - - + -
151D LEU* 3.6 35.8 - - + +
154D ALA* 4.2 21.5 - - + -
155D ASP* 4.7 6.7 - - - +
158D VAL* 5.8 1.8 - - + -
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLY 3.4 0.4 - - - -
83D LEU* 1.3 77.0 - - - +
85D GLN* 1.3 57.2 + - - +
87D PHE* 3.2 5.5 + - - +
88D GLN* 2.8 47.9 + - + +
138D LEU* 4.2 6.2 - - + +
141D ILE* 3.4 22.7 - - + +
142D GLU* 3.5 31.0 - - + +
146D ASN* 5.4 3.3 + - - -
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Residues in contact with GLN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LYS 4.9 1.2 - - - +
80D PHE* 3.2 33.0 - - - +
81D GLU* 3.0 54.5 + - + +
82D GLY 3.3 13.0 + - - +
84D THR* 1.3 77.5 - - - +
86D ILE* 1.3 57.3 + - - +
88D GLN* 3.4 17.1 + - + +
89D LYS* 3.0 51.0 + - + +
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Residues in contact with ILE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET* 3.5 30.2 - - + +
30D TRP* 3.4 38.8 - - + -
31D CYS* 3.9 13.2 - - - -
43D LEU* 4.0 20.6 - - + -
80D PHE* 3.6 33.2 - - + -
82D GLY 3.1 12.1 + - - +
83D LEU* 3.2 8.9 + - - +
85D GLN* 1.3 77.6 - - - +
87D PHE* 1.3 69.0 + - + +
89D LYS* 3.4 0.8 + - - -
90D ALA* 2.8 27.8 + - + +
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Residues in contact with PHE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ALA* 4.2 11.9 - - + -
42D PHE* 4.1 17.7 - + - -
43D LEU* 4.2 17.3 - - + -
83D LEU* 3.1 46.6 + - + +
84D THR 3.2 3.1 + - - +
86D ILE* 1.3 83.8 - - + +
88D GLN* 1.3 60.3 + - - +
90D ALA* 4.0 2.1 - - + +
91D TYR* 3.0 30.1 + - - +
134D PHE* 3.9 34.2 - + - -
137D ILE* 3.6 27.4 - - + -
138D LEU* 3.8 17.3 - - + +
141D ILE* 3.6 22.7 - - + -
158D VAL* 4.6 4.3 - - + -
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Residues in contact with GLN 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D THR* 2.8 27.4 + - - +
85D GLN* 3.6 18.6 + - - +
87D PHE* 1.3 77.4 - - - +
89D LYS* 1.3 57.6 + - + +
91D TYR* 3.4 1.9 + - - +
92D GLU* 3.0 40.4 + - + +
138D LEU* 3.9 23.3 - - + +
142D GLU* 3.5 21.4 + - - -
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Residues in contact with LYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 5.6 1.5 - - + +
27D MET* 3.8 11.9 - - + -
77D GLU* 4.0 28.6 + - + +
79D LYS 5.1 1.2 + - - -
80D PHE* 4.3 19.1 - - + -
85D GLN* 3.0 39.3 + - + +
86D ILE 3.6 4.0 - - - +
88D GLN* 1.3 77.5 - - + +
90D ALA* 1.3 56.3 + - - +
92D GLU* 3.4 11.9 + - - +
93D HIS* 2.9 28.8 + - - +
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Residues in contact with ALA 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 3.4 18.3 + - + -
27D MET* 3.9 9.6 - - + +
43D LEU* 5.1 1.6 - - + -
86D ILE* 2.8 18.2 + - + +
87D PHE* 4.0 4.9 - - + +
89D LYS* 1.3 77.6 - - - +
91D TYR* 1.3 56.9 + - - +
93D HIS* 3.1 6.7 + - - +
94D GLU* 2.8 34.2 + - - +
134D PHE* 3.6 29.4 - - + -
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE 3.0 20.0 + - - +
88D GLN 3.8 2.7 - - - +
90D ALA* 1.3 76.2 - - - +
92D GLU* 1.3 64.5 + - + +
94D GLU* 3.3 2.5 + - + +
95D GLN* 3.0 48.7 + - + +
131D GLU* 3.5 40.1 + - + -
134D PHE* 4.2 15.1 - - + +
135D LYS* 3.6 22.8 - - + +
138D LEU* 4.1 13.5 - - + -
1E MET* 3.4 27.0 - - + +
1001E ASP 4.8 1.9 + - - -
1002E GLN* 3.6 36.6 - - + +
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Residues in contact with GLU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN* 3.0 27.9 + - + +
89D LYS* 3.7 10.5 - - - +
91D TYR* 1.3 76.0 - - + +
93D HIS* 1.3 60.3 + - - +
95D GLN* 3.4 20.1 + - - +
96D HIS* 3.2 21.7 + - - +
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Residues in contact with HIS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LYS 5.2 0.9 - - - -
19D ASN* 4.4 15.5 - - - -
20D SER* 2.7 33.6 + - - -
23D LEU* 4.0 22.8 - - + +
24D TYR* 3.6 25.6 - + - -
89D LYS 2.9 18.6 + - - +
90D ALA* 3.1 8.3 + - - +
92D GLU* 1.3 74.1 - - - +
94D GLU* 1.3 67.1 + - - +
96D HIS* 3.1 16.8 + + - +
97D ILE* 3.0 39.4 + - + +
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Residues in contact with GLU 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 2.4 33.4 + - - +
46D HIS* 3.0 20.9 + - - -
50D GLU* 3.4 1.6 - - - +
90D ALA 2.8 16.1 + - - +
91D TYR* 3.8 6.5 - - + +
93D HIS* 1.3 75.8 - - - +
95D GLN* 1.3 57.1 + - - +
97D ILE* 3.3 3.7 + - - +
98D SER* 2.9 17.6 + - - -
127D GLN* 2.9 34.0 + - - +
130D GLU* 3.8 4.4 - - - +
131D GLU* 4.2 17.9 - - + -
134D PHE* 3.9 21.8 - - + -
1007D FE 2.3 27.2 - - - -
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Residues in contact with GLN 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.0 56.3 + - + +
92D GLU* 3.5 21.5 - - - +
94D GLU* 1.3 76.6 - - - +
96D HIS* 1.3 56.7 + - - +
98D SER* 3.2 4.0 + - - -
99D GLU* 3.0 31.0 + - - +
131D GLU* 3.5 23.6 - - - +
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Residues in contact with HIS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LYS* 3.3 37.6 + - + -
92D GLU 3.2 9.8 + - - +
93D HIS* 3.1 19.5 + + - +
95D GLN* 1.3 77.7 - - - +
97D ILE* 1.3 67.9 + - + +
99D GLU* 3.3 18.2 + - + +
100D SER* 2.9 28.3 + - - -
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 4.0 8.7 - - - +
16D LYS* 4.1 29.6 - - + +
17D GLU* 3.9 20.2 - - - +
20D SER* 4.0 15.7 - - - +
50D GLU* 5.5 1.6 - - - +
93D HIS* 3.0 37.2 + - + +
94D GLU* 3.7 9.6 - - - +
96D HIS* 1.3 86.7 - - + +
98D SER* 1.3 57.6 + - - +
100D SER* 2.6 20.2 + - - +
101D ILE* 2.9 19.3 + - + +
127D GLN* 3.7 24.9 - - - +
1006D FE 3.9 1.1 - - - -
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Residues in contact with SER 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLU 2.9 8.3 + - - -
95D GLN* 3.4 9.6 - - - -
97D ILE* 1.3 76.0 - - - +
99D GLU* 1.3 55.9 + - - +
101D ILE* 3.3 5.6 + - - +
102D ASN* 3.0 38.9 + - - +
127D GLN* 3.3 29.9 + - - +
128D HIS* 5.0 0.9 + - - -
131D GLU* 2.5 30.7 + - - -
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Residues in contact with GLU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN* 3.0 13.3 + - - +
96D HIS* 3.4 20.0 - - + +
98D SER* 1.3 74.6 - - - +
100D SER* 1.3 63.0 + - - +
102D ASN* 3.3 11.9 + - + +
103D ASN* 3.0 24.0 + - - +
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Residues in contact with SER 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 3.2 27.1 + - - -
16D LYS* 3.9 22.2 - - - +
96D HIS* 2.9 17.0 + - - -
97D ILE* 2.6 23.6 + - - -
99D GLU* 1.3 76.1 - - - +
101D ILE* 1.3 60.3 + - - +
103D ASN* 3.3 12.0 + - - +
104D ILE* 3.2 23.2 + - - +
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Residues in contact with ILE 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 3.7 8.5 - - - +
97D ILE* 2.9 18.4 + - + +
98D SER 3.3 5.8 + - - +
100D SER* 1.3 72.9 - - - +
102D ASN* 1.3 64.5 + - - +
104D ILE* 3.0 11.0 + - + +
105D VAL* 3.0 24.9 + - + +
120D LEU* 5.1 4.5 - - + -
123D TYR* 3.5 50.5 - - + +
124D VAL* 3.7 28.7 - - + -
127D GLN* 3.6 36.3 - - + -
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Residues in contact with ASN 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D SER* 3.0 26.6 + - - +
99D GLU* 3.6 11.1 - - + +
101D ILE* 1.3 76.6 - - - +
103D ASN* 1.3 57.2 + - - +
105D VAL* 3.4 2.7 + - - +
106D ASP* 2.9 31.4 + - - +
124D VAL* 5.0 3.8 - - - +
112E LYS* 3.2 33.9 + - + +
113E ASP* 4.8 3.2 + - - +
114E HIS* 3.5 32.0 + - + +
115E ALA* 4.3 5.4 + - - +
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 4.0 22.2 - - - +
99D GLU 3.0 13.2 + - - +
100D SER* 3.3 14.6 + - - +
102D ASN* 1.3 74.0 - - - +
104D ILE* 1.3 64.7 + - - +
106D ASP* 3.4 5.1 + - - +
107D HIS* 3.0 57.6 + - - -
112E LYS* 4.4 16.9 + - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.2 12.5 - - + +
9D LEU* 3.9 38.6 - - + +
10D LEU* 4.1 20.4 - - + -
13D GLN* 3.6 43.1 - - + +
100D SER 3.2 13.1 + - - +
101D ILE* 3.0 11.1 + - + +
103D ASN* 1.3 74.5 - - + +
105D VAL* 1.3 59.1 + - - +
107D HIS* 3.1 4.2 + - - +
108D ALA* 2.9 27.0 + - - +
116D THR* 5.1 0.2 - - + -
120D LEU* 3.9 24.7 - - + -
123D TYR* 5.4 0.4 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.0 20.7 + - + +
102D ASN* 3.8 4.3 - - - +
104D ILE* 1.3 75.7 - - - +
106D ASP* 1.3 61.1 + - - +
108D ALA* 3.2 9.2 + - - +
109D ILE* 3.1 22.5 + - - +
117D PHE* 3.5 20.8 - - + -
120D LEU* 3.9 23.6 - - + -
121D GLN* 4.6 4.3 - - - +
124D VAL* 3.8 26.7 - - + -
114E HIS* 3.4 38.1 - - + +
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Residues in contact with ASP 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASN 2.9 18.3 + - - +
103D ASN 3.7 4.5 - - - +
105D VAL* 1.3 77.9 - - - +
107D HIS* 1.3 62.1 + - - +
109D ILE* 3.3 11.2 + - - +
110D LYS* 3.0 61.5 + - - +
109E ILE* 4.4 10.2 - - - +
112E LYS* 3.5 39.0 + - + +
114E HIS* 4.0 8.7 + - - +
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Residues in contact with HIS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASP* 5.7 8.3 - - + -
6D ILE* 4.4 5.8 - - + -
9D LEU* 3.8 24.4 - - + +
103D ASN* 3.0 46.6 + - - +
104D ILE 3.5 7.4 - - - +
106D ASP* 1.3 79.5 + - - +
108D ALA* 1.3 60.5 + - - +
110D LYS* 3.4 16.7 + - + +
111D SER* 3.0 32.9 + - - -
112E LYS* 5.8 1.3 - - - -
----------------------------------------------------------
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.0 17.6 - - + +
104D ILE 2.9 13.1 + - - +
105D VAL* 3.5 13.2 - - - +
107D HIS* 1.3 77.2 - - - +
109D ILE* 1.3 60.3 + - - +
111D SER* 3.4 3.0 + - - -
112D LYS* 3.0 3.3 + - - -
113D ASP* 2.9 47.0 + - + +
114D HIS* 5.6 0.2 - - - -
116D THR* 4.5 5.8 - - + -
117D PHE* 4.1 17.5 - - - +
120D LEU* 5.0 0.2 - - + -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL 3.1 13.3 + - - +
106D ASP* 3.3 12.5 + - - +
108D ALA* 1.3 75.5 - - - +
110D LYS* 1.3 67.4 + - + +
112D LYS* 3.2 16.8 + - - +
114D HIS* 4.6 19.7 + - + -
117D PHE* 3.6 22.9 - - + -
109E ILE* 4.1 31.9 - - + -
114E HIS* 3.5 34.5 - - + +
----------------------------------------------------------
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Residues in contact with LYS 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D ASP* 3.0 48.5 + - - +
107D HIS* 3.8 18.6 - - + +
108D ALA 3.3 0.2 - - - -
109D ILE* 1.3 81.4 - - + +
111D SER* 1.3 57.9 + - - +
112D LYS* 3.3 6.9 + - - +
112E LYS* 4.8 7.3 - - - +
----------------------------------------------------------
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Residues in contact with SER 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 4.8 9.0 + - - -
6D ILE* 4.1 10.1 - - - +
107D HIS 3.0 19.3 + - - -
108D ALA* 3.7 5.0 + - - -
110D LYS* 1.3 75.1 - - - +
112D LYS* 1.3 70.2 + - - +
113D ASP* 3.2 14.0 + - - +
----------------------------------------------------------
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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