Contacts of the helix formed by residues 98 - 141 (chain C) in PDB entry 3UED
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 LEU 98 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 6.1 1.3 - - + -
93A PHE* 3.4 60.3 - - + +
94A GLU* 3.3 4.6 + - - +
96A LEU* 2.9 27.9 + - + +
97A THR 5.1 0.2 - - - -
98A LEU* 3.9 27.4 - - + -
101A PHE* 3.9 22.7 - - + -
10C TRP* 6.1 4.3 - - + -
97C THR* 1.3 69.7 - - - +
99C GLY* 1.3 58.0 + - - +
101C PHE* 4.2 11.2 - - + -
102C LEU* 2.6 47.3 + - + +
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Residues in contact with GLY 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 2.9 41.4 + - - +
97C THR* 4.1 0.4 - - - -
98C LEU* 1.3 75.6 - - - +
100C GLU* 1.3 63.7 + - - +
102C LEU* 3.3 2.4 + - - +
103C LYS* 2.8 26.0 + - - +
106C ARG* 4.6 2.5 + - - -
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C LYS* 2.9 31.1 + - - -
96C LEU* 3.7 18.3 - - + +
97C THR* 3.0 45.4 + - - +
99C GLY* 1.3 76.0 - - - +
101C PHE* 1.3 61.8 + - - +
103C LYS* 3.2 7.8 + - - +
104C LEU* 3.0 29.1 + - + +
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Residues in contact with PHE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.0 24.0 - - + -
10C TRP* 3.7 52.3 - + + -
13C PHE* 3.6 48.2 - + - -
93C PHE* 3.7 23.8 - + - -
96C LEU* 4.3 11.6 - - + +
97C THR 2.8 17.2 + - - +
98C LEU* 3.1 12.8 + - + +
100C GLU* 1.3 72.1 - - - +
102C LEU* 1.3 74.4 + - + +
104C LEU* 3.1 9.1 + - + +
105C ASP* 3.0 22.8 + - + +
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 4.9 8.1 - - - +
6A LEU* 4.5 23.3 - - + -
93A PHE* 4.7 17.3 - - + -
94A GLU* 3.9 22.9 - - - +
10C TRP* 4.6 16.4 - - + -
98C LEU* 2.6 29.9 + - + +
99C GLY* 3.9 3.1 - - - +
101C PHE* 1.3 85.1 - - + +
103C LYS* 1.3 62.7 + - - +
105C ASP* 3.3 7.3 + - + +
106C ARG* 3.0 46.2 + - - +
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY 2.8 22.0 + - - +
100C GLU* 3.4 8.3 - - - +
102C LEU* 1.3 70.7 - - - +
104C LEU* 1.3 62.5 + - + +
106C ARG* 3.2 25.9 + - + +
107C GLU* 3.1 21.3 + - + +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PHE* 4.4 14.4 - - + -
59C PHE* 3.3 37.8 - - + -
85C ALA* 4.6 10.5 - - + -
89C VAL* 4.0 32.3 - - + -
96C LEU* 4.2 29.4 - - + -
100C GLU* 3.0 19.8 + - + +
101C PHE* 3.1 7.2 + - - +
103C LYS* 1.3 75.6 - - + +
105C ASP* 1.3 60.0 + - - +
107C GLU* 3.2 5.6 + - - +
108C ARG 3.0 22.9 + - - -
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Residues in contact with ASP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TRP* 2.6 37.8 + - - -
13C PHE* 4.1 13.2 - - + -
101C PHE* 3.0 20.0 + - + +
102C LEU* 3.3 10.3 + - + +
104C LEU* 1.3 74.2 - - - +
106C ARG* 1.3 67.0 + - - +
108C ARG* 3.4 30.4 + - - -
109C ALA* 3.0 22.9 + - - +
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Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 5.2 6.9 + - - -
99C GLY* 4.6 2.4 + - - -
102C LEU* 3.0 36.8 + - - +
103C LYS* 3.5 32.8 - - - +
104C LEU 3.2 0.2 - - - -
105C ASP* 1.3 76.4 - - - +
107C GLU* 1.3 64.5 + - - +
109C ALA* 3.0 9.4 + - - +
110C LYS* 3.0 22.0 + - - +
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Residues in contact with GLU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 4.1 6.0 - - + -
83C GLY 4.9 4.5 - - - +
85C ALA* 3.4 31.9 + - - +
103C LYS* 3.1 13.8 + - + +
104C LEU* 3.2 11.6 + - - +
106C ARG* 1.3 75.8 - - - +
108C ARG* 1.3 57.2 + - - +
110C LYS* 3.3 8.2 + - + +
111C ASN* 2.8 45.0 + - - +
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ALA* 2.8 30.9 + - - +
10C TRP* 4.4 1.2 - - - -
12C PRO* 3.7 22.3 - - - +
13C PHE* 3.6 25.7 - - - -
58C PHE* 3.3 25.6 + - - +
59C PHE* 3.9 32.7 - - + +
61C PHE* 3.6 14.2 - - + -
104C LEU 3.0 16.8 + - - +
105C ASP* 3.4 25.2 + - - +
107C GLU* 1.3 75.1 - - - +
109C ALA* 1.3 58.8 + - - +
111C ASN* 3.1 3.1 + - - +
112C LYS* 2.9 26.2 + - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ASP* 3.0 12.7 + - - +
106C ARG* 3.0 12.8 + - - +
108C ARG* 1.3 77.3 - - - +
110C LYS* 1.3 61.8 + - - +
112C LYS* 3.3 9.8 + - - +
113C ILE* 3.1 30.5 + - + +
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ARG 3.0 11.3 + - - +
107C GLU* 3.7 12.1 - - + +
109C ALA* 1.3 74.4 - - - +
111C ASN* 1.3 60.7 + - - +
112C LYS 3.2 0.2 + - - -
113C ILE* 3.2 11.5 + - - +
114C ALA* 2.8 29.7 + - - +
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Residues in contact with ASN 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 3.1 48.6 + - - +
60C CYS* 3.7 17.0 - - - +
61C PHE* 4.0 7.5 - - + -
84C CYS* 5.7 1.0 - - - +
85C ALA 5.5 1.4 - - - +
107C GLU* 2.8 34.5 + - - +
108C ARG 3.1 3.3 + - - +
110C LYS* 1.3 74.4 - - - +
112C LYS* 1.3 57.6 + - - +
114C ALA* 3.2 9.0 + - - +
115C LYS* 2.9 29.1 + - - +
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 3.6 35.4 - - + -
108C ARG 2.9 12.5 + - - +
109C ALA* 3.5 11.9 - - - +
111C ASN* 1.3 73.7 - - - +
113C ILE* 1.3 62.2 + - + +
115C LYS* 3.1 5.3 + - + +
116C GLU* 2.9 55.8 + - - +
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Residues in contact with ILE 113 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ALA* 3.1 16.9 + - + +
110C LYS* 3.5 11.2 - - - +
112C LYS* 1.3 78.6 - - + +
114C ALA* 1.3 66.5 + - - +
115C LYS 3.0 0.3 + - - -
116C GLU* 3.1 13.6 + - - +
117C THR* 2.8 34.1 + - - +
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Residues in contact with ALA 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LYS 2.8 17.4 + - - +
111C ASN* 3.2 11.6 + - - +
113C ILE* 1.3 76.0 - - - +
115C LYS* 1.3 56.6 + - - +
117C THR* 3.7 5.3 - - - +
118C ASN* 2.9 31.1 + - - +
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Residues in contact with LYS 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLN* 5.3 3.8 - - - +
60C CYS 5.3 1.6 - - - +
61C PHE* 4.0 37.2 - - + +
62C LYS* 5.7 0.7 - - - -
63C GLU* 5.3 7.4 - - - +
111C ASN 2.9 13.8 + - - +
112C LYS* 3.6 8.7 - - + +
113C ILE 3.1 0.2 - - - -
114C ALA* 1.3 73.2 - - - +
116C GLU* 1.3 69.7 + - + +
118C ASN* 3.3 5.6 + - + +
119C ASN* 3.0 46.0 + - - +
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Residues in contact with GLU 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C LYS* 2.9 56.7 + - - +
113C ILE* 3.7 12.3 + - - +
115C LYS* 1.3 78.2 - - + +
117C THR* 1.3 61.9 + - - +
119C ASN* 3.2 10.2 + - - +
120C LYS* 3.0 39.6 + - - +
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Residues in contact with THR 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ILE* 2.8 29.6 + - - +
114C ALA* 3.7 6.7 - - - +
116C GLU* 1.3 77.9 - - - +
118C ASN* 1.3 66.0 + - - +
119C ASN 3.1 0.2 + - - -
120C LYS* 3.2 12.4 + - + +
121C LYS* 2.9 26.7 + - + +
----------------------------------------------------------
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Residues in contact with ASN 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ALA 2.9 17.4 + - - +
115C LYS* 3.8 6.7 - - + +
117C THR* 1.3 78.1 - - - +
119C ASN* 1.3 65.8 + - - +
121C LYS* 3.5 20.0 - - - +
122C LYS* 3.3 50.2 + - - +
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Residues in contact with ASN 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LYS* 3.0 36.1 + - - +
116C GLU* 3.4 13.6 - - - +
117C THR 3.0 0.2 - - - -
118C ASN* 1.3 77.8 - - - +
120C LYS* 1.3 67.0 + - + +
122C LYS* 3.0 11.7 + - - +
123C GLU* 3.0 39.7 + - - +
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Residues in contact with LYS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLU* 3.0 29.2 + - - +
117C THR* 3.6 11.2 - - - +
119C ASN* 1.3 79.1 - - + +
121C LYS* 1.3 57.2 + - - +
123C GLU* 3.8 10.8 + - - +
124C PHE* 2.9 31.6 + - - +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR* 2.9 18.0 + - + +
118C ASN* 3.5 24.7 - - - +
120C LYS* 1.3 75.9 - - - +
122C LYS* 1.3 54.9 + - + +
124C PHE* 3.1 7.2 + - - +
125C GLU* 2.7 72.1 + - + +
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Residues in contact with LYS 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ASN* 3.3 33.4 + - - +
119C ASN* 3.0 11.3 + - - +
121C LYS* 1.3 78.9 - - + +
123C GLU* 1.3 60.6 + - + +
125C GLU* 3.9 13.2 - - - +
126C GLU* 3.0 34.4 + - - +
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Residues in contact with GLU 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN* 3.0 36.1 + - - +
120C LYS* 3.8 8.9 - - - +
122C LYS* 1.3 75.7 - - + +
124C PHE* 1.3 62.3 + - - +
126C GLU* 3.3 7.2 + - - +
127C THR* 3.0 26.6 + - - -
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Residues in contact with PHE 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LYS 2.9 19.0 + - - +
121C LYS* 3.4 6.7 - - - +
123C GLU* 1.3 74.1 - - - +
125C GLU* 1.3 70.9 + - + +
127C THR* 3.2 8.5 + - + -
128C ALA* 2.9 37.3 + - + -
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Residues in contact with GLU 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS* 2.7 56.9 + - + +
122C LYS* 3.9 12.5 - - - +
123C GLU 3.3 0.2 - - - -
124C PHE* 1.3 82.9 - - + +
126C GLU* 1.3 58.5 + - + +
128C ALA* 3.3 9.2 + - + +
129C LYS* 3.0 32.9 + - + +
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Residues in contact with GLU 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS 3.0 19.7 + - - +
123C GLU* 3.6 7.6 - - - +
124C PHE 3.2 0.2 - - - -
125C GLU* 1.3 75.4 - - + +
127C THR* 1.3 64.1 + - - +
129C LYS* 3.3 31.8 + - - +
130C LYS* 3.1 36.3 + - - +
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Residues in contact with THR 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLU 3.0 14.7 + - - -
124C PHE* 3.2 12.0 + - + -
126C GLU* 1.3 72.3 - - - +
128C ALA* 1.3 67.6 + - - +
130C LYS* 3.2 23.2 + - + +
131C VAL* 3.0 35.7 + - + +
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Residues in contact with ALA 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PHE* 2.9 27.0 + - + +
125C GLU* 3.4 14.4 - - + +
127C THR* 1.3 77.1 - - - +
129C LYS* 1.3 62.8 + - + +
131C VAL* 3.3 5.6 + - - +
132C ARG* 2.9 26.9 + - - +
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Residues in contact with LYS 129 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLU* 3.0 16.5 + - + +
126C GLU* 3.6 35.5 + - - +
127C THR 3.2 0.4 - - - -
128C ALA* 1.3 76.9 - - - +
130C LYS* 1.3 62.5 + - + +
132C ARG* 3.7 5.9 - - - +
133C ARG* 2.9 24.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 130 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLU* 3.1 21.7 + - - +
127C THR* 3.2 30.3 + - + +
129C LYS* 1.3 74.9 - - - +
131C VAL* 1.3 59.9 - - + +
133C ARG* 3.1 7.7 + - - +
134C ALA* 2.9 30.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL 131 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C THR* 3.0 30.0 + - + +
128C ALA* 3.8 5.2 - - - +
130C LYS* 1.3 78.8 - - + +
132C ARG* 1.3 64.4 + - - +
134C ALA* 3.3 7.8 + - - +
135C ILE* 3.0 42.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 132 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ALA 2.9 18.4 + - - +
129C LYS* 3.7 6.5 - - - +
131C VAL* 1.3 76.4 - - - +
133C ARG* 1.3 64.9 + - - +
135C ILE* 3.1 8.8 + - - +
136C GLU* 2.9 46.8 + - + +
----------------------------------------------------------
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Residues in contact with ARG 133 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LYS 2.9 14.0 + - - +
130C LYS* 3.4 10.3 - - - +
132C ARG* 1.3 76.4 - - - +
134C ALA* 1.3 65.0 + - - +
136C GLU* 3.0 16.6 + - - +
137C GLN* 2.9 36.0 + - + +
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Residues in contact with ALA 134 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C LYS 2.9 16.6 + - - +
131C VAL* 3.7 7.9 - - - +
132C ARG 3.3 0.2 - - - -
133C ARG* 1.3 75.6 - - - +
135C ILE* 1.3 63.7 + - + +
137C GLN* 3.5 16.9 + - - +
138C LEU* 3.2 20.6 + - - +
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Residues in contact with ILE 135 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C VAL* 3.0 38.5 + - + +
132C ARG* 3.6 6.3 - - - +
134C ALA* 1.3 77.2 - - + +
136C GLU* 1.3 64.9 + - + +
138C LEU* 3.4 13.1 + - + +
139C ALA* 3.2 21.0 + - + +
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Residues in contact with GLU 136 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ARG* 2.9 44.2 + - + +
133C ARG* 3.5 18.4 - - - +
135C ILE* 1.3 75.4 - - + +
137C GLN* 1.3 54.9 + - - +
139C ALA* 3.0 9.4 + - - +
140C ALA* 2.7 36.2 + - - +
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Residues in contact with GLN 137 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ARG* 2.9 26.5 + - + +
134C ALA* 3.6 16.9 - - - +
136C GLU* 1.3 70.4 - - - +
138C LEU* 1.3 59.1 + - - +
140C ALA* 3.2 8.9 + - - +
141C MET* 2.8 32.9 + - + +
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Residues in contact with LEU 138 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C ALA 3.2 11.4 + - - +
135C ILE* 3.7 15.7 - - + +
136C GLU 3.2 0.4 - - - -
137C GLN* 1.3 79.7 - - - +
139C ALA* 1.3 61.7 + - - +
141C MET* 3.7 8.6 + - + +
142C ASP* 3.2 21.7 + - - +
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Residues in contact with ALA 139 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ILE* 3.2 13.3 + - + +
136C GLU* 3.0 10.8 + - - +
138C LEU* 1.3 76.0 - - - +
140C ALA* 1.3 62.0 + - - +
142C ASP* 3.1 27.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLU 2.7 16.7 + - - +
137C GLN* 3.3 14.1 - - - +
139C ALA* 1.3 70.0 - - - +
141C MET* 1.3 68.2 + - - +
142C ASP 3.0 6.1 + - - +
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Residues in contact with MET 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN* 2.8 20.2 + - + +
138C LEU* 4.0 10.8 - - + +
140C ALA* 1.3 72.1 - - - +
142C ASP* 1.3 66.4 + - - +
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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
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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) + - + + + + + -
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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