Contacts of the helix formed by residues 113 - 144 (chain C) in PDB entry 3E1J
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 ASP 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 6.4 0.4 - - - -
3C GLY* 5.8 0.3 - - - -
4C ASP* 5.5 3.4 + - + -
7C VAL* 3.4 29.2 - - + +
61C ARG* 2.8 25.1 + - - -
65C LEU* 3.7 11.1 - - - +
108C ALA* 2.8 16.5 + - + +
111C VAL* 3.3 6.4 + - + +
112C HIS* 1.3 72.7 - - - +
114C TYR* 1.3 56.4 + - - +
115C VAL 3.8 1.6 + - - -
116C SER* 2.6 28.0 + - - -
117C ARG* 3.0 26.2 + - - +
102H ARG* 4.7 7.4 + - - +
128H GLU* 4.2 1.7 - - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ASP* 3.3 39.9 + - - -
112C HIS* 2.9 51.4 + + + -
113C ASP* 1.3 73.2 - - - +
115C VAL* 1.4 58.2 + - - +
117C ARG* 3.4 8.1 + - - +
118C ASP* 2.9 27.9 + - - +
102H ARG* 3.5 21.9 - - - +
105H ILE* 3.5 32.8 - - + -
106H GLY* 3.4 15.4 - - - -
117H ARG* 3.6 20.4 + - - -
121H ILE* 4.1 21.0 - - + +
124H LEU* 4.1 14.4 - - + +
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Residues in contact with VAL 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ARG* 3.2 29.8 - - - +
113C ASP* 3.3 1.4 + - - -
114C TYR* 1.4 74.5 - - - +
116C SER* 1.3 65.2 + - - +
118C ASP* 3.1 8.0 + - + +
119C MET* 2.9 25.6 + - + +
102H ARG* 4.8 0.4 - - - +
121H ILE* 4.9 3.4 - - + +
124H LEU* 3.9 20.9 - - + -
125H ARG* 4.1 33.9 - - + +
128H GLU* 3.2 30.1 - - + +
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Residues in contact with SER 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 4.1 10.7 - - - +
11C LEU* 4.2 7.5 - - - +
61C ARG* 2.9 31.0 + - - +
65C LEU* 3.8 5.5 - - - +
108C ALA* 4.7 0.7 - - - -
113C ASP* 2.6 37.0 + - - -
115C VAL* 1.3 73.8 - - - +
117C ARG* 1.3 63.8 + - - +
119C MET* 3.3 7.2 + - - +
120C MET* 2.9 36.1 + - - +
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Residues in contact with ARG 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASP* 2.8 25.9 + - - -
114B TYR* 3.7 17.2 + - - -
117B ARG* 3.8 2.0 - - - +
251B SO4 2.7 41.7 + - - +
105C ILE* 3.3 42.7 + - + +
106C GLY* 4.3 1.0 - - - -
108C ALA* 4.0 6.3 - - + -
109C ASP* 3.2 42.6 + - - +
113C ASP 3.0 14.0 + - - +
114C TYR* 3.5 14.6 - - - +
115C VAL 3.1 0.4 - - - -
116C SER* 1.3 75.6 - - - +
118C ASP* 1.3 51.6 + - - +
120C MET* 3.0 15.3 + - - +
121C ILE* 2.8 40.0 + - + +
117H ARG* 4.1 2.9 - - - +
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Residues in contact with ASP 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 5.6 2.3 - - - +
251B SO4 5.0 7.1 + - - -
114C TYR 2.9 16.9 + - - +
115C VAL* 3.5 8.1 - - + +
117C ARG* 1.3 76.6 - - - +
119C MET* 1.3 63.1 + - - +
121C ILE* 3.3 10.8 + - - +
122C GLU* 3.2 32.0 + - - +
118H ASP* 5.6 1.6 - - - +
121H ILE* 4.1 17.2 - - + +
122H GLU* 3.3 25.5 - - - +
125H ARG* 4.1 21.7 + - - -
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Residues in contact with MET 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.6 1.8 - - - -
57C ARG* 3.5 63.7 + - + +
58C TYR* 4.4 15.9 - - - -
61C ARG* 3.6 33.9 - - + +
115C VAL* 2.9 18.0 + - + +
116C SER* 3.7 6.3 - - - +
118C ASP* 1.3 78.8 + - - +
120C MET* 1.3 62.6 + - - +
122C GLU* 3.4 3.3 + - - +
123C ILE* 3.2 32.1 + - + +
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Residues in contact with MET 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 5.8 1.1 - - + -
10C TYR* 6.2 0.2 - - + -
11C LEU* 4.0 15.0 - - + -
14C LEU* 3.6 31.2 - - + -
58C TYR* 4.4 10.5 - - + -
101C LEU* 3.7 11.1 - - + +
104C ALA* 3.6 36.6 - - + +
105C ILE* 3.6 16.8 - - + -
108C ALA* 3.6 19.7 - - + -
116C SER* 2.9 26.8 + - - +
117C ARG* 3.5 5.6 - - - +
119C MET* 1.3 78.8 - - + +
121C ILE* 1.3 58.4 + - - +
123C ILE* 3.2 6.8 + - - +
124C LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.2 20.2 - - + +
115B VAL* 5.0 4.1 - - + +
118B ASP* 4.0 34.1 - - + +
251B SO4 3.9 21.5 - - - +
105C ILE* 4.0 23.8 - - + -
117C ARG* 2.8 48.0 + - + +
118C ASP* 3.3 10.1 + - - +
120C MET* 1.3 75.5 - - - +
122C GLU* 1.3 66.7 + - - +
124C LEU* 3.3 4.6 + - - +
125C ARG* 3.0 22.3 + - + +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 3.3 29.3 - - - +
57C ARG* 4.2 19.3 - - - +
118C ASP* 3.2 21.5 + - - +
119C MET 3.9 6.5 - - - +
120C MET 3.3 0.2 - - - -
121C ILE* 1.3 81.0 - - - +
123C ILE* 1.3 61.7 + - - +
125C ARG* 3.2 30.2 + - - +
126C ASP* 3.1 27.0 + - - +
125H ARG* 6.4 0.4 - - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.7 18.6 - - - +
54C HIS* 3.7 41.1 - - + +
57C ARG* 3.9 13.9 - - + +
58C TYR* 3.6 44.2 - - + +
101C LEU* 4.1 8.1 - - + -
119C MET* 3.2 29.2 + - + +
120C MET* 3.6 6.7 - - - +
122C GLU* 1.3 75.3 - - - +
124C LEU* 1.3 57.6 + - - +
126C ASP* 2.9 20.0 + - - +
127C GLU* 2.9 19.5 + - - +
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Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TYR* 4.1 15.7 - - + -
115B VAL* 3.8 21.3 - - + +
98C ALA* 3.9 34.5 - - + +
101C LEU* 3.9 16.6 - - + -
102C ARG* 4.1 21.8 - - + +
105C ILE* 3.9 20.4 - - + -
120C MET 2.9 16.3 + - - +
121C ILE* 3.6 5.6 - - - +
123C ILE* 1.3 75.1 - - - +
125C ARG* 1.3 57.8 + - - +
127C GLU* 3.1 4.6 + - + +
128C GLU* 2.8 46.4 + - - +
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Residues in contact with ARG 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 5.2 13.3 - - - +
115B VAL* 4.2 27.7 - - + +
118B ASP* 4.2 17.7 + - - +
122B GLU* 6.4 0.2 - - - +
121C ILE* 3.0 13.2 + - + +
122C GLU* 3.3 32.5 + - - +
123C ILE 3.2 0.2 - - - -
124C LEU* 1.3 76.9 - - - +
126C ASP* 1.3 64.7 + - - +
128C GLU* 3.6 4.2 + - - +
129C GLY* 3.1 17.0 + - - -
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Residues in contact with ASP 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C ASP* 3.8 11.8 - - - +
54C HIS* 2.9 33.7 + - + -
57C ARG* 5.0 4.7 + - - -
122C GLU* 3.1 14.6 + - - +
123C ILE* 2.9 9.9 + - - +
125C ARG* 1.3 80.2 - - - +
127C GLU* 1.3 63.6 + - - +
129C GLY* 3.2 4.0 + - - -
130C HIS* 3.1 26.6 + - - +
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 2.7 28.9 - - - +
51C GLU* 2.8 23.9 - - - +
54C HIS* 3.4 8.5 + - - -
94C GLU* 2.6 29.6 - - - +
97C GLY 6.1 0.2 - - - -
98C ALA* 5.4 4.7 - - + +
101C LEU* 3.9 21.3 - - + -
123C ILE* 2.9 19.6 + - - +
124C LEU* 3.1 10.1 + - + +
126C ASP* 1.3 72.7 - - - +
128C GLU* 1.3 57.4 + - - +
130C HIS* 2.9 13.1 + - - +
131C ILE* 2.8 42.4 + - + +
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.8 11.0 - - + +
61B ARG* 2.8 36.4 + - - +
64B PHE* 3.4 31.9 - - + -
115B VAL* 3.2 16.2 - - + +
98C ALA* 5.2 0.9 - - - +
102C ARG* 2.7 30.6 + - - -
124C LEU* 2.8 27.1 + - - +
125C ARG* 3.7 7.9 - - - +
127C GLU* 1.3 75.6 - - - +
129C GLY* 1.3 54.3 + - - +
131C ILE* 3.3 12.8 + - - +
132C ASP* 2.9 28.1 + - - +
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Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG 3.1 13.6 + - - -
126C ASP* 3.5 5.8 - - - -
127C GLU 3.1 1.0 - - - -
128C GLU* 1.3 73.4 - - - +
130C HIS* 1.3 65.1 + - - +
132C ASP* 3.2 10.1 + - - +
133C TRP* 3.1 21.1 + - - +
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Residues in contact with HIS 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 4.0 4.5 + - - +
47C GLU* 3.2 42.5 - - + +
50C ASP* 3.3 34.4 + - + -
51C GLU* 3.5 21.0 + - - -
54C HIS* 4.7 0.4 - + - -
94C GLU* 3.0 29.3 + - - +
126C ASP* 3.1 13.0 + - - +
127C GLU* 2.9 15.8 + - - +
129C GLY* 1.3 71.8 - - - +
131C ILE* 1.3 67.3 + - - +
133C TRP* 3.1 3.7 + - - +
134C LEU* 2.9 30.0 + - - +
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Residues in contact with ILE 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 4.1 26.9 - - + -
64B PHE* 4.4 1.8 - - + -
91C LEU* 4.0 14.6 - - + -
94C GLU* 3.6 32.3 - - + +
95C LEU* 3.6 22.9 - - + -
98C ALA* 4.2 11.9 - - + -
127C GLU* 2.8 23.4 + - + +
128C GLU* 3.5 15.0 - - - +
130C HIS* 1.3 72.7 - - - +
132C ASP* 1.3 62.9 + - - +
134C LEU* 3.9 2.7 - - - +
135C GLU* 3.0 48.0 + - - +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.9 19.9 + - - +
64B PHE* 3.7 29.8 - - + +
128C GLU 2.9 13.8 + - - +
129C GLY* 3.2 13.4 + - - +
131C ILE* 1.3 76.8 - - - +
133C TRP* 1.3 58.0 + - - +
135C GLU* 3.4 5.0 + - - +
136C THR* 2.6 42.0 + - - -
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Residues in contact with TRP 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 4.2 10.4 - - - +
40C LEU* 4.2 15.9 - - + -
43C VAL* 3.5 46.6 - - + +
44C GLU* 3.7 18.2 - - + -
47C GLU* 4.1 13.7 - - - +
87C LEU* 4.7 5.4 - - + -
129C GLY 3.1 13.1 + - - +
130C HIS* 3.7 6.3 - - - +
132C ASP* 1.3 77.2 - - - +
134C LEU* 1.3 99.5 + - + +
136C THR* 3.2 7.7 + - - -
137C GLU* 3.0 61.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR* 3.6 25.1 - - + +
44C GLU* 4.0 11.0 - - - +
47C GLU* 4.9 0.9 - - - +
87C LEU* 4.1 20.8 - - + +
90C ASP* 4.3 5.2 - - + -
91C LEU* 4.1 32.5 - - + +
94C GLU* 4.1 12.3 - - + -
130C HIS* 2.9 28.4 + - + +
131C ILE* 3.9 4.5 - - - +
133C TRP* 1.3 104.2 - - + +
135C GLU* 1.3 64.7 + - - +
137C GLU* 3.3 4.4 + - - +
138C LEU* 3.0 30.1 + - + +
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Residues in contact with GLU 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 2.8 41.1 + - - +
64B PHE* 4.0 11.4 - - - +
66B GLU* 4.3 4.5 - - - +
91C LEU* 4.1 21.9 - - + +
95C LEU* 5.3 3.1 - - - +
131C ILE* 3.0 33.5 + - - +
132C ASP* 3.8 4.1 - - - +
134C LEU* 1.3 75.1 - - - +
136C THR* 1.3 65.3 + - - +
138C LEU* 3.3 9.7 + - - +
139C ASP* 2.9 32.3 + - - +
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Residues in contact with THR 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 3.4 20.1 + - - +
35A TRP* 3.4 28.9 - - - +
36A GLY* 3.7 9.4 - - - +
132C ASP* 2.6 32.8 + - - -
133C TRP* 3.2 7.6 + - - -
135C GLU* 1.3 77.3 - - - +
137C GLU* 1.3 59.7 + - - +
139C ASP* 3.1 7.6 + - + +
140C LEU* 2.8 34.0 + - + +
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Residues in contact with GLU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ARG* 3.3 21.2 + - - -
87C LEU* 4.1 11.0 - - + -
133C TRP* 3.0 61.2 + - + +
134C LEU* 3.7 7.4 - - - +
136C THR* 1.3 79.6 - - - +
138C LEU* 1.3 63.5 + - - +
140C LEU* 3.0 28.1 + - - +
141C ILE* 3.0 18.6 + - - +
149C TYR* 2.5 41.0 + - - +
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Residues in contact with LEU 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 3.9 32.6 - - + +
87C LEU* 3.7 28.5 - - + -
88C ARG* 4.0 39.0 + - - +
91C LEU* 3.8 29.8 - - + -
134C LEU 3.0 20.8 + - - +
135C GLU* 3.7 4.7 - - - +
137C GLU* 1.3 76.5 - - - +
139C ASP* 1.3 64.9 + - - +
141C ILE* 3.4 17.0 + - + +
142C GLN* 3.5 16.8 + - - +
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 5.6 4.4 - - + +
135C GLU* 2.9 23.8 + - - +
136C THR* 3.7 6.7 - - + +
138C LEU* 1.3 75.8 - - - +
140C LEU* 1.3 66.0 + - - +
142C GLN* 3.2 8.8 + - - +
143C LYS* 2.9 50.4 + - - +
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP 3.5 24.7 - - - +
36A GLY* 4.8 5.6 - - - +
37A LEU* 3.8 19.3 - - + -
150A LEU* 5.8 0.9 - - + -
154A ILE* 4.2 21.8 - - + -
39C ARG* 5.6 0.9 - - - +
136C THR* 2.8 20.6 + - + +
137C GLU* 3.0 32.3 + - - +
139C ASP* 1.3 77.3 - - - +
141C ILE* 1.3 62.8 + - - +
143C LYS* 4.3 11.0 - - + +
144C MET* 2.9 52.9 + - + +
149C TYR* 4.2 7.4 - - + -
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Residues in contact with ILE 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 4.3 8.1 - - + -
84C GLU* 4.3 27.4 - - + +
87C LEU* 4.2 17.5 - - + -
137C GLU 3.0 18.1 + - - +
138C LEU* 3.6 11.9 - - + +
139C ASP 3.2 0.2 - - - -
140C LEU* 1.3 76.7 - - - +
142C GLN* 1.3 70.7 + - - +
145C GLY* 3.0 28.6 + - - -
146C LEU* 3.8 27.0 + - + -
149C TYR* 3.6 41.5 - - + -
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Residues in contact with GLN 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN* 4.5 4.0 + - - -
84C GLU* 3.9 26.0 + - - -
88C ARG* 5.4 5.6 - - - +
138C LEU 3.5 11.7 + - - +
139C ASP* 3.2 10.3 + - - +
141C ILE* 1.3 90.0 + - - +
143C LYS* 1.3 67.1 + - + +
144C MET 3.6 0.2 + - - -
145C GLY* 3.8 5.2 + - - -
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Residues in contact with LYS 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 3.8 47.6 + - + +
37A LEU* 6.0 3.8 - - + +
146A LEU* 5.7 1.4 - - - +
147A GLN* 3.5 17.5 + - - +
150A LEU* 4.1 29.8 - - + +
139C ASP* 2.9 42.1 + - + +
140C LEU* 3.1 11.7 + - + +
142C GLN* 1.3 80.2 - - + +
144C MET* 1.3 58.0 + - + +
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Residues in contact with MET 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN* 3.4 44.2 - - - +
150A LEU* 4.4 6.7 - - + -
151A GLN* 3.7 27.6 - - - +
154A ILE* 3.2 34.1 - - + -
140C LEU* 2.9 43.1 + - + +
143C LYS* 1.3 76.1 - - + +
145C GLY* 1.3 66.6 + - - +
148C ASN* 3.4 22.0 + - + +
149C TYR* 3.8 27.1 - - - +
250C SO4 4.7 0.7 + - - -
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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