Contacts of the helix formed by residues 110 - 145 (chain C) in PDB entry 2VT4
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 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C TRP* 3.2 14.5 + - - -
108C LEU 3.6 2.2 + - - -
109C TRP* 1.3 78.1 - - - +
111C SER* 1.3 66.7 + - - -
112C PHE 3.2 2.9 + - - -
113C LEU 3.3 2.6 + - - -
114C CYS 3.0 17.7 + - - -
196C PRO* 4.4 13.6 + - - -
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C GLY* 1.3 72.2 - - - -
112C PHE* 1.3 63.3 + - - +
114C CYS* 3.2 21.3 - - - +
115C GLU* 3.3 11.5 + - - +
193C TYR 4.7 11.1 + - - -
194C GLN 5.6 0.3 + - - -
195C ASP 4.9 0.3 + - - -
196C PRO* 3.7 31.6 - - - +
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Residues in contact with PHE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B PRO* 4.0 35.0 - - + -
110C GLY 3.2 1.0 - - - -
111C SER* 1.3 78.6 - - - +
113C LEU* 1.3 83.5 + - + +
114C CYS 3.3 0.3 + - - -
115C GLU* 3.3 12.8 + - + +
116C LEU* 3.1 41.7 + - + +
178C MET* 5.4 9.0 - - - -
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Residues in contact with LEU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C PHE* 4.0 26.9 - - + -
107C TRP* 4.1 4.4 - - + -
109C TRP* 3.8 34.5 + - + +
110C GLY 3.3 2.8 + - - +
112C PHE* 1.3 100.5 - - + +
114C CYS* 1.3 53.9 + - - +
116C LEU* 3.6 16.8 - - + +
117C TRP* 2.7 36.7 + - - +
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Residues in contact with CYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C TRP* 3.5 17.2 - - + +
110C GLY 3.0 13.0 + - - +
111C SER* 3.2 15.9 - - - +
113C LEU* 1.3 78.2 - - - +
115C GLU* 1.3 62.6 + - - +
117C TRP* 3.6 2.6 - - - +
118C THR* 3.0 29.9 + - - -
182C TRP* 6.4 2.0 - - - -
196C PRO 5.6 0.4 - - - +
198C CYS 4.2 5.4 - - - +
199C CYS* 2.1 56.1 - - - -
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C SER 3.3 8.3 + - - +
112C PHE* 3.3 14.4 + - + +
114C CYS* 1.3 77.6 - - + +
116C LEU* 1.3 61.3 + - - +
118C THR* 3.2 7.6 + - - -
119C SER* 2.9 31.0 + - - -
177C ILE* 3.6 11.4 - - + +
178C MET* 3.3 23.5 - - + +
180C HIS* 2.7 41.6 + - - -
182C TRP* 3.6 27.2 + - + +
183C ARG* 4.0 8.7 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 3.1 30.6 + - + +
113C LEU* 3.6 28.0 - - + +
115C GLU* 1.3 79.5 - - - +
117C TRP* 1.3 62.6 + - - +
119C SER* 3.3 6.9 - - - -
120C LEU* 3.0 31.7 + - + +
174C PHE* 4.0 24.9 - - + -
178C MET* 3.9 13.3 - - - +
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Residues in contact with TRP 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LEU 4.3 2.9 - - - -
94C VAL* 3.0 36.0 + - + +
97C PHE* 3.9 20.8 - + + +
98C GLY* 3.8 22.9 - - - -
101C LEU* 3.6 24.7 - - + -
107C TRP* 3.7 16.6 - + + -
113C LEU 2.7 21.7 + - - +
114C CYS 3.6 0.4 - - - +
116C LEU* 1.3 71.7 - - - +
118C THR* 1.3 75.9 + - - +
120C LEU* 3.1 13.4 + - + +
121C ASP* 3.0 24.8 + - - +
199C CYS* 3.7 33.9 - - - -
333C TYR* 4.0 17.0 - + - -
400C P32 3.5 28.3 - - + -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C CYS* 3.0 16.3 + - - -
115C GLU* 3.2 10.3 + - - -
117C TRP* 1.3 88.4 - - - +
119C SER* 1.3 66.1 + - - +
121C ASP* 3.2 16.8 + - - +
122C VAL* 3.2 14.5 + - + +
177C ILE* 4.1 8.3 - - + -
182C TRP* 6.3 1.1 - - + -
199C CYS* 4.3 5.2 + - - -
201C PHE* 3.6 43.4 - - + +
400C P32 3.8 16.0 - - + +
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C GLU 2.9 15.2 + - - -
116C LEU* 3.3 9.2 - - - -
118C THR* 1.3 75.9 - - - +
120C LEU* 1.3 56.9 + - - -
122C VAL* 3.4 2.6 + - - +
123C LEU* 3.0 29.3 + - - +
173C SER 4.5 2.8 - - - +
174C PHE* 3.3 34.3 - - - -
177C ILE* 3.2 27.8 - - - +
178C MET* 3.3 18.1 - - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 4.5 14.1 - - + -
93C LEU* 3.6 39.5 - - + -
94C VAL* 4.4 8.3 - - + +
116C LEU* 3.0 23.7 + - + +
117C TRP* 3.4 15.3 - - + +
119C SER* 1.3 73.8 - - - +
121C ASP* 1.3 66.1 + - - +
123C LEU* 3.6 14.5 + - + +
124C CYS* 3.1 30.9 + - - -
174C PHE* 4.4 14.1 - - + -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C VAL* 5.8 0.5 - - - +
94C VAL* 3.8 21.4 - - + +
117C TRP* 3.0 15.3 + - + +
118C THR* 3.2 13.7 + - - +
120C LEU* 1.3 79.4 - - - +
122C VAL* 1.3 61.3 + - - +
124C CYS* 3.5 3.3 + - - +
125C VAL* 3.3 21.5 + - - +
333C TYR* 2.4 35.2 + - - -
400C P32 2.6 45.4 + - + +
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Residues in contact with VAL 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.2 19.2 + - + +
119C SER 3.9 3.4 - - - +
121C ASP* 1.3 74.2 - - - +
123C LEU* 1.3 65.6 + - - +
125C VAL* 3.3 2.4 + - - +
126C THR* 3.0 27.8 + - - -
173C SER* 3.1 33.2 - - - +
177C ILE* 3.7 19.5 - - + -
201C PHE* 4.7 3.8 - - + -
207C TYR* 5.0 2.0 - - - +
211C SER* 6.4 0.2 - - - -
400C P32 3.4 57.3 - - + -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C SER 3.0 17.2 + - - +
120C LEU* 3.7 16.2 - - + +
122C VAL* 1.3 77.8 - - - +
124C CYS* 1.3 57.1 - - - +
126C THR* 3.6 0.3 - - - -
127C ALA* 2.8 32.9 + - - +
166C TRP* 4.0 26.7 - - + +
169C SER* 3.3 20.6 - - - +
170C ALA* 3.3 39.0 - - + +
173C SER* 4.4 5.7 - - - -
174C PHE* 4.2 22.0 - - + -
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Residues in contact with CYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.7 24.4 - - + +
89C VAL* 3.6 32.8 - - - -
90C VAL* 3.8 23.3 - - + -
94C VAL* 4.7 1.1 - - - -
120C LEU* 3.1 21.5 + - - +
121C ASP* 3.9 4.0 - - - +
122C VAL 3.2 0.2 - - - -
123C LEU* 1.3 82.2 - - - +
125C VAL* 1.3 61.3 + - + +
127C ALA* 3.5 4.8 + - - +
128C SER* 3.0 28.6 + - - -
166C TRP* 4.8 8.1 - - - -
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Residues in contact with VAL 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C VAL* 6.4 1.1 - - + -
121C ASP* 3.3 21.3 + - - +
122C VAL 3.3 5.1 + - - +
124C CYS* 1.3 73.5 - - + +
126C THR* 1.3 66.5 + - - +
128C SER* 3.5 4.8 + - - -
129C ILE* 3.3 21.5 + - - +
215C SER 5.2 0.7 - - - +
216C PHE* 5.1 2.9 - - + -
299C PHE* 4.3 9.8 - - + -
303C TRP* 3.4 56.5 - - + +
307C PHE* 4.3 18.2 - - + -
400C P32 4.1 13.0 - - + -
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Residues in contact with THR 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 3.0 15.3 + - - +
123C LEU 3.6 3.1 - - - -
125C VAL* 1.3 78.2 - - - +
127C ALA* 1.3 57.3 + - - +
129C ILE* 3.4 2.8 - - - +
130C GLU* 3.0 46.8 + - + +
169C SER* 3.2 19.5 - - - +
172C VAL* 4.0 7.9 - - + -
173C SER* 2.9 28.2 + - - +
215C SER* 3.3 35.7 - - - +
400C P32 4.2 0.7 - - - -
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 4.9 1.3 - - + -
123C LEU 2.8 21.0 + - - +
124C CYS 4.0 2.5 - - - +
126C THR* 1.3 73.3 - - - +
128C SER* 1.3 56.8 + - - +
130C GLU* 3.9 2.4 - - - +
131C THR* 2.9 35.7 + - - -
165C VAL* 4.0 3.8 - - + +
166C TRP* 3.9 44.6 - - + +
169C SER* 3.2 17.0 + - - +
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Residues in contact with SER 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.9 19.7 - - - +
86C ALA* 4.2 12.2 - - - +
87C ASP* 4.7 8.7 + - - -
124C CYS 3.0 19.1 + - - -
125C VAL* 3.7 4.1 - - - -
126C THR 3.3 0.2 - - - -
127C ALA* 1.3 74.1 - - - +
129C ILE* 1.3 61.2 + - - +
131C THR* 2.9 6.2 + - - -
132C LEU* 2.8 32.2 + - - +
299C PHE* 3.7 24.8 - - - -
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C VAL 3.3 6.5 + - - +
126C THR 3.4 7.9 - - - +
128C SER* 1.3 79.6 - - - +
130C GLU* 1.3 66.0 + - - +
132C LEU* 3.4 3.7 + - + -
133C CYS* 3.0 23.4 + - - +
215C SER 3.3 26.9 - - - +
216C PHE* 4.4 10.5 - - + +
219C PRO* 3.7 29.4 - - + +
220C LEU* 4.1 11.7 - - + +
223C MET* 3.9 33.0 - - + -
299C PHE* 3.7 33.6 - - + -
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C THR* 3.0 31.1 + - + +
127C ALA 3.9 0.2 - - - +
129C ILE* 1.3 78.9 - - - +
131C THR* 1.3 56.8 + - - +
133C CYS* 3.1 23.1 - - - +
134C VAL* 3.3 13.3 + - - +
165C VAL* 3.1 36.4 - - + +
168C ILE* 3.3 27.3 - - - +
169C SER* 2.9 22.5 + - - -
172C VAL* 4.3 3.3 - - - +
214C ILE 5.3 1.7 - - - +
219C PRO* 4.7 15.9 - - + -
406C D10 4.3 12.0 - - + +
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Residues in contact with THR 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 3.6 34.1 - - + +
82C SER* 3.8 17.6 + - - +
83C LEU* 4.1 15.4 + - + -
127C ALA 2.9 22.0 + - - -
128C SER 2.9 5.3 + - - -
130C GLU* 1.3 72.4 - - - +
132C LEU* 1.3 66.3 + - - +
133C CYS 3.0 1.8 - - - -
134C VAL* 3.0 9.6 + - + +
135C ILE* 2.9 28.6 + - + +
162C ILE* 5.9 1.9 - - + +
165C VAL* 3.7 15.1 - - - +
166C TRP* 5.1 1.4 + - - -
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.6 31.0 - - + -
128C SER 2.8 22.3 + - - +
129C ILE* 3.7 8.1 - - + +
131C THR* 1.3 72.0 - - - +
133C CYS* 1.3 61.2 + - - +
135C ILE* 3.6 13.9 + - + +
136C ALA* 3.1 22.7 + - - +
223C MET* 3.7 17.9 - - - +
295C ILE* 3.8 18.2 - - + +
296C MET* 3.8 21.6 - - + +
299C PHE* 3.6 46.9 - - + -
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Residues in contact with CYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ILE 3.0 10.1 + - - +
130C GLU* 3.1 15.3 - - - +
131C THR 3.0 0.2 - - - -
132C LEU* 1.3 73.4 - - - +
134C VAL* 1.3 67.8 + - + +
136C ALA* 3.0 14.3 + - - +
137C ILE* 3.0 20.6 + - + +
219C PRO* 3.3 34.5 - - - -
222C ILE* 3.5 31.9 - - - -
223C MET* 3.7 12.0 - - - +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.9 35.9 - - + -
130C GLU 3.3 12.1 + - - +
131C THR* 3.0 9.1 + - + +
133C CYS* 1.3 80.2 - - + +
135C ILE* 1.3 64.1 + - - +
137C ILE* 3.1 8.4 + - + +
138C ASP* 2.8 27.4 + - + +
161C ILE* 3.9 18.2 - - + -
165C VAL* 3.8 24.0 - - + -
404C SOG 6.2 2.7 - - + -
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR* 5.1 7.0 - - + +
79C PHE* 3.8 26.9 - - + +
80C ILE* 4.4 15.0 - - + -
83C LEU* 4.1 13.7 - - + -
131C THR* 2.9 23.3 + - + +
132C LEU* 3.6 31.6 - - + +
134C VAL* 1.3 74.0 - - - +
136C ALA* 1.3 63.5 + - - +
138C ASP* 3.4 8.5 + - - +
139C ARG* 3.1 24.8 + - + +
292C LEU* 4.1 28.0 - - + -
295C ILE* 5.8 0.9 - - + -
296C MET* 3.8 16.4 - - + -
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Residues in contact with ALA 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 3.1 7.7 + - - +
133C CYS* 3.0 10.0 + - - +
135C ILE* 1.3 75.3 - - - +
137C ILE* 1.3 59.3 + - - +
139C ARG* 3.2 5.2 + - - +
140C TYR* 2.8 28.4 + - - +
223C MET* 4.4 15.7 - - + +
226C VAL* 3.8 15.3 - - + +
227C ALA* 4.5 2.7 - - - +
230C VAL* 4.0 2.4 - - - +
296C MET* 3.7 25.1 - - + -
405C SOG 4.2 11.4 - - + -
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Residues in contact with ILE 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C CYS* 3.0 21.5 + - + +
134C VAL* 3.7 10.1 - - + +
136C ALA* 1.3 74.6 - - - +
138C ASP* 1.3 57.3 + - - +
140C TYR* 3.5 4.1 + - + +
141C LEU* 3.0 44.7 + - + +
222C ILE* 4.4 19.5 - - + -
226C VAL* 3.7 27.1 - - + -
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Residues in contact with ASP 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 5.3 0.6 - - - +
76C THR* 3.7 10.2 + - - +
79C PHE* 4.3 24.9 - - + -
134C VAL* 2.8 23.6 + - + +
135C ILE* 3.5 8.9 - - - +
137C ILE* 1.3 71.1 - - - +
139C ARG* 1.3 87.8 + - - +
141C LEU* 3.2 9.5 + - - +
142C ALA* 3.0 21.1 + - - +
149C TYR* 2.4 37.4 + - - -
153C MET* 4.9 8.2 - - + +
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Residues in contact with ARG 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 5.7 0.8 - - - +
76C THR* 3.4 18.7 + - - +
135C ILE* 3.1 16.5 + - + +
136C ALA* 3.4 9.2 - - - +
138C ASP* 1.3 102.8 + - - +
140C TYR* 1.3 63.5 + - - +
142C ALA* 3.1 19.3 + - - +
143C ILE* 2.9 27.9 + - - +
149C TYR* 3.5 19.4 + - - -
230C VAL* 4.4 13.5 - - + -
289C LEU* 3.5 33.7 - - + +
292C LEU* 4.1 20.4 - - + -
405C SOG 5.2 4.7 - - + -
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Residues in contact with TYR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C ALA 2.8 15.4 + - - +
137C ILE* 3.8 6.1 - - + +
139C ARG* 1.3 73.0 - - - +
141C LEU* 1.3 73.0 + - + +
143C ILE* 3.8 3.1 + - + -
144C THR* 3.2 53.7 + - + +
226C VAL* 3.8 17.0 - - + -
229C ARG* 3.9 31.0 - - + -
230C VAL* 3.4 30.0 - - + +
233C GLU* 4.6 9.1 + - + -
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ILE* 3.0 36.9 + - + +
138C ASP* 3.7 6.5 - - - +
140C TYR* 1.3 88.5 - - + +
142C ALA* 1.3 60.2 + - - +
143C ILE 3.1 1.6 - - - -
144C THR* 4.1 5.4 - - - +
145C SER* 2.7 42.8 + - - +
149C TYR* 4.1 15.8 - - + +
153C MET* 5.5 8.3 - - + -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C ASP 3.0 16.6 + - - +
139C ARG* 3.1 29.4 + - - +
141C LEU* 1.3 76.4 - - - +
143C ILE* 1.3 62.4 + - - +
146C PRO* 3.4 24.4 - - - +
149C TYR* 3.8 28.0 - - + -
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C ARG 2.9 14.1 + - - +
140C TYR* 3.8 8.7 - - + +
142C ALA* 1.3 80.7 - - - +
144C THR* 1.3 76.5 + - + +
146C PRO* 3.9 5.7 - - - +
230C VAL* 4.2 21.5 - - + +
233C GLU* 3.8 19.8 - - + +
234C ALA* 4.3 9.6 - - - +
237C GLN* 4.0 36.8 + - - +
286C HIS* 6.1 0.4 - - - +
289C LEU* 4.0 26.5 - - + -
----------------------------------------------------------
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TYR* 3.2 53.6 + - + +
141C LEU* 3.8 4.7 + - - +
143C ILE* 1.3 85.8 - - + +
145C SER* 1.3 70.1 + - - +
146C PRO* 3.1 11.3 - - - +
233C GLU* 4.1 15.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 2.7 29.5 + - - +
144C THR* 1.3 84.5 + - - +
146C PRO* 1.3 64.9 - - - +
147C PHE 2.9 4.1 + - - -
148C ARG* 3.0 20.4 + - - -
149C TYR* 2.8 19.9 + - - +
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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