Contacts of the helix formed by residues 116 - 149 (chain C) in PDB entry 5B2G
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 LYS 116 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C LYS* 3.1 4.7 - - - -
115C ALA* 1.3 80.9 - - + +
117C THR* 1.3 59.6 + - - +
118C MET 3.0 2.2 - - - -
119C ILE* 2.9 40.3 + - + +
120C VAL* 3.0 18.1 + - + +
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 4.3 35.4 - - + +
100C VAL 5.5 1.6 - - - +
101C GLY* 5.3 5.6 - - - -
102C GLY 5.3 3.6 - - - +
114C LYS* 3.5 33.0 + - - +
116C LYS* 1.3 80.2 - - - +
118C MET* 1.3 59.5 + - - +
120C VAL* 3.5 9.2 + - + +
121C ALA* 3.0 27.2 + - - +
1262E VAL* 6.3 2.7 - - + -
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Residues in contact with MET 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1233A LEU* 6.4 2.0 - - + -
7C GLN* 3.7 34.3 - - - +
11C ILE* 4.5 14.1 - - + -
97C LEU 4.3 17.0 - - - +
98C SER* 3.9 29.2 - - - +
101C GLY* 4.5 13.9 - - - -
102C GLY 5.6 0.4 - - - +
114C LYS 4.8 4.9 - - - +
115C ALA* 3.7 18.6 + - - +
116C LYS 3.0 0.4 - - - -
117C THR* 1.3 79.1 - - - +
119C ILE* 1.3 58.4 + - - +
121C ALA* 3.7 3.2 - - - -
122C GLY 2.9 21.8 + - - -
181C LEU* 3.2 29.9 - - + +
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA 3.9 9.4 - - - +
116C LYS* 2.9 36.3 + - + +
118C MET* 1.3 75.4 - - - +
120C VAL* 1.3 65.1 + - + +
122C GLY 3.2 1.0 + - - -
123C VAL* 3.0 24.0 + - + +
181C LEU 3.6 17.3 - - - +
182C CYS* 3.3 37.0 - - + +
184C SER* 4.6 9.6 - - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 4.3 14.6 - - + -
116C LYS* 3.0 14.2 + - + +
117C THR* 3.6 13.2 - - + +
119C ILE* 1.3 73.2 - - + +
121C ALA* 1.3 57.4 + - - +
122C GLY 3.0 1.3 - - - -
123C VAL* 2.8 29.5 + - + +
124C VAL* 2.9 20.0 + - + +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLY 3.9 11.4 - - - +
97C LEU* 3.8 31.2 - - + -
98C SER* 4.4 8.1 - - - +
117C THR 3.0 15.2 + - - +
118C MET* 3.9 7.2 - - - +
120C VAL* 1.3 79.9 - - - +
122C GLY* 1.3 56.9 + - - +
124C VAL* 3.5 8.0 + - - +
125C PHE* 2.9 39.2 + - + -
181C LEU* 4.8 1.6 - - + -
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C MET 2.9 16.5 + - - -
119C ILE 3.5 5.6 - - - -
120C VAL 3.0 0.6 - - - -
121C ALA* 1.3 76.5 - - - +
123C VAL* 1.3 57.0 + - - +
125C PHE* 3.2 4.9 + - - +
126C LEU* 2.9 31.3 + - - +
178C GLY* 3.4 26.7 - - - -
181C LEU* 3.8 6.7 - - - +
182C CYS* 4.1 4.0 - - - -
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Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ILE* 3.0 21.5 + - + +
120C VAL* 2.8 17.6 + - + +
122C GLY* 1.3 71.2 - - - -
124C VAL* 1.3 63.0 + - + +
126C LEU* 3.1 13.8 + - + +
127C LEU* 2.9 41.9 + - + +
182C CYS* 4.0 10.3 - - - -
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C VAL* 3.0 42.5 - - + +
91C ALA* 4.3 2.2 - - - +
93C LEU* 4.8 4.3 - - + -
94C GLY* 3.7 15.5 - - - +
97C LEU* 4.8 7.6 - - + -
120C VAL* 2.9 25.3 + - + +
121C ALA* 3.6 14.1 - - - +
123C VAL* 1.3 79.5 - - + +
125C PHE* 1.3 62.6 + - - +
127C LEU* 3.4 6.5 + - + +
128C ALA* 3.1 22.7 + - - +
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Residues in contact with PHE 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 5.1 2.5 - - - -
14C ALA* 3.2 35.4 - - + -
15C VAL* 5.1 3.1 - - + -
91C ALA* 3.6 30.7 - - + -
94C GLY* 3.3 29.2 - - - -
95C VAL* 3.8 13.0 - - + -
98C SER* 4.6 6.1 - - - -
121C ALA* 2.9 24.6 + - + -
122C GLY 3.5 5.4 - - - +
124C VAL* 1.3 75.7 - - - +
126C LEU* 1.3 58.2 + - - +
128C ALA* 3.8 3.4 - - - +
129C GLY* 2.9 25.8 + - - -
174C LEU* 3.3 34.3 - - + +
178C GLY* 3.8 6.1 - - - +
181C LEU* 3.6 25.4 - - + -
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Residues in contact with LEU 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLY 2.9 20.2 + - - +
123C VAL* 3.1 18.4 + - + +
125C PHE* 1.3 77.0 - - - +
127C LEU* 1.3 61.6 + - + +
130C LEU* 3.1 29.0 + - - +
174C LEU 4.7 0.2 - - - -
175C LEU* 3.1 49.9 - - + +
178C GLY 4.1 4.5 - - - -
179C GLY* 3.8 9.9 - - - +
182C CYS* 4.4 14.4 - - + -
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C VAL* 5.0 8.3 - - + -
123C VAL* 2.9 37.0 + - + +
124C VAL* 3.8 7.6 - - + +
126C LEU* 1.3 76.8 - - + +
128C ALA* 1.3 59.7 + - - +
130C LEU* 3.2 15.0 + - + +
131C MET* 2.9 36.8 + - - +
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Residues in contact with ALA 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 3.4 30.5 + - - +
90C VAL* 4.1 6.9 - - + +
91C ALA* 3.8 21.3 - - + +
124C VAL 3.1 17.3 + - - +
125C PHE 3.8 4.0 - - - +
127C LEU* 1.3 75.4 - - - +
129C GLY* 1.3 56.9 + - - +
131C MET* 2.8 25.0 + - - +
132C VAL* 2.8 17.0 + - - +
174C LEU* 4.2 3.1 - - + -
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Residues in contact with GLY 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE 2.9 15.2 + - - -
126C LEU 4.2 0.7 - - - -
128C ALA* 1.3 77.0 - - - +
130C LEU* 1.3 57.2 + - - +
132C VAL* 3.0 4.4 + - - -
133C ILE* 2.9 25.7 + - - +
171C SER* 3.3 16.4 - - - -
174C LEU* 3.6 25.4 - - - +
175C LEU* 4.3 8.3 - - - -
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Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU 3.1 20.1 + - - +
127C LEU* 3.4 15.7 - - + +
128C ALA 3.2 0.2 - - - -
129C GLY* 1.3 74.2 - - - +
131C MET* 1.3 59.8 + - + +
133C ILE* 3.5 18.8 + - + +
134C VAL* 3.2 32.1 + - + +
175C LEU* 4.0 15.1 - - + +
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Residues in contact with MET 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.2 48.0 - - + +
86C ILE* 3.6 24.5 - - + +
87C SER* 3.5 22.0 - - - +
90C VAL* 5.4 5.6 - - - -
127C LEU* 2.9 18.3 + - + +
128C ALA* 2.8 11.7 + - - +
130C LEU* 1.3 75.2 - - - +
132C VAL* 1.3 60.3 + - - +
134C VAL* 4.5 5.8 - - + -
135C PRO* 2.8 26.8 - - - +
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 3.5 31.2 - - + -
24C CYS* 5.6 0.4 - - - -
84C VAL* 6.0 3.6 - - + -
87C SER* 3.1 27.4 - - - +
128C ALA 2.8 13.8 + - - +
129C GLY* 3.0 10.0 + - - +
131C MET* 1.3 75.8 - - - +
133C ILE* 1.3 66.2 + - - +
134C VAL 3.3 0.4 - - - -
135C PRO* 3.6 2.9 - - - +
136C VAL* 3.1 34.6 + - + +
167C GLY* 3.6 25.6 - - - +
170C ALA* 4.6 0.2 - - + -
171C SER* 3.7 10.1 - - - +
174C LEU* 4.2 6.3 - - + -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C GLY 2.9 9.8 + - - +
130C LEU* 3.6 22.0 - - + +
131C MET 3.4 0.2 - - - -
132C VAL* 1.3 77.8 - - - +
134C VAL* 1.3 61.2 + - + +
136C VAL* 4.9 1.1 - - - -
137C SER* 2.4 52.5 + - - +
168C TRP* 5.4 5.6 - - + +
171C SER* 3.2 26.9 - - - +
172C GLY* 6.1 0.2 - - - -
175C LEU* 3.6 29.8 - - + -
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 4.2 15.9 - - + -
130C LEU* 3.2 22.2 + - + +
131C MET* 4.3 5.2 - - + +
133C ILE* 1.3 81.8 - - + +
135C PRO* 1.3 73.1 - - + +
137C SER* 3.7 1.9 - - - -
138C TRP* 3.0 45.5 + - + +
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Residues in contact with PRO 135 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 4.3 2.2 - - + -
80C ALA* 4.1 20.0 - - + +
83C LEU* 3.5 31.4 - - + -
84C VAL* 4.2 16.4 - - + -
131C MET 2.8 29.2 - - - +
132C VAL* 3.6 4.9 - - - +
134C VAL* 1.3 91.1 - - + +
136C VAL* 1.3 60.3 + - + +
137C SER 3.2 0.9 + - - -
138C TRP* 4.1 12.5 - - + +
139C THR* 2.9 35.3 + - + +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C CYS* 4.2 7.2 - - - -
30C TRP* 3.6 22.9 - - + -
84C VAL* 5.1 2.7 - - + -
132C VAL* 3.1 33.6 + - + +
133C ILE* 4.3 1.8 - - - +
134C VAL 3.4 0.8 - - - -
135C PRO* 1.3 79.4 - - + +
137C SER* 1.3 59.1 + - - +
139C THR* 3.2 14.3 + - - -
140C ALA* 4.0 5.0 - - - +
164C LEU* 3.4 43.6 - - + +
167C GLY* 3.9 17.0 - - - -
168C TRP* 4.0 12.4 - - + +
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Residues in contact with SER 137 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 2.4 40.1 + - - +
134C VAL* 3.7 2.9 - - - -
135C PRO 3.1 0.2 - - - -
136C VAL* 1.3 77.6 - - - +
138C TRP* 1.3 60.2 + - - +
139C THR 3.3 0.4 - - - -
140C ALA* 3.2 18.5 + - - +
141C HIS* 3.2 8.7 + - - +
168C TRP* 3.1 30.5 + - - +
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Residues in contact with TRP 138 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASP* 3.4 56.5 - - + -
79C ALA* 5.5 5.8 - - + -
80C ALA* 5.9 1.6 - - + -
83C LEU* 4.8 10.4 - - + +
134C VAL* 3.0 46.2 + - + +
135C PRO* 4.1 7.2 - - + +
137C SER* 1.3 74.0 - - - +
139C THR* 1.3 74.0 + - + +
140C ALA 3.1 0.9 - - - -
141C HIS* 3.1 31.0 + + + +
142C ASN* 3.2 19.5 + - - -
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP* 3.6 29.2 - - + -
31C ARG* 5.5 4.7 + - - +
76C ASP* 5.7 0.4 - - + -
77C LEU* 4.3 22.9 - - + -
80C ALA* 4.7 8.1 - - + -
135C PRO* 2.9 29.5 + - + +
136C VAL 3.2 11.3 + - - -
138C TRP* 1.3 90.0 - - + +
140C ALA* 1.3 61.7 + - - +
142C ASN* 3.6 7.6 + - - +
143C ILE* 3.3 28.2 + - - +
164C LEU* 4.1 4.8 - - - +
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Residues in contact with ALA 140 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL 4.0 1.8 - - - +
137C SER 3.2 12.9 + - - +
138C TRP 3.1 0.4 - - - -
139C THR* 1.3 81.0 + - - +
141C HIS* 1.3 56.8 + - - +
143C ILE* 3.4 7.1 + - - +
144C ILE* 3.1 36.2 + - + +
160C MET* 4.1 7.6 - - - +
164C LEU* 3.9 20.0 - - + -
168C TRP* 3.5 30.5 - - + -
----------------------------------------------------------
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Residues in contact with HIS 141 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C SER 3.2 5.9 + - - +
138C TRP* 3.1 26.6 + + + +
140C ALA* 1.3 74.0 - - - +
142C ASN* 1.3 68.4 + - - +
143C ILE 3.1 4.5 - - - -
144C ILE* 3.4 8.4 + - - +
145C GLN* 2.8 52.6 + - + +
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Residues in contact with ASN 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 5.8 5.4 - - - +
76C ASP* 3.2 25.7 + - - +
138C TRP* 3.2 27.3 + - - +
139C THR* 3.6 8.2 + - - +
140C ALA 3.4 0.2 - - - -
141C HIS* 1.3 85.7 - - - +
143C ILE* 1.3 60.7 + - + +
145C GLN* 3.5 22.1 - - - +
146C ASP* 3.7 18.9 + - - +
158C ARG* 5.4 3.1 + - - -
227D ARG* 6.0 1.0 - - - -
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Residues in contact with ILE 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP 5.0 0.2 - - - -
31C ARG* 3.7 37.9 - - + +
139C THR* 3.3 18.8 + - - +
140C ALA* 3.4 8.0 + - - +
141C HIS 3.1 0.6 - - - -
142C ASN* 1.3 81.6 - - + +
144C ILE* 1.3 62.1 + - + +
146C ASP* 3.2 21.1 - - - +
147C PHE* 3.8 4.0 + - - +
158C ARG* 3.0 42.8 - - + +
159C GLU* 3.5 0.9 - - - -
160C MET* 3.5 24.7 - - + +
164C LEU* 4.0 23.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ALA* 3.1 22.2 + - + +
141C HIS* 4.0 8.3 - - - +
143C ILE* 1.3 76.2 - - + +
145C GLN* 1.3 61.9 + - - +
146C ASP 3.0 5.4 - - - -
147C PHE* 3.2 15.9 + - + +
148C TYR* 3.3 32.4 - - + +
160C MET* 4.4 24.7 - - + -
168C TRP* 5.9 1.6 - - + -
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C HIS* 2.8 36.4 + - + +
142C ASN* 3.5 24.7 - - - +
144C ILE* 1.3 76.6 - - - +
146C ASP* 1.3 57.2 + - - +
147C PHE 3.3 0.4 - - - -
148C TYR* 3.9 4.7 + - - +
149C ASN* 3.2 26.4 + - - +
231D SER* 5.1 4.8 + - - -
309D ASN 3.7 20.8 + - - -
310D TYR* 3.5 21.0 - - + +
311D PRO* 4.6 15.8 - - + +
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Residues in contact with ASP 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ASN 3.7 14.0 + - - +
143C ILE* 3.2 17.8 + - - +
144C ILE 3.0 0.6 - - - -
145C GLN* 1.3 78.9 - - - +
147C PHE* 1.3 62.5 + - - +
149C ASN* 3.6 22.7 + - - +
152C VAL* 3.0 32.4 - - - +
157C LYS* 4.6 4.2 - - - -
158C ARG* 3.5 19.6 + - + +
227D ARG* 2.6 42.8 + - - -
311D PRO* 6.0 1.7 - - - +
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Residues in contact with PHE 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE 3.8 4.9 + - - +
144C ILE* 3.2 14.3 + - + +
146C ASP* 1.3 79.2 - - - +
148C TYR* 1.3 95.4 + + + +
149C ASN 3.3 4.7 + - - +
157C LYS* 3.6 46.8 + - + +
158C ARG 5.7 1.5 + - - +
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Residues in contact with TYR 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C ILE* 3.3 35.4 + - + -
145C GLN* 3.9 4.0 + - - +
147C PHE* 1.3 98.0 - + - +
149C ASN* 1.3 64.6 + - - +
150C PRO* 3.1 12.0 - - - +
310D TYR* 3.6 20.0 + - - +
----------------------------------------------------------
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Residues in contact with ASN 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C GLN 3.2 21.6 + - - +
146C ASP* 3.6 19.6 + - - +
147C PHE 3.1 4.7 - - - +
148C TYR* 1.3 76.7 - - - +
150C PRO* 1.3 67.1 - - - +
151C LEU* 2.8 29.3 + - - +
152C VAL* 3.4 28.6 + - - +
157C LYS* 5.7 0.2 - - - -
310D TYR* 3.2 28.9 - - + +
311D PRO* 2.8 35.4 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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