Contacts of the helix formed by residues 130 - 167 (chain R) in PDB entry 6E3Y
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 ASN 130 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R ASP* 4.3 12.0 + - - +
99R GLU* 3.2 29.4 + - - +
126R GLN* 3.6 14.8 - - - +
127R CYS 3.7 6.8 - - - +
129R VAL* 1.3 78.0 - - + +
131R THR* 1.3 66.0 + - - +
132R HIS 3.3 2.9 - - - -
133R GLU* 2.9 40.9 + - + +
134R LYS* 3.3 10.6 + - - +
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Residues in contact with THR 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P SER* 4.7 4.7 - - - +
22P VAL* 4.5 5.4 - - + -
93R GLN 4.4 4.7 - - - +
94R ASP* 2.8 37.0 + - + +
95R PHE 5.2 0.4 - - - -
96R ASP* 4.0 11.5 + - + +
127R CYS 2.7 27.9 + - - -
128R ASN* 3.4 7.7 - - - -
129R VAL 3.5 1.6 - - - -
130R ASN* 1.3 79.7 + - - +
132R HIS* 1.3 58.3 + - - +
134R LYS* 3.1 7.3 + - - +
135R VAL* 2.9 41.1 + - + +
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Residues in contact with HIS 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P VAL* 4.5 20.6 - - + +
23P VAL* 4.1 25.0 - - + +
128R ASN 4.6 3.5 + - - +
129R VAL 4.7 4.9 + - - +
130R ASN 3.3 0.8 - - - -
131R THR* 1.3 77.6 - - - +
133R GLU* 1.3 60.6 + - - +
135R VAL* 3.4 2.6 + - - +
136R LYS* 3.0 40.6 + - + +
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Residues in contact with GLU 133 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R VAL 5.2 1.3 + - - +
130R ASN* 2.9 40.2 - - + +
132R HIS* 1.3 82.2 + - - +
134R LYS* 1.3 63.6 + - - +
136R LYS* 3.4 11.0 + - + +
137R THR* 2.9 36.7 + - - -
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Residues in contact with LYS 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P LEU* 4.2 29.3 - - + +
96R ASP* 2.8 43.6 + - - +
98R SER* 3.6 10.1 + - - -
130R ASN* 3.3 18.9 + - - +
131R THR* 3.1 7.3 + - + +
133R GLU* 1.3 84.2 - - - +
135R VAL* 1.3 61.2 + - + +
137R THR* 3.3 7.0 + - - -
138R ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P LEU* 5.5 5.4 - - + -
16P LEU* 5.3 6.7 - - + -
19P SER* 3.6 42.6 - - - +
20P GLY* 5.3 2.7 - - - +
22P VAL* 4.4 7.0 - - + -
23P VAL* 3.9 23.8 - - + +
131R THR* 2.9 25.4 + - + +
132R HIS* 3.9 4.5 - - - +
134R LYS* 1.3 77.9 - - + +
136R LYS* 1.3 57.5 + - - +
138R ALA* 3.7 5.6 - - - +
139R LEU* 2.9 40.9 + - + +
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Residues in contact with LYS 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P VAL* 5.0 3.8 - - + +
132R HIS* 3.0 33.7 + - + +
133R GLU* 3.6 11.2 - - + +
134R LYS 3.2 0.2 - - - -
135R VAL* 1.3 77.2 - - - +
137R THR* 1.3 60.1 + - - +
139R LEU* 3.7 9.9 + - + +
140R ASN* 3.3 36.1 + - - +
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Residues in contact with THR 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R GLU* 2.9 23.7 + - - -
134R LYS* 3.6 8.2 - - - -
135R VAL 3.2 0.2 - - - -
136R LYS* 1.3 75.2 - - - +
138R ALA* 1.3 59.8 + - - +
140R ASN* 3.2 9.1 + - - +
141R LEU* 3.0 40.1 + - + +
366R ASP* 5.7 0.9 - - - +
367R TYR* 3.6 27.3 + - + +
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Residues in contact with ALA 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P LEU* 4.0 9.7 - - + +
15P LEU* 3.9 24.0 - - + -
16P LEU* 4.2 19.7 - - + +
134R LYS 2.9 17.4 + - - +
135R VAL* 3.8 5.8 - - - +
137R THR* 1.3 76.4 - - - +
139R LEU* 1.3 57.4 + - - +
141R LEU* 3.4 13.1 + - + +
142R PHE* 2.9 28.1 + - - +
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Residues in contact with LEU 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU* 3.9 19.7 - - + -
23P VAL* 4.4 28.9 - - + -
135R VAL* 2.9 29.5 + - + +
136R LYS* 4.0 8.5 - - + +
137R THR 3.2 0.4 - - - -
138R ALA* 1.3 77.5 - - - +
140R ASN* 1.3 58.1 + - - +
142R PHE* 3.1 16.0 + - + +
143R TYR* 2.9 49.1 + - + +
200R ASN* 5.8 4.3 - - - +
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Residues in contact with ASN 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136R LYS* 3.3 26.6 + - - +
137R THR* 3.2 9.8 + - - +
139R LEU* 1.3 78.6 - - - +
141R LEU* 1.3 57.5 + - + +
143R TYR* 3.4 12.7 + - - +
144R LEU* 3.0 35.4 + - + +
367R TYR* 5.4 9.0 + - + +
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Residues in contact with LEU 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P LEU* 3.7 14.4 - - + -
137R THR* 3.0 32.9 + - + +
138R ALA* 3.6 13.5 - - + +
140R ASN* 1.3 77.7 - - - +
142R PHE* 1.3 56.3 + - - +
144R LEU* 3.4 13.2 - - + +
145R THR* 2.9 31.4 + - - -
366R ASP* 3.5 19.3 - - + +
367R TYR* 3.6 37.5 - - + -
370R HIS* 3.4 35.6 + - + +
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Residues in contact with PHE 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P LEU* 3.9 5.1 - - + +
16P LEU* 3.6 27.4 - - + -
138R ALA 2.9 15.0 + - - +
139R LEU* 3.1 18.8 + - + +
141R LEU* 1.3 74.1 - - - +
143R TYR* 1.3 82.8 + + - +
145R THR* 3.2 7.5 + - - -
146R ILE* 3.0 41.3 + - + +
195R LEU* 3.8 33.0 - - + -
196R THR* 3.6 39.7 - - + -
200R ASN* 4.4 22.0 - - - -
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Residues in contact with TYR 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R LEU* 2.9 45.8 + - + +
140R ASN* 3.4 13.7 + - - +
142R PHE* 1.3 92.7 - + - +
144R LEU* 1.3 58.5 + - - +
146R ILE* 3.2 19.3 + - + +
147R ILE* 2.9 36.4 + - + +
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Residues in contact with LEU 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R ASN* 3.0 22.0 + - + +
141R LEU* 3.4 28.3 - - + +
143R TYR* 1.3 73.9 - - - +
145R THR* 1.3 63.4 + - - +
147R ILE* 3.7 14.3 - - + +
148R GLY* 2.8 25.5 + - - -
367R TYR* 4.4 13.5 - - + -
370R HIS* 3.7 36.8 - - + +
371R ILE* 4.7 13.0 - - + +
374R HIS* 4.6 0.7 - - - +
375R PHE* 4.3 13.0 - - + -
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Residues in contact with THR 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P LEU* 4.6 3.3 - - - +
141R LEU 2.9 19.7 + - - -
142R PHE* 3.2 12.3 + - - +
144R LEU* 1.3 74.0 - - - +
146R ILE* 1.3 62.1 + - + +
148R GLY* 3.4 0.5 + - - -
149R HIS* 3.0 38.3 + - + +
191R THR* 5.3 3.4 - - + -
192R ILE* 6.2 3.6 - - + -
195R LEU* 3.7 27.4 - - + -
370R HIS* 3.9 4.7 + - - -
374R HIS* 2.9 46.7 + - + +
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Residues in contact with ILE 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142R PHE* 3.0 46.8 + - + +
143R TYR* 3.4 20.4 - - + +
145R THR* 1.3 79.0 - - + +
147R ILE* 1.3 59.2 + - + +
150R GLY* 2.9 27.0 + - - -
192R ILE* 3.7 23.0 - - + +
196R THR* 3.7 22.2 - - + -
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Residues in contact with ILE 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R TYR* 2.9 25.5 + - + +
144R LEU* 3.7 15.0 - - + +
145R THR 3.3 0.2 - - - -
146R ILE* 1.3 78.7 - - + +
148R GLY* 1.3 57.0 + - - +
150R GLY* 3.3 1.0 + - - -
151R LEU* 2.9 47.7 + - + +
375R PHE* 4.2 10.8 - - + -
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Residues in contact with GLY 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R LEU 2.8 15.1 + - - -
145R THR 3.8 1.1 - - - -
147R ILE* 1.3 77.0 - - - +
149R HIS* 1.3 56.2 + - - +
151R LEU* 3.3 2.3 + - - +
152R SER* 2.9 24.8 + - - -
374R HIS* 3.2 24.9 - - - +
375R PHE* 3.6 27.1 - - - -
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Residues in contact with HIS 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R THR* 3.0 25.0 + - + +
146R ILE 3.7 0.2 - - - -
148R GLY* 1.3 75.9 - - - +
150R GLY* 1.3 58.7 + - - +
152R SER* 3.9 4.4 - - - -
153R ILE* 3.3 21.0 + - - +
187R ASN* 5.1 2.7 - - - -
188R SER* 2.9 53.1 + - - +
191R THR* 4.3 19.3 - - + +
192R ILE* 4.0 19.3 - - + -
373R MET* 4.8 6.6 + - + +
374R HIS* 3.2 49.1 + + + -
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Residues in contact with GLY 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R ILE 2.9 18.7 + - - -
147R ILE* 3.7 2.2 - - - -
149R HIS* 1.3 77.3 - - - +
151R LEU* 1.3 63.8 + - - +
152R SER 3.3 0.4 - - - -
153R ILE* 3.7 4.4 + - - +
154R ALA* 3.5 22.3 + - - +
192R ILE* 4.6 5.6 - - - -
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Residues in contact with LEU 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R ILE* 2.9 31.3 + - + +
148R GLY 4.0 2.5 - - - +
150R GLY* 1.3 77.0 - - - +
152R SER* 1.3 63.0 + - - +
153R ILE 3.4 0.2 - - - -
154R ALA* 4.1 8.5 - - + +
155R SER* 3.5 21.1 + - - -
375R PHE* 4.0 24.2 - - + -
378R LEU* 4.0 22.4 - - + +
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Residues in contact with SER 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148R GLY 2.9 17.8 + - - -
149R HIS* 4.2 9.6 - - - -
150R GLY 3.3 0.2 - - - -
151R LEU* 1.3 76.9 - - - +
153R ILE* 1.3 59.3 + - - +
155R SER* 3.5 1.4 + - - -
156R LEU* 3.0 39.4 + - - +
184R PHE* 5.3 1.9 + - - +
188R SER* 4.4 10.1 + - - -
374R HIS 4.2 7.6 - - - -
375R PHE* 5.5 0.2 - - - -
377R GLY* 3.3 27.6 + - - -
378R LEU* 4.3 10.3 - - - +
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Residues in contact with ILE 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149R HIS 3.3 20.7 + - - +
150R GLY* 4.3 5.4 - - - +
151R LEU 3.4 0.4 - - - -
152R SER* 1.3 76.5 - - - +
154R ALA* 1.3 58.6 + - - +
156R LEU* 4.7 2.5 - - - -
157R LEU* 2.9 51.2 + - + +
185R VAL* 4.7 11.2 - - + +
188R SER* 3.3 23.3 - - - +
189R VAL* 4.0 30.3 - - + +
192R ILE* 4.7 8.3 - - + -
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Residues in contact with ALA 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150R GLY 3.5 15.8 + - - +
151R LEU* 4.4 10.1 - - + +
152R SER 3.4 0.4 - - - -
153R ILE* 1.3 81.1 - - - +
155R SER* 1.3 59.8 + - - +
157R LEU* 4.5 3.7 - - - +
158R ILE* 3.3 30.5 + - + +
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Residues in contact with SER 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R LEU 3.5 17.4 + - - -
152R SER 3.5 3.1 + - - -
153R ILE 3.2 0.6 - - - -
154R ALA* 1.3 77.8 - - - +
156R LEU* 1.3 60.5 + - - +
157R LEU 3.3 0.4 - - - -
158R ILE* 3.3 8.7 + - - +
159R SER* 3.0 29.1 + - - -
378R LEU* 3.9 21.8 + - - +
381R SER* 3.0 25.6 + - - -
382R THR* 4.9 0.5 + - - -
386R PHE* 3.7 14.6 - - - -
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Residues in contact with LEU 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R SER* 3.0 35.6 + - - +
153R ILE* 4.2 0.7 - - - +
155R SER* 1.3 75.0 - - - +
157R LEU* 1.3 60.9 + - - +
159R SER* 3.7 1.8 - - - -
160R LEU* 2.9 33.8 + - - +
181R PHE* 3.5 39.7 - - + +
184R PHE* 3.6 27.8 - - + -
185R VAL* 3.6 21.3 - - + -
377R GLY* 3.8 15.9 - - - +
380R VAL* 4.8 1.3 - - + -
381R SER* 3.7 19.7 - - - -
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Residues in contact with LEU 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R ILE* 2.9 40.6 + - + +
154R ALA* 4.5 4.5 - - - +
156R LEU* 1.3 76.4 - - - +
158R ILE* 1.3 60.9 + - + +
160R LEU* 4.0 8.9 - - + +
161R GLY* 2.9 26.9 + - - -
185R VAL* 3.7 30.7 - - + -
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Residues in contact with ILE 158 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R ALA* 3.3 18.8 + - + +
155R SER* 3.3 10.2 + - - +
157R LEU* 1.3 78.1 - - + +
159R SER* 1.3 57.9 + - - +
161R GLY* 3.4 1.4 + - - -
162R ILE* 2.9 41.1 + - + +
386R PHE* 3.7 28.3 - - + -
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Residues in contact with SER 159 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R SER 3.0 10.3 + - - -
156R LEU* 3.7 6.1 - - - -
157R LEU 3.3 0.4 - - - -
158R ILE* 1.3 76.6 - - - +
160R LEU* 1.3 62.6 + - - +
162R ILE* 3.2 3.1 - - - +
163R PHE* 3.0 30.8 + - - -
181R PHE* 3.8 21.3 - - - -
381R SER* 2.4 29.9 + - - -
385R CYS* 3.3 27.6 - - - -
386R PHE* 3.9 2.3 - - - -
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Residues in contact with LEU 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R LEU 2.9 20.8 + - - +
157R LEU* 4.0 10.1 - - + +
159R SER* 1.3 76.3 - - - +
161R GLY* 1.3 63.4 + - - +
163R PHE* 3.3 2.8 + - + +
164R PHE* 3.0 48.8 + - + -
178R LYS* 3.3 37.2 - - + +
181R PHE* 3.7 20.0 - - + +
182R PHE* 3.6 36.6 - - + +
185R VAL* 4.2 9.2 - - + -
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Residues in contact with GLY 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157R LEU 2.9 18.3 + - - -
158R ILE* 3.8 1.8 - - - -
160R LEU* 1.3 77.7 - - - +
162R ILE* 1.3 57.6 + - - +
164R PHE* 4.2 2.8 - - - +
165R TYR* 2.8 34.4 + - - +
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Residues in contact with ILE 162 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R ILE* 2.9 31.3 + - + +
159R SER 3.2 11.9 - - - +
161R GLY* 1.3 75.3 - - - +
163R PHE* 1.4 78.7 + - + +
165R TYR* 4.2 5.6 - - + -
166R PHE* 3.0 52.2 + - + +
169R LEU* 5.6 1.3 - - + -
385R CYS* 3.6 27.8 - - - -
386R PHE* 6.4 0.4 - - + -
391R VAL* 3.9 22.2 - - + -
395R LEU* 5.4 8.7 - - + -
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Residues in contact with PHE 163 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R SER 3.0 28.1 + - - +
160R LEU* 3.8 6.3 - - + +
161R GLY 3.3 0.2 - - - -
162R ILE* 1.4 86.1 - - + +
164R PHE* 1.3 61.9 + - - +
166R PHE* 4.0 5.0 + - - +
167R LYS* 4.0 7.4 + - - -
169R LEU* 4.8 15.3 + - + +
174R ILE* 3.6 42.8 - - + +
177R HIS* 4.9 10.3 - + + -
178R LYS* 3.8 34.4 + - + -
181R PHE* 3.5 31.9 - + - -
384R PHE 4.1 18.8 - - - -
385R CYS* 4.4 13.7 - - + -
391R VAL* 4.8 12.3 - - + -
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Residues in contact with PHE 164 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R LEU* 3.0 44.2 + - + +
161R GLY* 4.2 2.9 - - - +
163R PHE* 1.3 78.5 - - - +
165R TYR* 1.3 63.9 + - - +
166R PHE 3.5 0.2 + - - -
167R LYS* 3.7 13.9 + - - +
178R LYS* 3.6 46.7 - - + +
179R ASN* 6.1 0.4 - - - -
182R PHE* 6.5 0.2 - - + -
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Residues in contact with TYR 165 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 5.5 5.0 + - - -
161R GLY 2.8 25.4 + - - +
162R ILE* 3.9 5.2 - - + +
164R PHE* 1.3 72.7 - - - +
166R PHE* 1.3 87.3 + + - +
167R LYS* 3.5 3.1 + - - +
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Residues in contact with PHE 166 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 5.3 0.3 + - - -
162R ILE* 3.0 52.9 + - + +
163R PHE 4.7 1.8 - - - +
165R TYR* 1.3 92.5 - + - +
167R LYS* 1.3 68.0 + - - +
168R SER* 3.2 19.8 + - - +
169R LEU* 5.0 15.5 - - + -
391R VAL* 5.4 3.6 - - + -
394R ILE* 3.6 19.1 - - + -
395R LEU* 3.6 26.0 - - + -
398R ASN* 3.3 32.1 - - + -
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Residues in contact with LYS 167 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 3.6 34.3 + - - +
335B PHE* 3.7 12.0 - - - -
163R PHE 4.0 6.2 + - - -
164R PHE 3.7 14.4 + - - +
165R TYR 3.4 3.9 - - - +
166R PHE* 1.3 78.6 - - - +
168R SER* 1.3 57.5 + - - +
169R LEU 3.8 1.9 - - - +
170R SER* 4.9 10.3 + - - +
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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) + - + + + + + -
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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