Contacts of the helix formed by residues 116 - 153 (chain B) in PDB entry 6QVC
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 GLU 116 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY* 1.3 69.7 - - - -
117B ASP* 1.3 61.5 + - - +
118B GLY 3.2 0.7 - - - -
119B ILE* 3.2 27.2 + - + +
120B PHE* 3.1 21.1 + - - +
250B MET* 5.9 2.9 - - - +
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY* 2.7 20.8 + - - -
116B GLU* 1.3 71.9 + - - +
118B GLY* 1.3 67.3 + - - -
119B ILE 3.2 0.2 - - - -
120B PHE* 3.2 15.6 - - + +
121B LEU* 2.9 33.9 + - + +
304B ARG* 4.5 23.4 + - - +
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY 3.2 15.4 + - - -
117B ASP* 1.3 86.9 + - - +
119B ILE* 1.3 57.3 + - - +
121B LEU* 3.3 8.4 + - - +
122B VAL* 2.8 24.6 + - - +
307B PHE* 3.3 29.8 - - - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLY 3.1 10.9 + - - +
116B GLU* 3.2 35.1 + - + +
118B GLY* 1.3 74.1 - - - +
120B PHE* 1.3 64.9 + - - +
122B VAL* 3.2 17.0 + - + +
123B LEU* 3.1 30.6 + - + +
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B GLU 3.1 10.2 + - - +
117B ASP* 3.2 21.8 - - + +
119B ILE* 1.3 75.2 - - - +
121B LEU* 1.3 81.0 + - + +
123B LEU* 3.4 14.3 + - + +
124B LEU* 3.1 30.6 + - + +
243B ALA* 4.4 9.2 - - + -
246B LEU* 3.6 42.6 - - + -
247B SER* 3.9 16.4 - - - -
250B MET* 4.0 27.8 - - + -
266B ILE* 5.5 9.2 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 2.9 20.8 + - + +
118B GLY* 3.4 11.9 - - - +
119B ILE 3.2 0.4 - - - -
120B PHE* 1.3 92.6 - - + +
122B VAL* 1.3 57.9 + - - +
124B LEU* 3.3 11.5 + - + +
125B GLY* 2.9 24.9 + - - -
269B VAL* 3.7 29.8 - - + -
304B ARG* 3.6 43.5 - - + +
307B PHE* 4.1 18.2 - - + -
308B ALA* 4.0 18.1 - - + +
311B PHE* 5.9 0.7 - - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLY 2.8 12.1 + - - +
119B ILE* 3.2 34.2 + - + +
121B LEU* 1.3 74.5 - - - +
123B LEU* 1.3 66.2 + - + +
125B GLY* 3.5 0.8 + - - +
126B LEU* 3.0 27.1 + - + +
307B PHE* 4.4 13.7 - - + -
311B PHE* 3.5 47.0 - - + -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE* 3.1 33.5 + - + +
120B PHE* 3.5 20.2 - - + +
122B VAL* 1.3 77.1 - - + +
124B LEU* 1.3 63.6 + - - +
126B LEU* 3.7 9.4 - - + +
127B LEU* 3.0 26.1 + - + +
246B LEU* 3.7 32.1 - - + -
249B PHE* 6.1 2.2 - - + -
250B MET* 5.3 10.8 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 3.1 22.5 + - + +
121B LEU* 3.3 25.3 + - + +
123B LEU* 1.3 77.9 - - - +
125B GLY* 1.3 57.7 + - - +
127B LEU* 3.4 6.0 + - + +
128B MET* 3.0 37.4 + - + +
239B ALA 5.1 0.7 - - - +
242B CYS* 4.0 26.9 - - + +
243B ALA* 4.0 22.9 - - + +
246B LEU* 3.9 22.0 - - + -
269B VAL* 4.7 6.3 - - + +
270B GLY* 5.6 1.6 - - - -
273B VAL* 4.3 24.2 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU 2.9 14.5 + - - -
122B VAL* 4.0 1.3 - - - -
124B LEU* 1.3 75.1 - - - +
126B LEU* 1.3 59.2 + - - +
128B MET* 3.8 4.1 - - - +
129B ALA* 3.0 32.1 + - - +
273B VAL* 4.8 2.7 - - - +
308B ALA* 4.8 2.4 - - - +
311B PHE* 5.0 5.2 - - - -
312B SER* 3.2 31.4 + - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.0 19.2 + - + +
123B LEU* 3.7 9.6 - - + +
124B LEU 3.3 0.2 - - - -
125B GLY* 1.3 75.7 - - - +
127B LEU* 1.3 65.5 + - + +
129B ALA* 4.0 2.1 - - - +
130B LEU* 3.1 46.5 + - + +
311B PHE* 4.7 15.1 - - + -
315B VAL* 4.8 18.5 - - + +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 3.0 17.7 + - + +
124B LEU* 3.8 6.7 - - + +
126B LEU* 1.3 78.3 - - + +
128B MET* 1.3 65.8 + - + +
130B LEU* 3.2 16.6 + - + +
131B VAL* 3.0 46.8 + - + +
212B PHE* 5.9 0.9 - - + -
242B CYS* 4.4 25.4 - - + -
246B LEU* 6.5 0.2 - - + -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 3.0 27.4 + - + +
125B GLY 3.3 3.8 + - - +
127B LEU* 1.3 81.0 - - + +
129B ALA* 1.3 57.2 + - - +
131B VAL* 3.3 8.1 + - - +
132B SER* 3.0 23.6 + - - -
235B PHE* 4.1 14.8 - - + -
238B ILE* 4.4 9.6 - - - -
239B ALA* 3.6 36.3 - - + +
242B CYS* 3.8 25.6 - - + -
273B VAL* 3.7 24.2 - - + -
277B CYS* 3.3 26.6 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLY 3.0 17.0 + - - +
126B LEU 4.0 0.4 - - - +
128B MET* 1.3 76.1 - - - +
130B LEU* 1.3 60.4 + - - +
132B SER* 4.0 1.0 - - - -
133B TRP* 3.0 31.5 + - - +
277B CYS* 3.6 10.9 - - - -
312B SER 3.7 21.8 - - - +
315B VAL* 3.9 24.2 - - + -
316B PHE* 4.0 12.0 - - - +
319B LEU* 5.2 1.9 - - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.1 40.1 + - + +
127B LEU* 3.5 18.4 - - + +
129B ALA* 1.3 77.3 - - - +
131B VAL* 1.3 58.3 + - + +
133B TRP* 3.6 8.2 + - + +
134B SER* 3.0 29.3 + - - -
315B VAL* 5.7 1.3 - - + -
319B LEU* 3.7 27.3 - - + +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.0 38.4 + - + +
128B MET* 3.8 9.0 - - - +
129B ALA 3.3 0.2 - - - -
130B LEU* 1.3 79.9 - - + +
132B SER* 1.3 56.6 + - - +
134B SER* 3.3 7.9 + - - -
135B MET* 3.0 46.2 + - + +
212B PHE* 5.3 12.3 - - + -
216B VAL* 4.8 9.0 - - + -
235B PHE* 5.0 0.9 - - + -
238B ILE* 5.0 11.2 - - + -
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Residues in contact with SER 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET 3.0 17.4 + - - -
129B ALA 4.0 2.5 - - - -
130B LEU 3.4 0.2 - - - -
131B VAL* 1.3 75.0 - - - +
133B TRP* 1.3 61.6 + - - +
135B MET* 3.2 14.0 - - - +
136B ASP* 3.0 27.8 + - - +
231B LYS* 3.7 14.2 + - - -
235B PHE* 3.6 18.9 - - - -
277B CYS* 3.2 24.7 + - - -
316B PHE* 3.5 11.0 - - - -
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Residues in contact with TRP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA 3.0 18.4 + - - +
130B LEU* 4.0 7.9 - - + +
132B SER* 1.3 76.1 - - - +
134B SER* 1.3 69.8 + - - +
136B ASP* 2.8 22.4 - - - +
137B TYR* 2.9 66.1 + + + +
316B PHE* 3.9 25.4 - + + +
319B LEU* 3.4 35.5 - - + +
320B ALA* 4.8 13.9 - - + +
323B ASN* 4.4 22.7 - - + -
324B LYS* 4.3 17.2 - - + +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU 3.0 19.6 + - - -
131B VAL* 3.5 8.7 - - - -
132B SER 3.2 0.4 - - - -
133B TRP* 1.3 88.9 - - - +
135B MET* 1.3 63.6 + - - +
137B TYR* 3.6 2.7 - - - +
138B VAL* 3.1 34.1 + - - +
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Residues in contact with MET 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.0 35.7 + - + +
132B SER* 3.2 12.3 - - - +
134B SER* 1.3 78.6 - - - +
136B ASP* 1.3 63.5 + - + +
138B VAL* 3.9 1.1 - - - -
139B SER* 3.0 27.8 + - - -
216B VAL* 3.7 19.7 - - + -
219B LEU* 4.2 21.1 - - + -
220B THR* 3.8 27.8 - - + +
223B LEU* 4.5 7.8 - - + +
231B LYS* 4.6 9.9 - - - -
235B PHE* 3.6 38.6 - - + -
238B ILE* 5.1 1.1 - - + -
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B SER 3.0 13.8 + - - +
133B TRP* 2.8 31.6 - - - +
135B MET* 1.3 74.8 - - - +
137B TYR* 1.3 61.6 + - - +
139B SER* 3.6 6.4 - - - -
140B ALA* 2.9 31.2 + - - +
223B LEU* 4.2 14.4 - - + -
231B LYS* 3.9 14.4 + - - +
316B PHE* 3.3 25.6 - - - -
421B ARG* 4.9 17.5 + - - +
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TRP* 2.9 62.1 + + + +
134B SER* 3.6 3.1 - - - +
136B ASP* 1.3 82.6 + - - +
138B VAL* 1.3 75.5 + - + +
140B ALA* 3.3 6.1 + - + +
141B LYS* 3.0 63.9 + - + +
324B LYS* 4.1 34.3 + - + -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER* 3.1 24.0 + - - +
135B MET* 4.1 2.9 - - - +
137B TYR* 1.3 89.0 - - + +
139B SER* 1.3 63.0 + - - +
141B LYS* 3.8 6.4 - - + +
142B SER* 3.0 26.5 + - - -
220B THR* 4.6 15.5 - - + -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET 3.0 19.4 + - - -
136B ASP* 3.6 5.2 - - - -
138B VAL* 1.3 77.0 - - - +
140B ALA* 1.3 56.7 + - - +
142B SER* 2.6 23.0 + - - -
143B LEU* 3.0 16.2 + - - +
220B THR* 4.7 5.8 - - - +
223B LEU* 3.3 29.8 + - - +
224B GLY* 3.3 23.8 - - - -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 2.9 18.1 + - - +
137B TYR* 3.8 5.4 - - + +
139B SER* 1.3 76.3 + - - +
141B LYS* 1.3 59.1 + - + +
143B LEU* 3.3 7.1 + - - +
144B GLN* 3.0 32.8 + - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B TYR* 3.0 65.8 + - + +
138B VAL* 3.4 7.8 + - + +
139B SER 3.3 0.2 - - - -
140B ALA* 1.3 75.4 - - + +
142B SER* 1.3 66.0 + - - +
144B GLN* 3.2 27.6 + - - +
145B ALA* 3.0 23.9 + - - +
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 3.0 17.4 + - - -
139B SER* 2.6 25.1 + - - -
141B LYS* 1.3 75.4 - - - +
143B LEU* 1.3 56.9 + - - +
145B ALA* 3.3 7.6 + - - +
146B TYR* 3.0 26.9 + - - +
167B PHE* 4.8 17.7 - - - -
171B LEU* 6.4 1.8 - - - -
224B GLY* 4.1 14.2 + - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B SER* 3.0 19.3 + - - +
140B ALA* 3.7 8.1 - - - +
141B LYS 3.2 0.2 - - - -
142B SER* 1.3 76.9 + - - +
144B GLN* 1.3 65.9 + - + +
146B TYR* 3.1 18.3 + - + +
147B LYS* 3.1 33.5 + - + +
224B GLY 4.3 16.6 - - - +
225B SER 5.3 1.3 - - - +
226B GLY* 5.1 5.4 - - - +
419B MET* 3.6 47.1 - - + -
422B GLU* 4.4 6.7 - - - +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 3.0 16.9 + - - +
141B LYS* 3.2 42.8 + - - +
143B LEU* 1.3 80.5 - - + +
145B ALA* 1.3 57.2 + - - +
147B LYS* 4.1 6.3 - - - +
148B TRP* 2.9 32.0 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS 3.0 18.9 + - - +
142B SER* 3.6 8.1 - - - +
144B GLN* 1.3 78.3 - - + +
146B TYR* 1.3 57.2 + - - +
148B TRP* 4.0 16.8 - - + -
149B SER* 3.0 35.0 + - - +
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Residues in contact with TYR 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B SER 3.0 14.3 + - - +
143B LEU* 3.1 21.7 + - + +
145B ALA* 1.3 77.3 - - - +
147B LYS* 1.3 78.9 + - + +
149B SER* 4.2 1.5 - - - -
150B TYR* 3.0 32.7 + + + +
163B VAL* 4.3 11.5 - - + +
164B TRP* 3.2 55.6 + + - -
167B PHE* 3.4 52.0 - + + -
168B PRO* 4.0 13.6 - - + +
226B GLY* 6.2 1.8 - - - -
419B MET* 5.0 11.9 - - + -
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Residues in contact with LYS 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.1 33.8 + - + +
144B GLN* 4.2 5.8 - - - +
146B TYR* 1.3 93.5 - - + +
148B TRP* 1.3 57.7 + - - +
150B TYR* 3.6 11.2 - - + +
151B ALA* 3.0 31.2 + - - +
417B GLU* 3.8 41.5 + - + +
419B MET* 4.3 10.1 - - + -
422B GLU* 4.1 14.4 - - - +
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Residues in contact with TRP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN 2.9 21.2 + - - +
145B ALA* 3.6 16.4 - - + +
146B TYR 3.2 0.2 - - - -
147B LYS* 1.3 77.8 - - - +
149B SER* 1.3 71.1 + - - +
151B ALA* 3.3 3.6 + - - +
152B GLN* 2.7 75.3 + - + +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 3.0 17.8 + - - +
146B TYR* 4.3 1.6 - - - -
148B TRP* 1.3 87.2 - - - +
150B TYR* 1.3 64.6 + - - +
152B GLN* 3.7 14.8 + - - -
153B MET* 3.1 31.5 + - - +
163B VAL* 5.8 5.2 - - - -
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TYR* 3.0 28.7 + + + +
147B LYS* 3.6 12.3 - - + +
149B SER* 1.3 77.5 - - - +
151B ALA* 1.3 67.4 + - + +
153B MET* 4.1 3.5 - - - +
160B GLN* 3.1 66.0 + - + +
163B VAL* 3.7 31.6 - - + +
164B TRP* 4.0 31.9 - + - -
406B PHE* 3.9 7.3 - + - -
407B PRO* 3.8 22.9 - - + +
408B PRO* 4.0 6.6 - - - +
417B GLU* 4.8 17.5 - - + -
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LYS 3.0 17.1 + - - +
148B TRP* 3.7 4.3 - - - +
150B TYR* 1.3 85.5 - - + +
152B GLN* 1.3 60.8 + - + +
153B MET 3.2 5.4 + - - -
154B GLN* 3.9 9.7 + - - -
155B PRO* 5.1 2.6 - - - +
160B GLN* 3.9 8.4 + - - +
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TRP* 2.7 78.4 + - + +
149B SER* 3.2 14.2 + - - +
151B ALA* 1.3 76.0 - - + +
153B MET* 1.3 68.3 + - - +
154B GLN* 4.9 0.2 - - - -
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Residues in contact with MET 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER* 3.1 19.5 + - - +
150B TYR 4.1 4.5 - - - +
151B ALA 3.2 0.2 + - - -
152B GLN* 1.3 83.1 - - - +
154B GLN* 1.4 76.3 + - + +
156B SER* 5.7 0.2 - - - -
159B LEU* 3.3 47.8 - - + +
160B GLN* 3.6 17.5 - - + +
163B VAL* 3.7 20.2 - - + -
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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