Contacts of the helix formed by residues 113 - 148 (chain B) in PDB entry 5UNG
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 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TRP* 2.9 30.5 + - - -
111B LEU* 3.9 0.4 - - - +
112B PHE* 1.3 78.7 - - - +
114B PRO* 1.4 72.4 - - - +
115B VAL* 3.3 3.4 - - - -
116B MET 3.6 0.2 + - - -
117B CYS* 3.3 5.5 + - - +
184B VAL* 4.0 3.1 - - - -
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Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B GLY* 1.4 80.9 - - - +
115B VAL* 1.3 69.9 + - + +
117B CYS* 3.5 13.5 + - + +
118B LYS* 3.6 15.3 + - - +
183B ASP* 3.5 25.1 - - - +
184B VAL* 3.8 26.0 - - + +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE 5.9 0.2 - - - +
113B GLY* 3.3 1.0 - - - -
114B PRO* 1.3 84.0 - - + +
116B MET* 1.4 59.2 + - + +
118B LYS* 3.2 13.5 + - - +
119B VAL* 3.1 36.4 + - + +
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TRP* 3.3 5.3 - - - -
112B PHE* 3.6 42.5 + - + +
113B GLY 3.6 2.6 + - - -
115B VAL* 1.4 76.9 - - + +
117B CYS* 1.4 58.5 + - - +
118B LYS 3.3 0.2 - - - -
119B VAL* 3.7 16.4 - - + -
120B PHE* 3.0 66.2 + - + +
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Residues in contact with CYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TRP* 3.7 10.0 - - - +
113B GLY 3.3 13.4 + - - +
114B PRO* 3.5 11.7 - - + +
115B VAL 3.2 0.2 - - - -
116B MET* 1.4 76.7 - - - +
118B LYS* 1.4 56.2 + - - +
121B GLY* 3.4 22.5 + - - -
182B ARG* 3.9 7.5 - - - +
183B ASP* 3.5 29.6 - - - -
184B VAL* 3.8 7.0 - - + -
195B CYS* 2.0 58.0 - - - -
1201B 8ES 4.8 0.3 - - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B PRO 3.7 10.3 - - - +
115B VAL* 3.2 11.1 + - - +
117B CYS* 1.4 75.9 - - - +
119B VAL* 1.4 59.1 + - - +
122B SER* 2.7 36.5 + - - -
178B THR 5.1 0.3 - - - +
179B PHE* 2.8 54.1 + - + +
180B TYR* 3.5 17.2 + - - +
181B PHE 4.6 0.4 - - - -
182B ARG* 3.0 34.5 + - - +
183B ASP* 4.3 14.7 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.1 28.1 + - + +
116B MET* 3.6 15.2 + - + -
118B LYS* 1.4 75.1 - - + +
120B PHE* 1.4 69.5 + - + +
122B SER* 3.9 2.7 - - - -
123B PHE* 3.0 32.9 + - + +
179B PHE* 5.1 10.1 - - + -
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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
----------------------------------------------------------
96B THR* 5.0 3.1 - - + +
99B LEU* 3.7 40.2 - - + -
100B TRP* 4.2 12.6 - - + -
110B TRP* 3.7 26.0 - + + -
112B PHE* 4.6 7.4 - + - -
116B MET* 3.0 66.7 + - + +
119B VAL* 1.4 77.5 - - + +
121B GLY* 1.3 58.8 + - - +
123B PHE* 3.8 15.4 - + + +
124B LEU* 3.1 29.6 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TRP* 5.6 0.4 - - - -
117B CYS 3.4 20.1 + - - -
118B LYS 4.1 0.2 - - - -
119B VAL 3.3 0.8 - - - -
120B PHE* 1.3 78.1 - - - +
122B SER* 1.4 57.9 + - - +
124B LEU* 3.5 6.3 - - - +
125B THR* 3.0 26.5 + - - -
178B THR* 3.4 12.3 - - - +
182B ARG* 5.1 0.9 - - - -
1201B 8ES 3.9 24.7 - - - +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LYS 2.7 23.4 + - - -
119B VAL* 3.9 3.4 - - - -
121B GLY* 1.4 72.6 - - - +
123B PHE* 1.4 55.1 + - - +
124B LEU 3.2 0.2 - - - -
125B THR* 3.3 1.8 + - - +
126B LEU* 2.8 39.0 + - - +
175B SER* 3.8 15.5 - - - -
178B THR* 3.9 8.0 - - - +
179B PHE* 3.3 37.6 + - - +
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.4 50.9 - - + -
95B ALA* 5.4 2.9 - - + -
96B THR* 3.7 20.0 - - + -
119B VAL* 3.0 21.6 + - + +
120B PHE* 3.8 14.1 - + + +
122B SER* 1.4 75.4 - - - +
124B LEU* 1.3 60.8 + - - +
126B LEU* 3.9 8.9 - - + +
127B ASN* 2.8 51.2 + - - -
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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
----------------------------------------------------------
93B LEU* 3.5 19.1 - - + +
96B THR* 3.4 28.7 - - + +
100B TRP* 3.5 15.5 - - + +
120B PHE 3.1 17.6 + - - +
121B GLY 3.5 4.3 - - - +
122B SER 3.2 0.2 - - - -
123B PHE* 1.3 76.7 - - - +
125B THR* 1.4 56.4 - - - +
128B MET* 3.0 30.4 + - - +
308B PHE* 3.7 7.4 - - + -
1201B 8ES 3.5 82.8 - - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLY 3.0 16.0 + - - -
122B SER 3.3 4.6 + - - -
124B LEU* 1.4 73.0 - - - +
126B LEU* 1.4 59.1 + - - +
128B MET* 3.7 5.6 - - - +
129B PHE* 3.0 63.0 + - + -
175B SER* 4.0 13.7 - - - -
178B THR* 3.5 28.0 + - - +
1201B 8ES 3.5 33.0 + - + -
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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 SER* 2.8 22.3 + - - +
123B PHE* 3.9 9.6 - - + +
125B THR* 1.4 72.6 - - - +
127B ASN* 1.3 63.0 + - - +
130B ALA* 2.9 28.6 + - - +
168B TRP* 3.8 34.3 - - + +
171B ALA* 3.3 26.7 - - + +
172B CYS* 3.8 32.1 - - + -
175B SER* 3.8 9.3 - - - +
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Residues in contact with ASN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA 3.5 20.4 - - - +
92B LEU* 3.5 26.2 - - - +
93B LEU* 4.0 13.6 - - + +
123B PHE* 2.8 60.8 + - - +
124B LEU 4.2 0.9 - - - +
126B LEU* 1.3 77.7 - - - +
128B MET* 1.4 59.7 + - - +
130B ALA* 3.8 5.3 - - - +
131B SER* 3.1 27.9 + - - -
168B TRP* 3.8 18.9 - - - -
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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
----------------------------------------------------------
93B LEU* 3.8 18.3 - - + +
124B LEU 3.0 20.7 + - - +
125B THR* 3.7 3.1 - - - +
127B ASN* 1.4 75.3 - - - +
129B PHE* 1.4 92.3 + - + +
131B SER* 3.3 4.0 + - - -
132B ILE* 3.1 51.2 + - + +
219B GLY* 5.3 2.9 - - - -
269B TRP* 3.8 28.3 - - + -
273B HIS* 6.4 1.8 - - + +
1201B 8ES 3.4 56.5 - - + -
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B THR* 3.0 34.2 + - + +
126B LEU 4.0 2.5 - - - +
128B MET* 1.4 85.3 - - + +
130B ALA* 1.4 55.8 + - - +
132B ILE* 3.3 5.2 + - + -
133B PHE* 2.8 73.5 + + + -
171B ALA* 4.0 8.1 - - + -
174B SER* 3.7 19.3 - - - -
214B MET 5.5 0.4 - - - -
215B LYS* 5.5 2.0 - - - -
218B LEU* 3.9 24.7 - - + -
219B GLY* 3.8 31.0 - - - -
1201B 8ES 3.5 39.3 - + - -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA* 3.8 10.1 - - + -
126B LEU 2.9 18.8 + - - +
127B ASN* 3.8 5.2 - - - +
128B MET 3.4 0.2 - - - -
129B PHE* 1.4 74.6 - - - +
131B SER* 1.4 55.7 + - - +
133B PHE* 4.1 3.3 - - - -
134B PHE* 3.1 40.4 + - + -
167B VAL* 4.8 2.7 - - + -
168B TRP* 3.7 36.1 - - + -
171B ALA* 3.7 9.9 - - + +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.3 13.2 - - - +
89B ALA* 3.8 7.4 - - - +
90B ASP* 2.7 27.9 + - - -
93B LEU* 4.7 6.5 - - - +
127B ASN 3.1 19.9 + - - -
128B MET* 3.4 7.9 - - - -
129B PHE 3.2 0.2 - - - -
130B ALA* 1.4 73.3 - - - +
132B ILE* 1.4 65.9 + - - +
134B PHE 3.4 1.0 + - - -
135B ILE* 3.2 30.5 + - - +
269B TRP* 6.1 1.0 - - - -
310B ASN* 5.0 1.6 + - - -
311B SER* 4.2 2.6 + - - -
314B ASN* 3.8 10.4 + - - -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 3.1 47.4 + - + +
129B PHE* 3.8 6.3 - - + +
131B SER* 1.4 75.7 - - - +
133B PHE* 1.3 67.0 + - + +
135B ILE* 3.3 14.2 + - + +
136B THR* 2.8 28.4 + - - -
219B GLY* 3.9 21.3 - - - +
223B PRO* 3.8 33.2 - - + -
265B PHE* 4.1 16.6 - - + -
269B TRP* 4.2 22.4 - - + +
273B HIS* 5.9 0.2 - - - +
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE* 2.8 61.4 + + + +
132B ILE* 1.3 80.2 - - + +
134B PHE* 1.4 57.7 + - - +
136B THR* 3.4 12.7 - - + -
137B CYS* 3.0 31.0 + - - -
167B VAL* 3.7 33.0 - - + -
170B MET* 4.1 37.2 - - + -
171B ALA 4.3 0.4 - - - -
174B SER* 4.2 7.6 - - - -
218B LEU* 4.1 24.7 - - + -
223B PRO* 5.7 3.6 - - + -
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.7 36.5 - + + +
85B ASN* 3.7 36.1 - - + -
86B LEU* 4.2 19.3 - - + -
130B ALA* 3.1 30.1 + - + +
131B SER 4.0 3.4 - - - +
133B PHE* 1.4 73.5 - - - +
135B ILE* 1.4 59.7 + - - +
137B CYS* 3.5 7.1 + - + +
138B MET* 3.0 32.2 + - - +
164B VAL* 4.0 14.1 - - + -
167B VAL* 3.6 33.2 - - + -
168B TRP* 3.4 36.1 - + - -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU* 3.8 13.2 - - + -
131B SER* 3.2 23.4 + - - +
132B ILE* 3.4 11.9 - - + +
133B PHE 3.3 0.2 - - - -
134B PHE* 1.4 74.8 - - - +
136B THR* 1.4 58.2 + - - +
138B MET* 3.3 7.9 + - - +
139B SER* 3.1 28.4 + - - +
227B ILE* 3.8 25.4 - - + -
261B VAL* 5.6 2.7 - - + +
265B PHE* 4.4 14.4 - - + -
310B ASN* 3.6 14.1 - - - +
314B ASN* 3.5 35.0 - - - +
318B TYR* 3.4 21.7 + - - +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ILE 2.8 16.3 + - - -
133B PHE* 3.4 15.8 - - + -
135B ILE* 1.4 75.6 - - - +
137B CYS* 1.4 56.2 + - - +
139B SER* 3.3 4.5 + - - -
140B VAL* 3.1 33.5 + - + +
223B PRO* 3.6 22.5 - - + +
226B PHE* 3.7 39.9 - - + -
227B ILE* 4.4 11.3 - - - +
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Residues in contact with CYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 4.4 21.7 - - + -
133B PHE 3.0 21.6 + - - +
134B PHE* 3.7 12.1 - - - +
135B ILE 3.4 0.2 - - - -
136B THR* 1.4 73.2 - - - +
138B MET* 1.4 60.4 + - - +
140B VAL* 3.4 8.2 + - - +
141B ASP* 2.9 30.4 + - - +
163B ILE* 4.0 15.7 - - + -
167B VAL* 3.7 26.9 - - - -
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Residues in contact with MET 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 4.0 16.4 - - - +
82B TYR* 3.8 26.9 - - + -
83B ILE* 3.8 27.4 - - + -
86B LEU* 5.1 6.5 - - + -
134B PHE 3.0 17.7 + - - +
135B ILE* 3.4 10.8 - - - +
137B CYS* 1.4 75.7 - - - +
139B SER* 1.4 51.9 + - - +
141B ASP* 3.4 6.2 + - - +
142B ARG* 2.8 63.1 + - + +
318B TYR* 3.7 39.5 - - + +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.1 15.0 + - - +
136B THR 3.3 9.4 + - - -
138B MET* 1.4 76.3 - - - +
140B VAL* 1.4 55.2 + - - +
142B ARG* 3.5 8.8 + - - +
143B TYR 3.0 22.2 + - - -
226B PHE 4.8 0.4 - - - -
227B ILE* 3.7 33.0 + - - +
230B CYS* 3.4 29.8 - - - +
234B ILE* 4.9 0.3 - - - +
261B VAL* 4.7 10.0 - - - +
318B TYR* 5.1 1.8 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 3.1 18.8 + - + +
137B CYS* 3.7 7.4 - - - +
138B MET 3.3 0.2 - - - -
139B SER* 1.4 74.6 - - - +
141B ASP* 1.4 55.8 + - - +
143B TYR* 3.3 4.9 + - + +
144B GLN* 2.9 53.7 + - - +
226B PHE* 4.3 22.9 - - + -
230B CYS* 3.8 18.4 - - - -
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Residues in contact with ASP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.4 13.9 - - - +
79B SER* 3.7 24.4 + - - -
82B TYR* 4.2 23.6 - - + -
137B CYS 2.9 18.4 + - - +
138B MET* 3.7 8.4 - - - +
140B VAL* 1.4 72.7 - - - +
142B ARG* 1.4 58.6 + - - +
144B GLN* 3.6 10.9 + - - +
145B SER* 2.7 42.0 + - - -
159B GLN* 5.7 1.7 + - - -
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B MET* 2.8 40.0 + - + +
139B SER* 3.8 7.9 - - - +
141B ASP* 1.4 74.8 - - - +
143B TYR* 1.4 63.6 + - - +
145B SER* 3.5 11.9 + - - -
146B VAL* 3.4 21.5 + - - +
234B ILE* 3.9 12.0 - - + +
257B MET* 4.0 13.3 + - - +
258B ALA* 4.8 2.7 - - - +
261B VAL* 3.8 30.7 - - - +
317B LEU 3.7 19.6 + - - -
318B TYR* 4.1 16.7 + - - +
322B GLY* 4.1 10.5 + - - -
325B PHE* 3.7 59.2 - - + +
329B LEU* 5.0 1.0 - - - +
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Residues in contact with TYR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B SER 3.0 17.9 + - - +
140B VAL* 3.3 6.5 + - + +
142B ARG* 1.4 75.5 - - - +
144B GLN* 1.4 69.7 + - + +
146B VAL* 3.2 14.1 + - + +
147B ILE* 3.3 42.8 + - + +
148B TYR* 5.9 1.3 - + - -
229B THR* 4.7 5.8 - - + -
230B CYS* 3.6 39.3 - - + +
233B GLY* 3.6 31.7 - - - -
234B ILE* 3.8 9.6 - - + +
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 2.9 40.4 + - - +
141B ASP* 3.8 11.7 + - - +
142B ARG 3.4 0.2 - - - -
143B TYR* 1.4 82.5 - - + +
145B SER* 1.4 56.6 + - - +
147B ILE* 4.0 6.1 - - + -
148B TYR* 3.0 50.8 + - + +
151B LEU* 3.8 24.0 - - + +
159B GLN* 6.1 2.0 - - - +
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 2.7 29.6 + - - -
142B ARG* 3.6 10.5 - - - -
143B TYR 3.3 0.4 - - - -
144B GLN* 1.4 74.9 - - - +
146B VAL* 1.3 60.0 + - - +
148B TYR 4.0 4.3 - - - -
149B PRO* 3.4 23.1 - - - +
151B LEU* 5.6 3.3 - - - +
152B SER* 5.7 9.2 + - - +
325B PHE* 6.4 0.2 - - - -
329B LEU* 3.8 21.9 - - - +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG 3.4 15.9 - - - +
143B TYR* 3.2 7.7 + - + +
145B SER* 1.3 74.4 - - - +
147B ILE* 1.3 65.3 + - + +
148B TYR 3.4 0.2 - - - -
149B PRO* 3.6 15.8 - - - +
234B ILE* 3.8 27.8 - - + -
237B HIS* 3.5 40.4 - - + +
238B LEU* 3.8 18.8 - - + -
329B LEU* 3.8 28.9 - - + -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 3.3 46.0 + - + +
144B GLN* 4.0 4.7 - - - +
146B VAL* 1.3 80.0 - - + +
148B TYR* 1.3 99.2 + - + +
149B PRO* 3.5 7.1 - - - +
237B HIS* 4.2 28.0 + - + -
240B LYS* 6.2 0.4 - - - +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 5.9 1.8 - + - -
144B GLN* 3.0 39.8 + - + +
145B SER* 3.6 5.4 - - - +
147B ILE* 1.3 111.8 - - + +
149B PRO* 1.4 64.2 - - - +
150B PHE* 3.2 37.9 + + + -
151B LEU* 3.5 22.5 + - + +
152B SER 4.9 0.2 + - - -
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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