Contacts of the helix formed by residues 137 - 164 (chain A) in PDB entry 2Y60
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 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LYS* 6.5 0.7 - - - -
132A GLU* 2.9 16.8 + - - -
135A HIS 3.2 0.4 + - - -
136A PRO* 1.3 72.6 - - - +
138A PHE* 1.3 57.7 + - - +
139A GLN 3.5 2.2 - - - -
140A ASP* 3.5 13.3 + - - +
141A PHE* 2.9 31.0 + - - +
1335A SO4 4.8 0.9 + - - -
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 4.5 11.9 - - + -
58A THR* 5.3 1.8 - - - -
61A PHE* 3.6 57.9 - + + -
103A PHE* 3.9 10.5 - + - -
129A TRP* 3.7 24.0 - + - -
130A PRO* 3.9 20.4 - - + -
135A HIS* 3.1 25.6 + - + +
136A PRO 3.2 3.1 + - - +
137A GLY* 1.3 74.3 - - - +
139A GLN* 1.3 64.4 + - - +
141A PHE* 3.2 12.3 + + - +
142A ALA* 2.8 35.4 + - + +
186A LEU* 3.8 23.1 - - + -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TRP* 3.4 59.6 - - + +
130A PRO* 5.3 2.2 - - + +
132A GLU* 4.7 12.5 + - - +
135A HIS 4.6 1.0 + - - -
137A GLY 3.5 0.2 - - - -
138A PHE* 1.3 81.0 - - + +
140A ASP* 1.3 63.9 + - - +
142A ALA* 3.2 1.4 + - - +
143A GLU* 2.9 58.7 + - - +
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Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 4.8 9.6 + - - +
137A GLY* 3.5 15.6 + - - +
138A PHE 3.2 0.4 - - - -
139A GLN* 1.3 83.8 - - - +
141A PHE* 1.3 64.3 + - - +
143A GLU* 3.9 12.8 - - - +
144A GLN* 3.0 25.1 + - - +
1335A SO4 3.6 9.3 + - - +
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Residues in contact with PHE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASN 5.5 0.9 - - - -
53A ARG* 3.5 28.9 - - + +
54A LEU* 3.5 47.1 - - + -
57A LYS* 3.6 41.7 - - + -
58A THR* 5.0 1.8 - - - -
137A GLY 2.9 19.4 + - - +
138A PHE* 3.5 11.9 - + - +
140A ASP* 1.3 76.3 - - - +
142A ALA* 1.3 65.6 + - + +
144A GLN* 3.3 2.1 + - - +
145A TYR* 2.8 38.6 + + + +
1335A SO4 3.3 26.4 + - - +
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Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 2.8 39.7 + - + +
129A TRP* 3.6 26.7 - - + -
138A PHE* 2.8 29.0 + - + +
141A PHE* 1.3 84.8 - - + +
143A GLU* 1.3 63.7 + - - +
145A TYR* 3.2 2.3 + - - -
146A TYR 3.0 13.2 + - - -
186A LEU* 5.4 1.3 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 4.8 0.9 - - - -
108A PRO* 4.0 35.5 - - + +
127A ASN* 5.4 0.2 + - - -
129A TRP* 3.9 20.0 + - + -
139A GLN* 2.9 50.0 + - - +
140A ASP* 3.9 12.1 - - - +
142A ALA* 1.3 74.7 - - - +
144A GLN* 1.3 66.9 + - - +
146A TYR* 3.2 11.9 + - - +
147A TRP* 3.2 22.7 + - + +
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Residues in contact with GLN 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASP 3.0 18.5 + - - +
141A PHE* 3.7 3.8 - - + +
143A GLU* 1.3 76.7 - - - +
145A TYR* 1.3 64.4 + - - +
147A TRP* 3.1 18.3 + - - +
148A ASP* 2.9 51.6 + - - +
1335A SO4 3.8 29.2 + - - +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.0 16.4 - - + -
54A LEU* 3.6 39.7 - - + +
105A TYR* 3.7 15.7 - - - +
141A PHE* 2.8 33.2 + + + +
142A ALA 3.6 4.0 - - - +
143A GLU 3.2 0.2 - - - -
144A GLN* 1.3 72.6 - - - +
146A TYR* 1.3 67.4 - - - +
148A ASP* 3.0 10.9 + - + +
149A VAL* 2.9 46.4 + - + +
184A VAL* 4.3 19.7 - - + -
186A LEU* 5.5 1.1 - - + -
222A VAL 5.4 0.2 + - - -
249A TYR* 2.7 41.6 + - - -
282A LEU* 4.7 10.2 + - + -
283A PRO 6.0 0.4 - - - -
284A PHE* 5.3 3.3 - - + +
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Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 4.0 11.7 - + + -
106A LEU* 3.5 21.5 - - - -
107A ASN* 3.4 20.4 - - - +
108A PRO* 3.5 21.8 - - + -
142A ALA 3.0 13.1 + - - +
143A GLU 3.2 11.6 + - - +
145A TYR* 1.3 75.8 - - - +
147A TRP* 1.4 85.2 + + - +
149A VAL* 3.5 9.1 - - - +
150A PHE* 2.8 32.8 + + - +
180A THR* 3.5 11.2 - - + +
182A ALA* 2.7 39.2 + - + +
184A VAL* 3.8 19.5 - - + -
284A PHE* 3.9 18.7 - + - -
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Residues in contact with TRP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ASN* 3.5 17.7 - - - -
108A PRO* 3.8 21.0 - - + +
109A ASN* 3.5 33.7 - - - -
143A GLU* 3.2 24.9 + - + +
144A GLN* 3.1 20.1 + - - +
146A TYR* 1.4 96.4 - + - +
148A ASP* 1.3 59.5 + - - +
150A PHE* 3.5 26.4 - + - +
151A GLY* 2.9 25.1 + - - -
177A PRO* 3.6 29.8 - - + -
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Residues in contact with ASP 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.5 29.0 - - + +
50A ASN 5.8 0.7 + - - -
144A GLN* 2.9 46.5 + - - +
145A TYR* 3.0 15.5 + - + +
147A TRP* 1.3 76.3 - - - +
149A VAL* 1.3 58.2 + - - +
151A GLY* 3.3 2.9 + - - -
152A LEU* 3.1 21.3 + - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 3.7 13.0 - - + -
145A TYR* 2.9 53.3 + - + +
146A TYR* 3.5 8.3 - - - +
148A ASP* 1.3 72.3 - - - +
150A PHE* 1.3 62.2 + - - +
152A LEU* 3.8 1.3 - - + +
153A SER* 2.8 34.6 + - - -
222A VAL* 3.8 22.7 - - + -
249A TYR* 4.4 2.2 - - + -
284A PHE* 3.5 42.0 - - + -
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Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A TYR* 2.8 23.8 + + + +
147A TRP* 3.5 27.8 - + + +
148A ASP 3.3 0.2 - - - -
149A VAL* 1.3 77.6 - - - +
151A GLY* 1.3 60.3 + - - +
153A SER* 3.1 3.0 + - - -
154A SER* 2.8 46.0 + - - -
175A PHE* 3.3 53.5 - + - -
176A LYS 4.0 4.7 - - - -
177A PRO* 3.6 29.4 - - + -
180A THR* 3.7 24.5 - - + -
284A PHE* 4.0 11.4 - + + -
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Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.0 8.7 - - - -
147A TRP 2.9 15.4 + - - -
148A ASP* 3.7 3.4 - - - -
149A VAL 3.3 0.2 - - - -
150A PHE* 1.3 80.0 - - - +
152A LEU* 1.3 65.8 + - - +
154A SER* 3.3 7.5 + - - -
155A ALA* 3.1 21.1 + - - +
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.1 14.1 - - + -
18A PHE* 3.8 23.6 - - + -
44A ALA* 5.0 1.6 - - + -
47A HIS* 3.7 26.2 - - + +
49A ILE* 3.9 22.2 - - + -
148A ASP 3.1 7.2 + - - +
149A VAL* 3.8 6.1 - - - +
151A GLY* 1.3 75.1 - - - +
153A SER* 1.4 59.0 + - - +
155A ALA* 3.1 3.4 + - + +
156A LEU* 2.8 43.5 + - + +
222A VAL* 4.0 16.8 - - + -
249A TYR* 3.7 34.5 - - + -
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Residues in contact with SER 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A VAL 2.8 23.6 + - - -
150A PHE 3.1 4.0 + - - -
152A LEU* 1.4 73.4 - - - +
154A SER* 1.3 62.3 + - - +
156A LEU* 3.3 10.9 + - - +
157A LEU* 2.8 33.5 + - - +
175A PHE* 3.9 9.0 - - - -
220A ILE* 4.6 0.8 - - - +
222A VAL* 3.4 10.6 - - - +
284A PHE* 3.2 23.2 - - - -
286A VAL* 3.3 24.6 - - - +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PHE* 2.8 29.1 + - - -
151A GLY* 3.5 10.5 - - - -
153A SER* 1.3 78.1 - - - +
155A ALA* 1.3 62.2 + - - +
157A LEU* 3.2 7.2 + - - +
158A LYS* 3.1 36.1 + - - +
172A ALA* 4.4 8.0 - - - +
175A PHE* 3.5 21.5 + - - -
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 6.3 0.7 - - + -
17A LEU* 3.3 38.0 - - + +
18A PHE* 3.8 25.8 - - + -
151A GLY 3.1 9.6 + - - +
152A LEU* 3.1 9.7 + - + +
154A SER* 1.3 79.1 - - - +
156A LEU* 1.3 62.3 + - + +
158A LYS* 3.1 20.5 + - - +
159A GLY 3.2 9.0 + - - -
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.8 33.9 - - + -
17A LEU* 4.1 4.9 - - + -
32A ILE* 4.5 2.6 - - + +
42A PHE* 4.2 14.6 - - + -
44A ALA* 4.2 9.0 - - + -
152A LEU* 2.8 34.3 + - + +
153A SER* 3.6 6.7 - - - +
155A ALA* 1.3 78.2 - - + +
157A LEU* 1.3 56.2 + - - +
159A GLY* 3.0 4.0 + - - -
160A TYR* 2.9 34.3 + - + -
220A ILE* 4.0 12.8 - - + -
222A VAL* 3.9 18.4 - - + -
251A ILE* 3.6 29.2 - - + -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER 2.8 16.7 + - - +
154A SER* 3.2 5.6 + - - +
156A LEU* 1.3 77.2 - - - +
158A LYS* 1.3 61.4 + - - +
160A TYR* 4.4 4.9 - - + +
161A ALA* 3.0 23.4 + - - +
168A GLU 4.2 1.6 - - - +
171A PHE* 3.8 31.4 - - + +
172A ALA* 4.4 9.2 - - + +
175A PHE* 3.9 39.9 - - + -
219A LEU* 3.7 27.6 - - + -
220A ILE* 4.1 26.0 - - + -
257A MET* 5.0 0.7 - - + -
286A VAL* 4.0 11.0 - - + -
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Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.3 22.6 + - + +
18A PHE* 6.3 0.2 - - - +
25A LYS* 5.5 1.8 - - - +
154A SER* 3.1 24.3 + - - +
155A ALA* 3.1 10.6 + - - +
157A LEU* 1.3 75.4 - - - +
159A GLY* 1.3 58.8 + - - +
161A ALA* 3.4 2.4 + - - +
162A LEU* 3.0 37.1 + - + +
168A GLU* 3.3 52.4 + - + +
169A ASN* 4.0 18.1 - - - +
172A ALA* 4.7 7.2 - - + -
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Residues in contact with GLY 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.9 20.5 - - - +
29A ALA* 3.6 9.8 - - - +
32A ILE* 3.9 16.8 - - - -
155A ALA 3.2 5.1 + - - -
156A LEU 3.0 7.7 + - - -
158A LYS* 1.3 77.3 - - - +
160A TYR* 1.3 58.1 + - - +
162A LEU* 3.4 4.3 + - - -
163A ALA* 2.9 29.3 + - - +
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Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.6 18.3 - - + +
36A SER* 3.5 17.1 + - - -
42A PHE* 3.3 23.4 - + - -
156A LEU* 2.9 29.6 + - + -
157A LEU* 3.9 8.3 - - + +
159A GLY* 1.3 71.3 - - - +
161A ALA* 1.3 67.0 + - - +
163A ALA* 3.3 5.7 + - - +
164A LEU* 3.1 28.3 + - + +
171A PHE* 4.0 15.0 - - + -
220A ILE* 3.7 33.2 - - + -
251A ILE* 3.4 15.7 - - + +
252A ASN* 4.2 6.8 - - - -
253A CYS* 3.4 25.1 - - - -
257A MET* 3.9 13.7 - - + -
265A TYR* 3.9 15.7 - + - -
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 3.0 17.5 + - - +
158A LYS 3.6 4.9 - - - +
160A TYR* 1.3 77.6 - - - +
162A LEU* 1.3 62.4 + - - +
164A LEU* 3.1 8.8 + - - -
166A LYS* 3.0 28.0 + - - +
167A GLU 3.3 24.0 - - - +
168A GLU* 3.8 8.5 - - - +
170A PHE* 3.8 15.0 - - + +
171A PHE* 3.7 13.8 - - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 5.1 0.9 - - + -
22A GLN* 5.4 2.2 - - - +
25A LYS* 3.9 40.8 - - + +
26A MET* 4.2 30.1 - - + +
29A ALA* 3.7 15.5 - - + +
158A LYS 3.0 23.5 + - - +
159A GLY* 5.0 2.0 - - - -
161A ALA* 1.3 76.9 - - - +
163A ALA* 1.3 64.0 + - - +
165A GLY* 3.0 14.0 + - - -
166A LYS 3.6 17.5 - - - +
167A GLU* 4.4 1.3 - - - -
168A GLU* 4.0 25.1 - - + +
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA* 3.4 29.3 - - - +
32A ILE* 4.5 2.0 - - + -
33A ASP* 3.9 16.4 - - + +
159A GLY 2.9 16.9 + - - +
160A TYR* 3.5 8.7 - - - +
161A ALA 3.2 0.2 - - - -
162A LEU* 1.3 77.9 - - - +
164A LEU* 1.3 57.4 + - - +
165A GLY 3.2 0.9 + - - -
264A TYR* 5.2 1.6 + - - -
265A TYR* 3.1 26.6 + - + +
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR 3.1 14.5 + - - +
161A ALA 3.1 6.5 + - - +
163A ALA* 1.3 74.4 - - - +
165A GLY* 1.3 61.0 + - - +
166A LYS* 3.4 14.0 - - + +
171A PHE* 3.5 32.5 - - + -
257A MET* 4.2 1.6 - - + -
261A THR* 3.8 24.7 - - + -
264A TYR* 3.7 23.1 - - + -
265A TYR* 3.5 33.4 - - + -
297A PHE* 4.1 14.2 - - + -
299A PRO* 3.8 18.7 - - + +
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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