Contacts of the helix formed by residues 179 - 206 (chain B) in PDB entry 3H90
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 ASP 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B HIS* 4.0 22.5 + - - +
110B PRO* 4.6 11.6 - - - +
111B MET 5.1 1.0 + - - -
112B THR* 4.7 16.5 + - - -
164B ILE* 3.7 25.4 - - - +
178B ALA* 1.3 81.5 - - - +
180B ALA* 1.3 55.9 + - - +
181B LEU 3.5 0.2 - - - -
182B PHE* 2.9 10.6 + - + +
183B ALA* 2.6 42.0 + - + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLY 3.8 10.3 - - - +
104B HIS* 3.7 22.7 + - - +
105B LEU* 3.7 31.2 - - + -
106B ILE* 5.8 0.7 - - + -
178B ALA* 3.2 9.2 - - + +
179B ASP* 1.3 76.4 - - - +
181B LEU* 1.3 57.5 + - - +
182B PHE 2.9 0.9 + - - -
183B ALA* 4.5 2.9 - - - +
184B LEU* 2.7 39.9 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 5.4 0.9 - - - +
177B ARG* 6.0 5.2 - - + +
178B ALA 4.5 5.6 + - - +
179B ASP 3.5 0.8 - - - -
180B ALA* 1.3 77.4 - - - +
182B PHE* 1.3 78.4 + - + +
184B LEU* 4.8 8.2 - - + +
185B GLY* 3.5 19.1 + - - -
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Residues in contact with PHE 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASN* 3.2 36.6 - - - +
163B ALA* 4.6 19.3 - - + -
164B ILE* 6.3 1.1 - - + -
178B ALA 5.4 3.6 - - - +
179B ASP* 2.9 12.2 + - - +
181B LEU* 1.3 101.6 - - + +
183B ALA* 1.3 63.1 + - - +
184B LEU 3.2 1.3 - - - -
185B GLY* 4.0 0.4 - - - -
186B ILE* 3.2 36.0 + - + +
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Residues in contact with ALA 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.1 39.0 - - + +
100B THR* 5.5 1.3 - - + -
101B GLY* 4.3 9.9 - - - +
104B HIS* 4.8 9.4 - - + +
161B ASN* 5.5 0.2 - - - +
179B ASP* 2.6 30.8 + - + +
180B ALA* 4.1 1.3 - - - +
182B PHE* 1.3 72.2 - - - +
184B LEU* 1.3 58.4 + - - +
186B ILE* 5.0 2.9 - - - -
187B GLY 3.5 11.2 + - - -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU 4.6 0.7 - - - -
98B PHE* 3.7 23.3 - - + -
101B GLY* 3.8 14.3 - - - +
102B ILE* 3.5 37.7 - - + +
105B LEU* 4.7 8.7 - - + -
180B ALA 2.7 23.0 + - - +
181B LEU* 4.9 8.5 - - + +
183B ALA* 1.3 71.8 - - - +
185B GLY* 1.3 59.6 + - - +
186B ILE 3.2 0.4 - - - -
187B GLY* 3.0 16.1 + - - -
188B ILE* 3.0 32.6 + - + +
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Residues in contact with GLY 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B LEU 3.5 18.7 + - - -
182B PHE* 3.5 1.3 + - - -
184B LEU* 1.3 85.6 - - - +
186B ILE* 1.3 60.2 + - - +
188B ILE* 3.8 7.4 + - - +
189B TYR* 3.4 22.2 + - - +
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.0 20.6 - - + -
156B SER* 5.0 6.5 - - - +
159B MET* 3.6 53.4 - - + +
161B ASN* 4.3 13.5 - - - +
182B PHE* 3.2 22.8 + - + +
183B ALA* 5.0 2.2 - - - -
185B GLY* 1.3 73.9 - - - +
187B GLY* 1.3 62.4 + - - +
188B ILE 3.1 0.5 + - - -
189B TYR* 3.1 4.4 + - - -
190B ILE* 2.8 50.2 + - + +
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA* 3.4 25.5 - - - +
97B LEU* 4.2 6.2 - - - +
98B PHE* 3.9 14.9 - - - +
183B ALA 3.5 10.7 + - - -
184B LEU 3.0 8.5 + - - -
186B ILE* 1.3 79.5 - - - +
188B ILE* 1.3 58.4 + - - +
191B LEU* 3.2 25.3 + - - +
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Residues in contact with ILE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.6 33.0 - - + -
184B LEU* 3.0 26.4 + - + +
185B GLY* 4.0 9.2 - - - +
187B GLY* 1.3 74.3 - - - +
189B TYR* 1.3 64.2 + - + +
191B LEU* 3.1 8.3 + - - +
192B TYR* 2.9 33.2 + - + +
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Residues in contact with TYR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 5.9 1.3 - - + -
155B GLN* 5.4 5.3 + - + -
159B MET* 4.1 26.7 - - + -
185B GLY 3.4 14.8 + - - +
186B ILE* 3.1 4.3 + - - +
188B ILE* 1.3 82.3 - - + +
190B ILE* 1.3 76.5 + - + +
192B TYR* 3.7 12.8 + + - +
193B SER* 3.0 49.9 + - - -
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.9 24.0 - - + +
93B SER* 6.4 0.2 - - - -
94B ALA* 3.8 17.0 - - + -
152B LEU* 4.3 19.2 - - + +
155B GLN* 4.7 2.9 - - + -
156B SER* 4.1 33.9 - - - +
159B MET* 4.3 6.5 - - - -
186B ILE* 2.8 41.1 + - + +
189B TYR* 1.3 91.9 - - + +
191B LEU* 1.3 54.6 + - - +
193B SER* 3.1 2.4 + - - -
194B ALA* 2.7 34.0 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B SER* 3.3 41.0 + - - +
94B ALA* 3.4 10.2 - - + +
95B LEU* 4.5 25.1 - - + +
98B PHE* 5.7 7.4 - - + -
187B GLY 3.2 21.1 + - - +
188B ILE* 3.1 5.5 + - - +
190B ILE* 1.3 76.1 - - - +
192B TYR* 1.3 62.9 + - - +
194B ALA* 3.4 3.3 + - - -
195B LEU* 3.1 44.8 + - + +
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Residues in contact with TYR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 2.9 21.5 + - + +
189B TYR* 3.8 13.7 - + - +
191B LEU* 1.3 76.8 - - - +
193B SER* 1.3 69.8 + - - +
195B LEU* 3.3 8.4 + - - +
196B ARG* 3.1 51.9 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B LEU* 3.7 25.8 - - - +
189B TYR* 3.0 40.6 + - - -
190B ILE* 3.1 5.4 + - - -
192B TYR* 1.3 86.4 - - - +
194B ALA* 1.3 57.4 + - - +
196B ARG* 4.1 5.6 - - - +
197B MET* 3.1 25.3 + - - +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER* 2.6 32.8 + - - +
90B ILE* 3.8 27.1 - - + -
91B SER* 3.6 27.2 + - - +
152B LEU* 3.6 8.7 - - + +
190B ILE 2.7 19.4 + - - +
191B LEU 3.9 1.1 - - - +
192B TYR 3.2 0.4 - - - -
193B SER* 1.3 71.6 - - - +
195B LEU* 1.3 59.1 + - - +
197B MET* 3.6 4.0 - - - +
198B GLY 3.3 5.0 + - - -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER* 4.8 1.1 - - - +
91B SER* 3.5 17.5 - - - +
191B LEU* 3.1 39.2 + - + +
192B TYR* 3.9 5.8 - - - +
194B ALA* 1.3 76.1 - - - +
196B ARG* 1.3 66.0 + - - +
197B MET 3.0 1.6 - - - -
198B GLY* 3.0 2.4 + - - -
199B TYR* 2.9 26.3 + - - +
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Residues in contact with ARG 196 (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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192B TYR* 3.1 45.3 + - + +
193B SER* 4.1 5.8 - - - +
195B LEU* 1.3 75.3 - - - +
197B MET* 1.3 61.1 + - - +
199B TYR* 3.9 34.5 + - - +
200B GLU* 3.5 37.8 + - - +
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 4.2 11.9 - - + +
87B SER* 4.1 16.2 - - - -
90B ILE* 6.3 0.4 - - + -
145B GLN* 3.6 25.8 - - + +
148B ARG* 3.9 33.9 - - - +
149B ALA* 3.8 28.9 - - + +
152B LEU* 4.3 13.0 - - + -
193B SER 3.1 22.6 + - - +
194B ALA* 3.6 8.7 - - - +
196B ARG* 1.3 77.3 - - - +
198B GLY* 1.3 62.9 + - - +
199B TYR 3.4 0.3 + - - -
200B GLU* 3.5 11.3 + - - +
201B ALA* 3.3 17.8 + - - +
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.4 6.8 - - - +
87B SER* 3.1 26.7 - - - -
194B ALA 3.3 4.2 + - - -
195B LEU* 3.0 6.4 + - - -
197B MET* 1.3 78.2 - - - +
199B TYR* 1.3 59.1 + - - +
201B ALA* 3.3 8.7 + - - +
202B VAL* 3.0 32.6 + - - +
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU 2.9 16.0 + - - +
196B ARG* 4.0 33.4 - - - +
198B GLY* 1.3 73.9 - - - +
200B GLU* 1.3 66.4 + - + +
202B VAL* 2.9 18.2 + - + +
203B GLN* 2.8 65.6 + - + +
208B ARG* 4.9 6.0 + - - -
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLN* 3.7 10.4 + - - +
148B ARG* 2.8 38.2 + - - +
196B ARG* 3.5 30.6 + - + +
197B MET* 3.5 11.5 + - - +
199B TYR* 1.3 84.9 - - + +
201B ALA* 1.3 61.6 + - - +
203B GLN* 3.5 8.6 + - - +
204B SER* 3.1 26.0 + - - -
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER* 3.5 23.3 - - - +
83B ALA* 4.2 9.9 - - + -
84B LEU* 3.8 17.5 - - + +
145B GLN* 4.1 12.5 - - - +
197B MET 3.3 10.0 + - - +
198B GLY* 3.3 11.7 - - - +
199B TYR 3.0 0.4 - - - -
200B GLU* 1.3 77.3 - - - +
202B VAL* 1.3 62.9 + - - +
204B SER* 3.3 4.2 + - - -
205B LEU* 3.1 27.9 + - - +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.6 26.0 - - + -
198B GLY 3.0 14.0 + - - +
199B TYR* 2.9 32.3 + - + +
201B ALA* 1.3 67.0 - - - +
203B GLN* 1.3 67.8 + - + +
204B SER 3.0 1.8 - - - -
205B LEU* 2.8 10.1 + - - +
206B LEU* 2.8 41.6 + - + +
81D LEU* 3.9 17.9 - - + -
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Residues in contact with GLN 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 2.8 58.6 + - + +
200B GLU* 3.6 9.0 - - - +
202B VAL* 1.3 79.5 - - + +
204B SER* 1.3 53.7 + - - +
206B LEU* 2.5 33.3 - - - +
208B ARG* 2.6 63.5 + - - +
62D TYR* 4.5 4.6 + - - -
71D HIS* 3.0 25.4 + - - -
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.3 21.4 - - - -
80B SER* 3.8 17.5 - - - -
145B GLN* 4.0 12.4 + - - -
200B GLU 3.1 16.1 + - - -
201B ALA 3.7 5.4 - - - -
202B VAL 3.0 0.4 - - - -
203B GLN* 1.3 73.5 - - - +
205B LEU* 1.3 59.5 + - - +
206B LEU 2.9 13.8 - - - +
207B ASP* 4.2 1.9 - - - -
208B ARG* 4.7 2.9 + - - +
238B GLN* 4.8 14.2 + - - +
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Residues in contact with LEU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.7 20.5 + - + +
80B SER* 4.1 21.5 - - - +
81B LEU* 3.6 30.3 - - + -
84B LEU* 3.6 31.4 - - + -
201B ALA 3.1 17.2 + - - +
202B VAL* 2.8 7.5 + - - +
204B SER* 1.3 75.9 - - - +
206B LEU* 1.3 63.3 + - - +
207B ASP 3.7 0.2 + - - -
77D LYS* 3.5 30.7 + - - +
81D LEU* 3.9 20.0 - - + -
205D LEU* 4.3 17.8 - - + +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 2.8 24.7 + - + +
203B GLN* 2.5 50.7 - - - +
204B SER 2.9 6.8 - - - +
205B LEU* 1.3 73.3 - - - +
207B ASP* 1.3 53.7 + - - +
208B ARG 2.6 6.8 + - - -
62D TYR* 4.3 23.1 - - + -
71D HIS* 4.2 14.8 - - + +
75D HIS* 5.3 6.7 - - - +
77D LYS* 3.9 9.9 - - + -
78D ALA* 3.6 29.6 - - + +
81D LEU* 3.4 26.7 - - + -
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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