Contacts of the helix formed by residues 182 - 208 (chain B) in PDB entry 3JRQ
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 SER 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B VAL* 3.7 3.8 - - - -
181B ASN* 1.3 75.7 - - - +
183B GLU* 1.3 62.8 + - - +
184B GLU* 3.3 22.8 + - - +
185B ASP* 2.9 37.6 + - - -
186B THR* 2.9 28.6 + - - -
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Residues in contact with GLU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 5.4 6.6 - - - +
56B ARG 3.4 18.9 - - - +
57B CYS* 3.9 13.4 - - + -
58B SER 4.6 0.5 + - - -
177B VAL* 4.0 20.9 - - + +
182B SER* 1.3 73.7 - - - +
184B GLU* 1.3 73.5 + - + +
186B THR* 3.8 1.8 - - - -
187B ARG* 3.0 49.5 + - - +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B SER* 3.2 15.8 + - - +
183B GLU* 1.3 95.3 + - + +
185B ASP* 1.3 64.4 + - - +
187B ARG* 3.8 11.5 - - - +
188B LEU* 2.9 25.6 + - - +
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Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ILE* 3.2 34.8 - - + +
299A GLN* 5.3 1.6 + - - +
300A TRP* 4.3 0.7 - - + -
180B GLY 5.0 0.5 - - - +
181B ASN* 3.0 31.0 + - + +
182B SER* 2.9 39.0 + - - +
184B GLU* 1.3 77.5 - - - +
186B THR* 1.3 60.1 + - - +
188B LEU* 3.1 8.1 + - - +
189B PHE* 2.9 30.3 + - - +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TRP* 3.6 22.9 - - + -
57B CYS* 3.9 14.1 - - + -
144B LEU* 5.0 3.8 - - + -
173B TYR* 5.4 0.7 - - + -
175B VAL* 3.6 30.5 - - + -
176B ASP 4.4 2.0 - - - +
177B VAL* 3.7 4.4 - - - +
178B PRO* 3.3 27.2 - - + +
181B ASN* 4.2 0.3 - - - +
182B SER 2.9 19.2 + - - -
183B GLU* 3.8 4.3 - - - -
184B GLU 3.2 0.4 - - - -
185B ASP* 1.3 80.0 - - - +
187B ARG* 1.3 64.0 + - - +
189B PHE* 3.3 2.8 + - - +
190B ALA* 3.0 24.0 + - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B CYS* 3.8 6.5 - - - -
58B SER 2.9 25.5 + - - +
59B SER* 3.5 12.9 + - - -
173B TYR* 3.4 10.5 - - - +
183B GLU* 3.0 48.8 + - - +
184B GLU* 3.8 10.5 - - - +
186B THR* 1.3 79.9 - - - +
188B LEU* 1.3 57.3 + - - +
191B ASP* 2.7 53.8 + - - +
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Residues in contact with LEU 188 (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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296A LYS* 3.7 41.1 - - + +
298A ILE* 4.0 25.4 - - + -
306A PHE* 4.1 29.8 - - + +
184B GLU 2.9 14.9 + - - +
185B ASP* 3.1 9.2 + - - +
187B ARG* 1.3 78.4 - - - +
189B PHE* 1.4 60.5 + - - +
191B ASP* 4.3 2.6 - - + +
192B THR* 2.8 34.1 + - - +
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Residues in contact with PHE 189 (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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298A ILE* 4.2 9.6 - - + +
300A TRP* 3.6 29.2 - + + -
306A PHE 3.7 10.5 + - - -
307A GLY* 3.5 36.3 - - - -
308A VAL* 4.2 11.0 - - + -
1B A8S 3.1 42.4 - - + -
114B LEU* 5.9 1.3 - - + -
115B PRO* 3.7 12.8 - - + -
144B LEU* 3.9 24.9 - - + -
185B ASP 2.9 18.6 + - - +
186B THR 3.3 3.6 + - - +
188B LEU* 1.4 75.9 - - - +
190B ALA* 1.3 67.3 + - - +
192B THR* 3.5 3.3 - - - -
193B VAL* 3.2 31.3 + - + +
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A8S 4.1 22.2 - - + -
144B LEU* 5.3 5.4 - - + -
147B TYR* 4.8 3.1 - - + -
173B TYR* 3.5 35.2 - - + +
175B VAL* 5.7 0.4 - - + -
186B THR* 3.0 14.2 + - + +
189B PHE* 1.3 81.7 - - + +
191B ASP* 1.3 63.6 + - - +
193B VAL* 3.2 2.3 + - - +
194B ILE* 3.1 28.3 + - - +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.2 20.2 + - - -
60B LEU 5.6 0.2 - - - +
61B LEU* 3.4 23.6 - - + +
173B TYR* 2.7 29.3 + - - -
187B ARG* 2.7 42.2 + - - +
188B LEU* 4.3 3.6 - - + +
190B ALA* 1.3 74.1 - - - +
192B THR* 1.3 56.0 + - - +
194B ILE 4.6 0.2 - - - +
195B ARG* 2.9 32.4 + - - +
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.6 43.5 - - + +
308A VAL* 4.3 11.7 - - + -
320A LEU* 4.6 7.4 - - + -
188B LEU* 2.8 25.0 + - - +
189B PHE 3.5 4.7 - - - -
191B ASP* 1.3 77.0 - - - +
193B VAL* 1.3 61.9 + - - +
195B ARG* 4.0 4.5 - - - +
196B LEU* 3.2 36.7 + - + +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 4.7 9.6 - - + -
1B A8S 3.6 43.5 - - + -
88B PHE* 4.0 26.9 - - + -
114B LEU* 6.0 1.3 - - + -
189B PHE* 3.2 34.5 + - + +
190B ALA 3.2 6.0 + - - +
192B THR* 1.3 73.8 - - - +
194B ILE* 1.3 66.8 + - - +
195B ARG 3.2 0.5 + - - -
196B LEU* 3.2 8.9 + - - +
197B ASN* 3.0 29.2 + - - +
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B A8S 3.4 22.9 - - + -
61B LEU* 4.0 15.0 - - + -
147B TYR* 3.2 22.9 - - - +
171B GLU* 3.6 31.2 - - + +
173B TYR* 3.4 28.5 - - + -
190B ALA 3.1 17.3 + - - +
191B ASP 4.3 2.0 - - - +
193B VAL* 1.3 74.4 - - - +
195B ARG* 1.3 57.7 + - - +
197B ASN* 3.3 9.2 + - - +
198B LEU* 2.9 48.0 + - + +
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Residues in contact with ARG 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 3.9 31.2 - - + +
62B ALA 2.7 39.7 + - - +
63B GLN* 3.9 11.3 + - - -
191B ASP 2.9 21.1 + - - +
192B THR* 4.0 5.6 - - - +
193B VAL 3.1 0.4 - - - -
194B ILE* 1.3 78.1 - - - +
196B LEU* 1.3 58.6 + - + +
198B LEU* 3.3 8.0 + - - +
199B GLN* 2.9 60.5 + - - +
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Residues in contact with LEU 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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238A GLU* 4.7 5.6 - - - +
319A TYR* 3.7 53.8 - - + +
320A LEU* 5.1 0.9 - - + -
87B HIS* 3.4 25.1 + - + -
88B PHE* 3.9 21.1 - - + -
192B THR* 3.2 33.0 + - + +
193B VAL 3.2 4.0 + - - +
195B ARG* 1.3 78.8 - - + +
197B ASN* 1.3 63.7 + - - +
199B GLN* 3.4 19.1 + - - +
200B LYS 3.0 17.7 + - - -
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Residues in contact with ASN 197 (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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1B A8S 3.8 16.8 + - - +
85B TYR* 3.2 31.5 - - + -
86B LYS* 3.7 27.3 - - - +
87B HIS* 3.3 27.3 + - - +
88B PHE* 4.4 5.2 - - - -
171B GLU* 5.4 5.1 + - - +
193B VAL* 3.0 31.3 + - - +
194B ILE* 3.5 10.1 - - - +
196B LEU* 1.3 73.4 - - - +
198B LEU* 1.3 58.7 + - + +
200B LYS* 3.2 1.3 + - - +
201B LEU 2.8 23.2 + - - -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU* 4.0 22.0 - - + +
62B ALA 5.0 0.2 - - - -
63B GLN* 3.6 29.5 - - + +
85B TYR* 5.2 4.3 - - + +
151B THR* 5.6 1.8 - - + -
169B VAL* 3.9 26.7 - - + +
171B GLU* 4.3 19.3 - - + +
194B ILE* 2.9 40.8 + - + +
195B ARG* 3.6 12.6 - - - +
196B LEU 3.2 0.2 - - - -
197B ASN* 1.3 76.4 - - - +
199B GLN* 1.3 61.8 + - - +
201B LEU* 3.5 17.7 - - + +
202B ALA* 2.8 27.9 + - - +
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Residues in contact with GLN 199 (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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238A GLU* 5.3 3.1 - - - +
63B GLN* 3.8 16.4 - - - +
195B ARG* 2.9 41.9 + - - +
196B LEU* 3.8 24.0 - - - +
198B LEU* 1.3 77.6 - - - +
200B LYS* 1.3 57.5 + - - +
202B ALA* 3.6 5.1 - - - +
203B SER* 3.1 28.4 + - - -
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Residues in contact with LYS 200 (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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83B GLN 4.0 15.2 + - - -
84B ILE 3.6 16.6 + - - -
85B TYR* 2.9 26.5 - - - +
86B LYS 4.0 7.1 + - - -
87B HIS* 3.5 41.9 + - + +
196B LEU 3.0 18.6 + - - +
197B ASN 3.6 0.9 - - - +
199B GLN* 1.3 74.7 - - - +
201B LEU* 1.3 64.1 + - - +
203B SER* 3.7 5.4 - - - -
204B ILE* 3.0 42.2 + - + +
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Residues in contact with LEU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.0 17.3 - - + -
72B VAL* 4.2 4.3 - - + +
75B VAL* 3.6 26.5 - - + -
76B VAL* 3.7 27.4 - - + -
85B TYR* 3.8 22.8 - - + +
151B THR* 5.9 0.2 - - + -
169B VAL* 4.3 5.4 - - + -
197B ASN 2.8 14.6 + - - +
198B LEU* 3.5 27.6 - - + +
200B LYS* 1.3 78.4 - - - +
202B ALA* 1.3 63.7 + - - +
204B ILE* 4.5 1.3 - - + -
205B THR* 2.8 57.0 + - + +
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Residues in contact with ALA 202 (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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63B GLN* 4.0 17.0 - - - +
65B ILE* 3.7 28.2 - - + +
198B LEU 2.8 17.9 + - - +
199B GLN* 3.6 6.3 - - - +
201B LEU* 1.3 78.9 - - - +
203B SER* 1.3 63.8 + - - +
205B THR* 3.3 1.2 + - - -
206B GLU* 3.0 37.2 + - - +
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Residues in contact with SER 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLN 3.1 13.9 + - - -
200B LYS* 3.7 8.3 - - - -
202B ALA* 1.3 79.7 - - - +
204B ILE* 1.3 63.9 + - - +
206B GLU* 3.7 8.9 + - - +
207B ALA* 3.3 23.4 + - - +
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 4.8 5.6 - - + -
84B ILE* 2.6 54.1 - - + +
85B TYR* 3.6 12.3 - - + -
200B LYS* 3.0 35.5 + - + +
201B LEU* 3.9 3.8 - - - +
203B SER* 1.3 73.0 - - - +
205B THR* 1.3 64.6 + - + +
207B ALA* 3.3 13.4 + - - +
208B MET* 3.3 31.0 + - + +
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 3.2 24.4 - - - +
67B ALA* 3.8 10.2 - - - +
71B THR* 4.0 4.4 - - - +
72B VAL* 3.8 26.7 - - + +
75B VAL* 4.0 7.2 - - + -
201B LEU* 2.8 52.6 + - + -
202B ALA 3.3 0.2 + - - -
204B ILE* 1.3 75.7 - - + +
206B GLU* 1.3 55.0 + - - +
208B MET* 3.2 46.6 + - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG 4.4 2.8 - - - +
65B ILE* 3.7 11.9 - - + -
66B HIS* 2.8 60.5 + - + +
67B ALA* 4.2 4.7 - - - -
202B ALA* 3.0 29.4 + - - +
203B SER* 4.3 5.9 + - - +
205B THR* 1.3 72.2 - - - +
207B ALA* 1.3 62.9 + - - +
208B MET 3.3 7.4 - - - +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B SER 3.3 18.4 + - - +
204B ILE* 3.6 8.1 - - - +
205B THR 3.3 0.2 - - - -
206B GLU* 1.3 72.5 - - - +
208B MET* 1.3 66.1 + - + +
209B ASN 3.9 5.4 - - - +
210B ARG* 5.1 5.6 - - - +
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Residues in contact with MET 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.0 38.6 - - + +
74B SER* 5.1 1.6 - - - +
75B VAL* 3.6 20.6 - - + -
84B ILE* 6.2 0.2 - - - -
204B ILE* 3.3 16.4 - - + +
205B THR* 3.2 41.4 + - + +
206B GLU 3.5 8.5 - - - +
207B ALA* 1.3 82.2 - - - +
209B ASN* 1.3 69.3 + - - +
210B ARG* 4.4 15.3 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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