Contacts of the helix formed by residues 196 - 221 (chain B) in PDB entry 6VDK
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 ALA 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER 4.9 0.3 - - - +
82B GLY 5.3 7.2 - - - +
83B TYR* 5.3 5.4 - - + +
183B HIS* 3.4 24.5 - - + +
184B ASN* 3.2 24.0 + - - +
187B ARG 5.3 0.4 - - - +
195B SER* 1.3 89.1 + - - +
197B GLY* 1.3 56.2 + - - +
198B GLU 3.4 2.0 - - - -
199B ARG* 3.4 24.3 + - - +
200B ILE* 3.4 20.3 - - - +
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Residues in contact with GLY 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASN* 3.9 11.8 + - - -
185B PHE* 5.8 3.0 - - - -
195B SER* 3.8 4.0 + - - -
196B ALA* 1.3 77.6 - - - +
198B GLU* 1.3 61.4 + - - +
199B ARG 3.3 1.3 - - - -
200B ILE* 3.2 18.7 - - - +
201B VAL* 2.9 35.5 + - - +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ILE* 4.1 34.2 - - + +
188B LYS* 6.0 0.2 - - - -
194B TYR* 3.1 38.0 - - + +
195B SER* 3.8 29.3 + - - +
196B ALA 3.4 0.8 - - - -
197B GLY* 1.3 79.3 - - - +
199B ARG* 1.3 57.5 + - - +
201B VAL* 3.3 10.3 - - - +
202B ASP* 3.0 37.0 + - - +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 3.3 31.8 + - - +
82B GLY 5.8 1.6 + - - -
187B ARG 4.9 1.4 + - - -
188B LYS 5.1 0.8 - - - -
189B GLY 3.6 18.4 + - - +
190B GLY* 4.6 5.3 - - - +
194B TYR* 2.7 53.9 + - + +
195B SER 3.3 18.8 + - - -
196B ALA* 3.4 28.0 + - - +
198B GLU* 1.3 79.5 - - - +
200B ILE* 1.3 55.1 + - - +
202B ASP* 3.3 11.0 + - - +
203B ILE* 2.9 26.2 + - - +
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 4.8 6.5 - - + +
81B SER* 3.3 26.9 - - - +
83B TYR* 3.7 50.9 - - + +
108B TRP* 4.6 17.9 - - + +
184B ASN* 5.6 0.4 - - - +
196B ALA 3.4 17.0 - - - +
197B GLY* 3.2 22.7 - - - +
199B ARG* 1.3 74.3 - - - +
201B VAL* 1.3 67.4 + - + +
203B ILE* 3.2 9.5 - - + +
204B ILE* 2.9 36.2 + - + +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TRP* 5.5 12.1 - - + -
109A PRO* 6.6 0.2 - - + -
201A VAL* 4.2 17.2 - - + +
204A ILE* 4.9 23.8 - - + +
205A ALA* 4.9 15.0 - - + +
208A ILE* 5.8 4.5 - - + -
108B TRP* 6.3 0.9 - - - +
197B GLY* 2.9 21.6 + - - +
198B GLU* 3.3 20.4 - - - +
200B ILE* 1.3 81.5 - - + +
202B ASP* 1.3 62.3 + - - +
204B ILE* 4.1 9.6 - - + +
205B ALA* 2.9 31.7 + - - +
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Residues in contact with ASP 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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205A ALA* 5.4 6.2 - - - +
209A GLN* 5.2 12.1 - - - +
194B TYR* 5.8 6.9 - - - -
198B GLU* 3.0 27.8 + - - +
199B ARG* 3.4 12.8 - - - +
201B VAL* 1.3 79.9 - - - +
203B ILE* 1.3 57.7 + - - +
205B ALA* 3.8 4.1 - - - +
206B THR* 2.9 37.7 + - + +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 5.2 1.6 - - - +
58B PRO* 4.4 13.2 - - + +
78B HIS* 3.8 14.1 - - + +
80B ALA* 3.5 37.9 - - + +
81B SER* 3.7 20.4 - - - -
199B ARG 2.9 11.3 + - - +
200B ILE 3.2 14.1 - - - +
202B ASP* 1.3 76.3 - - - +
204B ILE* 1.3 61.6 + - + +
206B THR* 2.9 20.2 + - - +
207B ASP* 2.9 18.9 + - + +
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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
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201A VAL* 3.7 26.9 - - + -
58B PRO* 5.3 5.4 - - + -
78B HIS* 4.9 12.8 - - + +
108B TRP* 3.7 32.3 - - + +
109B PRO* 5.2 18.4 - - + -
200B ILE* 2.9 31.0 + - + +
201B VAL* 4.1 9.0 - - + +
203B ILE* 1.3 81.5 - - + +
205B ALA* 1.3 59.0 + - - +
207B ASP* 3.3 7.6 + - - +
208B ILE* 2.9 43.3 + - + +
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Residues in contact with ALA 205 (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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201A VAL* 3.8 20.4 - - + +
202A ASP* 6.3 0.2 - - - -
205A ALA* 4.4 13.5 - - + -
201B VAL 2.9 20.0 + - - +
202B ASP* 3.8 5.2 - - - +
204B ILE* 1.3 75.7 - - - +
206B THR* 1.3 59.5 + - + +
208B ILE* 3.3 5.6 + - - +
209B GLN* 2.9 44.3 + - - +
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Residues in contact with THR 206 (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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20B ARG* 3.7 21.4 + - - +
202B ASP* 2.9 20.3 + - + +
203B ILE* 2.9 24.9 + - - +
205B ALA* 1.3 77.1 - - + +
207B ASP* 1.3 56.2 + - - +
209B GLN* 3.3 13.6 + - - +
210B THR* 2.9 32.7 + - - +
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Residues in contact with ASP 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B CYS 4.9 2.6 - - - +
58B PRO* 3.5 38.2 - - + +
109B PRO* 5.4 6.9 - - - +
203B ILE 2.9 19.6 + - - +
204B ILE* 3.3 7.4 + - - +
206B THR* 1.3 76.8 + - - +
208B ILE* 1.3 65.3 + - - +
210B THR* 3.3 10.6 - - - +
211B LYS* 2.9 50.4 + - - +
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Residues in contact with ILE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A TYR* 6.5 0.4 - - + -
198A GLU* 4.4 31.4 - - + +
201A VAL* 5.4 4.3 - - + -
109B PRO* 5.8 6.5 - - + -
204B ILE* 2.9 31.1 + - + +
205B ALA* 3.3 7.8 + - - +
207B ASP* 1.3 79.9 - - - +
209B GLN* 1.3 60.1 + - + +
211B LYS* 3.4 22.1 - - + +
212B GLU* 2.9 46.9 + - + +
271J TYR* 5.2 4.5 - - + -
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Residues in contact with GLN 209 (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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19B TRP* 5.9 0.7 - - - -
20B ARG* 4.2 19.3 + - - +
205B ALA* 2.9 31.7 + - - +
206B THR* 3.7 11.1 - - - +
208B ILE* 1.3 78.2 - - + +
210B THR* 1.3 58.3 + - - +
212B GLU* 3.4 3.1 + - - +
213B LEU* 2.9 36.2 + - + +
269J ARG* 5.8 7.3 + - - +
270J ASP 5.8 2.0 + - - -
271J TYR* 4.5 19.0 - - + +
274J GLN* 4.7 15.6 - - - +
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Residues in contact with THR 210 (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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19B TRP* 4.2 17.8 + - - -
20B ARG* 4.2 12.7 - - - +
34B LYS* 5.8 2.4 + - - +
206B THR 2.9 22.0 + - - +
207B ASP* 3.3 15.3 - - - +
209B GLN* 1.3 75.9 - - - +
211B LYS* 1.3 62.7 + - + +
213B LEU* 3.3 6.3 + - - +
214B GLN* 2.9 27.2 + - - +
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Residues in contact with LYS 211 (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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111B LYS* 5.3 15.3 - - - +
207B ASP* 2.9 43.4 + - - +
208B ILE* 3.4 23.8 - - + +
210B THR* 1.3 77.9 - - + +
212B GLU* 1.3 61.2 + - + +
214B GLN* 3.5 9.1 + - + +
215B LYS* 2.8 34.2 + - + +
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Residues in contact with GLU 212 (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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194A TYR* 4.2 20.2 + - - -
208B ILE* 2.9 28.1 + - + +
209B GLN 4.0 3.1 - - - +
211B LYS* 1.3 78.0 - - + +
213B LEU* 1.3 62.1 + - + +
215B LYS* 3.4 20.1 + - + +
216B GLN* 2.8 27.1 + - + +
270J ASP* 4.8 0.3 - - - +
271J TYR* 3.2 34.9 - - + +
272J GLY* 4.3 8.2 + - - -
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TRP* 5.2 10.3 - - + -
30B PRO* 4.3 19.3 - - + -
31B VAL* 4.8 11.2 - - + -
34B LYS* 6.4 2.7 - - + -
209B GLN* 2.9 26.8 + - + +
210B THR* 3.7 7.4 - - - +
211B LYS 3.3 0.2 - - - -
212B GLU* 1.3 77.1 - - - +
214B GLN* 1.3 58.6 + - - +
216B GLN* 3.1 29.0 + - - +
217B ILE* 2.9 30.4 + - - +
271J TYR 4.0 6.1 - - - +
274J GLN* 3.7 46.4 - - + +
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Residues in contact with GLN 214 (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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210B THR 2.9 16.7 + - - +
211B LYS* 3.6 9.9 - - + +
213B LEU* 1.3 75.6 - - - +
215B LYS* 1.3 57.9 + - - +
217B ILE* 3.2 15.0 + - - +
218B THR* 2.9 37.9 + - + +
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Residues in contact with LYS 215 (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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188A LYS* 4.4 11.3 - - - +
211B LYS* 2.8 23.9 + - - +
212B GLU* 3.4 22.5 - - + +
213B LEU 3.2 0.2 - - - -
214B GLN* 1.3 76.9 - - - +
216B GLN* 1.3 62.1 + - - +
218B THR* 3.3 20.6 - - + +
219B LYS* 4.4 1.4 - - - +
24C SER* 3.4 37.6 + - - +
25C ASP* 2.6 38.1 + - - +
27C ASN* 3.8 12.7 + - - +
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Residues in contact with GLN 216 (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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31B VAL* 5.2 10.3 - - + +
212B GLU 2.8 14.2 + - - +
213B LEU* 3.1 34.1 + - + +
215B LYS* 1.3 77.5 - - - +
217B ILE* 1.3 63.2 + - + +
219B LYS* 2.5 44.7 + - - +
220B ILE* 3.3 7.1 - - + +
271J TYR 5.2 1.9 - - - +
272J GLY* 5.5 4.0 - - - -
274J GLN* 4.8 7.4 + - - +
275J MET* 4.6 25.1 + - - +
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Residues in contact with ILE 217 (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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31B VAL* 4.3 28.0 - - + -
213B LEU 2.9 15.7 + - - +
214B GLN* 3.3 30.1 - - - +
216B GLN* 1.3 74.6 - - + +
218B THR* 1.3 65.0 + - - +
219B LYS 3.2 3.4 - - - -
220B ILE* 3.1 34.4 + - + -
221B GLN* 3.4 14.0 + - + +
241B LEU 5.1 4.9 - - - +
242B LEU* 5.2 4.5 - - + +
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Residues in contact with THR 218 (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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214B GLN* 2.9 26.7 + - + +
215B LYS* 3.3 26.0 - - + +
217B ILE* 1.3 77.7 - - - +
219B LYS* 1.3 56.2 + - - +
221B GLN* 2.9 34.1 + - - +
222B ASN* 3.4 1.6 - - - +
27C ASN* 3.4 16.9 + - - +
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LYS 4.4 2.5 - - - +
216B GLN* 2.5 45.7 + - - +
218B THR* 1.3 78.4 - - - +
220B ILE* 1.3 81.9 + - + +
221B GLN 3.3 2.2 - - - -
222B ASN* 3.1 18.7 + - - +
223B PHE* 3.2 29.2 - - + -
27C ASN* 3.4 38.1 - - + +
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLN* 3.3 19.7 - - + +
217B ILE* 3.1 23.5 + - + +
219B LYS* 1.3 100.1 - - + +
221B GLN* 1.3 59.8 + - - +
223B PHE* 2.8 42.2 + - + +
241B LEU* 3.4 51.1 + - + +
242B LEU 5.2 2.7 - - - +
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Residues in contact with GLN 221 (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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217B ILE* 3.4 10.3 + - + +
218B THR* 2.9 36.4 + - - +
220B ILE* 1.3 77.4 - - - +
222B ASN* 1.3 86.9 + - - +
223B PHE 4.1 3.4 - - - +
224B ARG* 5.7 1.9 + - - -
240B LYS* 6.0 2.1 - - - +
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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