Contacts of the helix formed by residues 198 - 221 (chain B) in PDB entry 1UXI
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 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B SER 5.3 0.4 - - - -
196B PHE 4.3 1.2 + - - -
197B ILE* 1.3 75.0 - - - +
199B PRO* 1.3 69.1 - - + +
200B ASP* 3.3 17.9 - - - +
201B ARG* 3.2 7.7 + - + +
202B LEU* 2.9 25.5 + - - +
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Residues in contact with PRO 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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194B SER 5.9 0.7 - - - +
197B ILE 3.7 2.4 - - - +
198B ALA* 1.3 87.6 - - + +
200B ASP* 1.3 56.7 + - - +
202B LEU* 3.7 9.7 - - + +
203B ALA* 2.9 30.3 + - - +
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Residues in contact with ASP 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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198B ALA* 3.3 21.0 - - - +
199B PRO* 1.3 73.8 - - - +
201B ARG* 1.3 80.4 + - - +
203B ALA* 3.4 7.5 + - - +
204B GLN* 3.2 29.1 + - - +
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Residues in contact with ARG 201 (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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159B GLU* 2.9 46.5 + - + +
197B ILE* 3.6 12.6 - - + -
198B ALA* 3.2 7.3 + - + +
200B ASP* 1.3 87.0 - - - +
202B LEU* 1.3 60.6 + - - +
204B GLN* 3.0 37.1 + - - +
205B ILE* 2.9 40.2 + - - +
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Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.9 26.9 - - + +
156B ILE* 5.7 1.1 - - + -
183B PRO* 3.8 28.0 - - + -
193B VAL* 4.5 17.0 - - + -
194B SER* 4.6 11.2 - - - -
197B ILE* 3.5 34.9 - - + +
198B ALA 2.9 16.4 + - - +
199B PRO* 3.7 9.2 - - + +
201B ARG* 1.3 77.5 - - - +
203B ALA* 1.3 56.5 + - - +
205B ILE* 3.1 9.2 + - + +
206B VAL* 2.8 32.6 + - + +
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Residues in contact with ALA 203 (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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199B PRO 2.9 19.5 + - - +
200B ASP* 3.6 8.1 - - - +
202B LEU* 1.3 73.8 - - - +
204B GLN* 1.3 65.1 + - + +
206B VAL* 3.4 10.3 + - - +
207B GLU* 3.0 22.0 + - - +
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Residues in contact with GLN 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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200B ASP* 3.2 15.0 + - - +
201B ARG* 3.0 47.1 + - - +
203B ALA* 1.3 73.5 - - - +
205B ILE* 1.3 57.8 + - - +
207B GLU* 3.0 8.6 + - - +
208B ARG* 2.7 36.3 + - - +
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Residues in contact with ILE 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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152B TYR* 3.8 28.5 - - + +
155B PHE* 3.7 30.4 - - + +
156B ILE* 4.4 3.1 - - + -
159B GLU* 3.7 24.0 - - + +
197B ILE* 3.7 34.1 - - + -
201B ARG* 2.9 26.7 + - - +
202B LEU* 3.3 10.3 - - + +
204B GLN* 1.3 76.0 - - - +
206B VAL* 1.3 58.3 + - - +
208B ARG* 3.2 8.8 + - - +
209B THR* 2.8 32.1 + - - -
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Residues in contact with VAL 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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152B TYR* 4.4 8.5 - - + -
181B PRO* 3.4 27.7 - - + +
183B PRO* 4.0 27.4 - - + -
202B LEU* 2.8 21.4 + - + +
203B ALA* 3.5 12.3 - - - +
204B GLN 3.2 0.2 - - - -
205B ILE* 1.3 76.6 - - - +
207B GLU* 1.3 62.5 + - - +
209B THR* 3.3 7.0 + - - -
210B ARG* 3.1 41.2 + - - +
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Residues in contact with GLU 207 (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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203B ALA 3.0 13.9 + - - +
204B GLN* 3.0 11.5 + - - +
206B VAL* 1.3 73.8 - - - +
208B ARG* 1.3 67.6 + - - +
210B ARG* 3.2 23.1 + - - +
211B LYS* 3.1 55.7 + - - +
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Residues in contact with ARG 208 (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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44A LEU* 3.8 19.0 - - - +
155B PHE* 3.4 40.8 - - + +
158B MET* 4.2 10.5 - - - +
204B GLN 2.7 16.9 + - - +
205B ILE* 3.5 10.8 - - - +
207B GLU* 1.3 72.7 - - - +
209B THR* 1.3 53.6 + - - +
211B LYS* 3.1 5.2 + - - +
212B GLY* 2.6 36.9 + - - -
215B GLU* 2.6 40.3 + - - +
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Residues in contact with THR 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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148B ASP* 3.5 25.7 - - - +
151B ARG* 4.8 6.9 + - + -
152B TYR* 3.3 37.6 - - + +
155B PHE* 3.6 10.9 - - - -
171B LEU* 3.7 17.3 - - + -
179B MET* 3.9 12.0 - - - +
181B PRO* 4.6 6.1 - - + -
205B ILE 2.8 16.9 + - - -
206B VAL* 3.4 10.3 - - - -
207B GLU 3.2 0.2 - - - -
208B ARG* 1.3 77.0 - - - +
210B ARG* 1.3 63.2 + - - +
212B GLY* 3.1 12.5 + - - -
213B GLY 4.9 0.3 + - - -
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Residues in contact with ARG 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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88B ARG* 5.1 5.5 + - - -
176B GLY 4.2 3.3 - - - +
177B ASP* 3.3 38.5 + - - +
178B GLU* 5.0 5.0 + - - +
179B MET* 3.2 45.8 + - + +
180B VAL* 4.8 4.0 - - - +
181B PRO* 4.2 8.5 - - + +
206B VAL* 3.1 31.1 + - - +
207B GLU* 3.2 25.4 + - - +
209B THR* 1.3 76.8 - - - +
211B LYS* 1.3 64.6 + - + +
212B GLY 3.8 0.3 + - - -
213B GLY 5.1 0.9 + - - -
291B LEU* 3.7 35.6 - - - +
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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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177B ASP* 3.6 35.9 + - - +
207B GLU* 3.1 46.1 + - - +
208B ARG* 3.3 4.5 - - - +
210B ARG* 1.3 82.7 - - - +
212B GLY* 1.3 65.6 + - - +
213B GLY 3.2 2.7 - - - -
214B GLY* 3.0 8.2 + - - +
215B GLU* 2.8 24.8 + - + +
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Residues in contact with GLY 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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48A GLU* 4.7 1.1 - - - +
151B ARG* 3.7 21.4 + - - -
155B PHE* 5.1 3.6 - - - -
208B ARG 2.6 18.9 + - - -
209B THR* 3.1 11.0 + - - -
210B ARG 3.4 0.2 - - - -
211B LYS* 1.3 72.8 - - - +
213B GLY* 1.3 59.5 + - - +
215B GLU* 3.5 14.6 - - - +
216B ILE* 3.4 24.8 + - - +
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Residues in contact with GLY 213 (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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88B ARG* 4.0 8.0 - - - +
151B ARG* 3.3 29.1 - - - +
209B THR 4.9 0.4 + - - -
210B ARG 5.1 0.4 + - - -
211B LYS 3.2 0.6 - - - -
212B GLY* 1.3 73.7 - - - +
214B GLY* 1.3 65.4 + - - +
216B ILE* 3.3 4.9 + - - +
217B VAL* 3.0 25.5 + - - +
225B ALA 5.4 0.5 + - - -
1311B FUM 3.6 22.1 - - - +
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Residues in contact with GLY 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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82B ARG* 3.8 22.1 - - - +
88B ARG* 4.9 1.2 - - - +
211B LYS* 3.0 9.0 + - - +
213B GLY* 1.3 72.1 - - - +
215B GLU* 1.3 66.3 + - - +
217B VAL* 3.1 6.4 + - - +
218B ASN* 2.9 35.6 + - - -
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Residues in contact with GLU 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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44A LEU* 3.3 23.2 - - + +
48A GLU* 4.6 0.2 - - - +
155B PHE* 4.2 5.5 - - - -
208B ARG* 2.6 52.8 + - - +
211B LYS* 2.8 13.8 + - + +
212B GLY* 3.5 13.3 - - - +
213B GLY 3.2 0.2 - - - -
214B GLY* 1.3 77.3 - - - +
216B ILE* 1.3 61.5 + - - +
218B ASN* 3.5 9.4 + - - +
219B LEU* 3.4 27.0 + - + +
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Residues in contact with ILE 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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41A GLY* 4.2 13.9 - - - +
44A LEU* 4.2 16.6 - - + -
45A ASP* 3.8 22.4 - - + +
48A GLU* 3.3 28.3 - - - +
151B ARG* 4.0 2.9 - - - +
212B GLY 3.4 10.7 + - - +
213B GLY 3.3 6.9 + - - +
214B GLY 3.2 0.8 - - - -
215B GLU* 1.3 73.7 - - - +
217B VAL* 1.3 66.0 + - - +
219B LEU* 3.1 8.0 + - - +
220B LEU* 2.9 46.5 + - + +
225B ALA* 3.8 30.3 - - + +
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Residues in contact with VAL 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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82B ARG* 4.0 20.0 - - + +
83B LYS 3.7 6.7 - - - +
84B PRO* 3.4 36.1 - - + +
213B GLY 3.0 20.4 + - - +
214B GLY* 3.1 11.0 + - - +
216B ILE* 1.3 76.4 - - - +
218B ASN* 1.3 60.0 + - - +
221B LYS* 2.9 28.4 + - - -
223B GLY 3.7 10.4 - - - +
224B SER* 3.8 28.3 - - - -
1311B FUM 4.0 9.0 - - - +
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Residues in contact with ASN 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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84B PRO* 3.6 26.1 - - - +
85B GLY 4.2 4.9 + - - -
214B GLY* 2.9 25.5 + - - +
215B GLU* 3.8 8.7 - - - +
216B ILE 3.2 0.2 - - - -
217B VAL* 1.3 77.9 - - - +
219B LEU* 1.3 60.9 + - + +
221B LYS* 3.1 30.7 - - - +
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Residues in contact with LEU 219 (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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36A GLU 4.3 0.5 - - - +
37A GLY* 3.5 43.7 - - - +
38A VAL* 3.8 1.2 + - - +
40A GLN* 3.9 15.3 - - + +
41A GLY* 3.5 26.9 - - - +
44A LEU* 4.6 13.9 - - + -
215B GLU* 3.4 21.1 - - + +
216B ILE* 3.1 9.5 + - - +
218B ASN* 1.3 77.4 - - + +
220B LEU* 1.3 65.9 + - - +
221B LYS* 3.2 13.7 - - - +
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Residues in contact with LEU 220 (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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37A GLY 4.8 0.2 - - - -
38A VAL* 3.9 22.5 - - + +
41A GLY* 4.0 2.9 - - - -
42A LYS* 3.8 45.5 - - + +
45A ASP* 5.4 1.6 - - - +
216B ILE* 2.9 30.7 + - + +
219B LEU* 1.3 74.0 - - - +
221B LYS* 1.3 61.0 + - - +
222B THR* 2.6 24.7 + - - +
223B GLY* 3.5 28.7 - - - +
224B SER 3.7 17.3 - - - +
225B ALA* 4.3 1.3 - - - +
226B TYR* 4.4 14.4 - - + -
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Residues in contact with LYS 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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35A VAL* 6.0 1.6 - - + +
36A GLU* 3.9 26.4 + - - +
37A GLY* 5.3 1.1 - - - -
38A VAL* 6.3 0.9 - - + -
83B LYS* 4.9 3.3 - - - +
84B PRO* 3.3 34.5 - - + +
217B VAL 2.9 17.3 + - - -
218B ASN* 3.1 21.1 - - - +
219B LEU* 3.2 12.3 + - - +
220B LEU* 1.3 74.9 - - - +
222B THR* 1.3 64.2 + - + +
223B GLY 3.5 1.8 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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