Contacts of the helix formed by residues 186 - 207 (chain B) in PDB entry 1XV9
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 PRO 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B SER 4.1 3.8 - - - +
185B LEU* 1.3 84.5 - - + +
187B ILE* 1.3 56.4 + - - +
188B GLU* 4.6 13.5 - - + +
189B ASP* 2.8 38.8 + - - +
190B GLN 3.1 8.5 + - - -
276B THR* 4.0 1.3 - - - +
277B GLN* 3.3 44.4 - - + +
280B GLU* 5.1 1.1 - - - +
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ARG* 4.9 0.7 - - - +
185B LEU 3.4 2.0 + - - -
186B PRO* 1.3 70.7 - - - +
188B GLU* 1.3 65.6 + - + +
189B ASP 2.9 1.7 + - - -
190B GLN* 3.0 32.5 + - - +
191B ILE* 2.9 43.6 + - + +
691F HIS* 4.1 16.4 - - + +
694F LEU* 4.5 25.1 - - + +
695F GLN* 6.1 0.7 - - - -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.1 11.4 + - + +
187B ILE* 1.3 77.7 - - + +
189B ASP* 1.3 60.1 + - - +
191B ILE* 4.1 9.6 - - - +
192B SER* 2.6 31.8 + - - -
274B GLY 3.9 3.7 - - - +
276B THR* 4.9 15.9 + - + +
259C SER* 5.5 6.9 - - - +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.6 9.3 - - + +
186B PRO* 2.8 15.7 + - + +
188B GLU* 1.3 82.6 - - - +
190B GLN* 1.3 55.9 + - - +
191B ILE 3.1 1.8 - - - -
192B SER* 3.6 5.1 - - - -
193B LEU* 2.7 41.1 + - + +
274B GLY 3.5 4.2 - - - +
275B VAL* 4.2 2.5 - - - -
276B THR* 2.5 46.7 + - - +
277B GLN* 3.1 29.5 + - - +
281B ILE* 4.6 14.1 - - + +
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Residues in contact with GLN 190 (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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182B PHE* 3.2 54.5 + - + +
183B ARG* 3.4 31.6 + - - +
185B LEU* 3.0 32.2 + - + +
186B PRO 3.1 3.0 + - - +
187B ILE* 3.1 33.1 - - - +
189B ASP* 1.3 76.0 - - - +
191B ILE* 1.3 57.4 + - - +
193B LEU 3.3 0.2 + - - -
194B LEU* 2.9 30.7 + - - +
694F LEU* 3.5 19.6 - - + +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ILE* 2.9 29.4 + - + +
188B GLU* 4.1 8.5 - - - +
190B GLN* 1.3 77.5 - - - +
192B SER* 1.3 52.7 + - - +
194B LEU* 2.9 8.0 + - - +
195B LYS* 2.7 60.9 + - + +
687F HIS* 3.9 21.3 - - + +
690F LEU* 4.5 13.2 - - + -
691F HIS* 3.5 43.7 - - + +
694F LEU* 4.1 12.1 - - + -
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLU 2.6 24.7 + - - -
189B ASP* 3.2 5.7 + - - -
191B ILE* 1.3 78.7 - - - +
193B LEU* 1.3 57.3 + - - +
195B LYS* 3.9 13.5 - - - +
196B GLY* 3.2 21.1 + - - -
272B ARG* 3.9 10.1 - - - +
273B PRO* 3.3 21.1 + - - +
274B GLY* 3.4 23.4 + - - -
275B VAL* 3.9 7.2 - - - -
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Residues in contact with LEU 193 (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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182B PHE* 3.4 29.2 - - + -
185B LEU* 3.6 21.3 - - + -
189B ASP 2.7 24.5 + - - +
190B GLN 3.6 4.3 - - - +
192B SER* 1.3 72.0 - - - +
194B LEU* 1.3 61.8 + - - +
196B GLY 3.9 0.2 - - - -
197B ALA* 2.9 34.1 + - - +
267B LEU* 3.5 21.7 - - + +
268B PHE* 4.0 14.6 - - + -
269B SER 3.5 22.0 - - - +
272B ARG* 3.9 7.9 - - + -
275B VAL* 4.2 4.9 - - + -
281B ILE* 3.8 21.3 - - + -
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B VAL* 5.2 6.5 - - + -
173B ILE* 4.0 22.9 - - + -
176B THR* 3.9 20.9 - - + +
182B PHE* 3.9 10.8 - - + -
190B GLN 2.9 18.4 + - - +
191B ILE* 3.5 4.7 - - - +
193B LEU* 1.3 76.7 - - - +
195B LYS* 1.3 64.5 + - + +
196B GLY 3.1 1.3 - - - -
198B ALA* 2.7 41.3 + - + +
267B LEU* 3.9 19.3 - - + -
346B ILE* 4.4 11.2 - - + -
690F LEU* 5.5 4.3 - - + -
694F LEU* 3.9 34.3 - - + -
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Residues in contact with LYS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ILE* 2.7 49.7 + - + +
192B SER* 3.9 10.8 - - - +
194B LEU* 1.3 73.1 - - - +
196B GLY* 1.3 59.8 + - - +
197B ALA 5.3 0.2 - - - -
273B PRO* 5.7 4.3 - - - -
323B ASN* 4.3 8.7 - - - +
345B GLU 3.0 22.9 + - - +
346B ILE* 3.0 32.2 - - - +
348B SER* 2.7 36.0 + - - +
687F HIS* 3.3 14.8 + - - +
690F LEU* 4.4 8.5 - - + -
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Residues in contact with GLY 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 SER 3.2 17.0 + - - -
194B LEU 3.1 0.4 - - - -
195B LYS* 1.3 79.8 - - - +
197B ALA* 1.3 57.5 + - - +
200B GLU* 3.3 0.2 - - - +
272B ARG* 3.1 36.2 + - - -
273B PRO* 6.2 2.2 - - - -
323B ASN* 3.0 21.8 + - - -
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Residues in contact with ALA 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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193B LEU 2.9 20.4 + - - +
196B GLY* 1.3 77.3 - - - +
198B ALA* 1.3 52.1 + - - +
199B VAL 3.3 2.0 - - - -
200B GLU* 2.7 35.6 + - - +
201B ILE* 3.1 29.0 + - + -
266B ALA 4.0 0.4 - - - -
267B LEU* 3.3 27.1 - - + +
272B ARG* 3.3 11.2 - - - +
323B ASN* 3.6 0.7 + - - +
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Residues in contact with ALA 198 (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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169B VAL* 4.5 14.4 - - + -
172B VAL* 4.2 11.9 - - + +
173B ILE* 6.3 0.7 - - + -
193B LEU 4.1 0.2 + - - -
194B LEU* 2.7 32.4 + - + +
197B ALA* 1.3 71.1 - - - +
199B VAL* 1.3 63.2 + - + +
201B ILE* 3.4 13.1 + - - +
202B CYS* 3.2 28.2 + - - -
346B ILE* 3.6 21.5 - - + -
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Residues in contact with VAL 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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169B VAL* 5.8 1.3 - - + -
195B LYS 5.6 0.2 + - - -
197B ALA 2.8 4.4 + - - -
198B ALA* 1.3 72.6 - - + +
200B GLU* 1.3 67.3 + - - +
202B CYS* 3.1 22.7 + - - +
203B HIS* 3.4 24.1 + - + +
322B ILE* 4.8 0.7 - - + -
323B ASN* 3.3 35.1 + - - +
326B TYR* 4.0 38.4 - - + -
343B LEU* 4.3 10.5 - - + -
346B ILE* 4.2 18.1 - - + +
347B CYS* 4.6 4.7 - - - -
1001D CI2 4.6 6.5 - - + +
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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
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196B GLY 3.3 11.0 - - - +
197B ALA 2.7 13.3 + - - +
199B VAL* 1.3 77.7 - - - +
201B ILE* 1.3 60.3 + - - +
202B CYS 3.3 0.5 + - - -
203B HIS* 3.3 6.0 + - - +
204B ILE* 2.9 28.1 + - - +
266B ALA* 4.1 14.1 - - + +
272B ARG* 3.3 25.3 + - - -
316B LEU* 4.3 6.6 - - - +
319B LEU* 2.9 54.8 - - + +
320B ARG* 3.6 11.3 + - - +
322B ILE* 5.6 0.4 - - + -
323B ASN* 2.9 33.1 + - + +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 4.6 8.3 - - + -
172B VAL* 4.0 27.8 - - + -
175B PHE* 5.3 6.1 - - + -
176B THR* 5.4 1.6 - - + -
194B LEU* 5.3 0.7 - - + -
197B ALA* 3.1 35.3 + - + +
198B ALA* 3.5 18.2 - - - +
200B GLU* 1.3 76.8 - - - +
202B CYS* 1.3 60.7 + - - +
204B ILE* 3.4 10.9 - - + +
205B VAL* 3.1 29.4 + - + +
263B ALA* 4.3 18.8 - - + +
266B ALA* 4.3 12.8 - - + -
267B LEU* 4.0 19.7 - - + -
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Residues in contact with CYS 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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128B MET* 5.6 2.8 - - - +
165B ASN* 5.6 2.9 - - - +
168B MET* 4.2 35.1 - - + +
169B VAL* 4.4 13.5 - - - -
172B VAL* 3.4 22.9 - - - -
198B ALA 3.3 15.9 - - - -
199B VAL* 3.1 11.9 + - - +
201B ILE* 1.3 73.4 - - - +
203B HIS* 1.3 57.8 + - + +
205B VAL* 3.0 8.5 + - - +
206B LEU* 2.7 37.1 + - - +
1001D CI2 6.0 4.9 - - + -
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Residues in contact with HIS 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 VAL* 3.4 22.7 + - + +
200B GLU 3.3 7.5 + - - +
202B CYS* 1.3 78.0 - - + +
204B ILE* 1.3 64.9 + - - +
206B LEU* 3.3 8.1 - - - +
207B ASN* 2.9 23.0 + - - +
238B PHE* 5.5 1.2 - + - -
242B LEU* 3.5 20.4 - - + -
245B PHE* 4.1 3.8 - + + -
246B HIS* 3.3 28.8 + + + -
319B LEU* 4.0 15.0 - - + -
322B ILE* 3.5 33.2 - - + +
1001D CI2 3.2 47.7 + - + +
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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
----------------------------------------------------------
200B GLU 2.9 19.7 - - - +
201B ILE* 3.4 13.0 - - - +
203B HIS* 1.3 78.6 - - - +
205B VAL* 1.3 65.7 + - + +
207B ASN* 3.5 11.4 + - - +
208B THR* 4.2 6.1 - - - +
245B PHE* 5.1 0.6 - - + -
249B LEU* 4.6 9.0 - - + -
259B TYR* 4.2 29.5 - - + +
262B LEU* 4.2 27.4 - - + +
263B ALA* 3.8 17.7 - - + +
266B ALA* 3.8 24.7 - - + -
316B LEU* 5.1 0.2 - - + -
319B LEU* 3.6 25.4 - - + -
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Residues in contact with VAL 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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121B HIS* 4.6 8.3 - - + +
125B MET* 4.0 32.8 - - + -
126B GLY* 3.9 18.6 - - - +
128B MET* 4.4 5.8 - - + -
129B PHE* 3.4 28.2 - - + -
172B VAL* 6.0 0.4 - - + -
201B ILE* 3.1 18.8 - - + +
202B CYS* 3.0 6.8 + - - +
204B ILE* 1.3 76.2 - - + +
206B LEU* 1.3 61.3 + - - +
208B THR* 2.7 40.0 + - + +
259B TYR* 6.4 0.2 - - - -
263B ALA* 5.6 3.6 - - + -
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 5.6 0.2 - - - +
129B PHE* 3.5 26.4 - - + -
132B PHE* 5.2 3.1 - - + -
168B MET* 5.1 13.2 - - + -
202B CYS 2.7 21.8 + - - +
203B HIS* 3.3 10.5 - - - +
205B VAL* 1.3 72.5 - - - +
207B ASN* 1.3 57.2 + - - +
208B THR 2.8 5.9 + - - -
209B THR* 2.8 29.9 + - - +
210B PHE 3.8 0.9 + - - -
217B PHE* 3.0 50.2 - - + -
219B CYS* 4.7 4.9 - - - -
246B HIS* 4.0 7.4 - - + +
1001D CI2 4.0 41.5 - - + -
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Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS 2.9 9.8 + - - +
204B ILE 3.7 4.5 - - - +
205B VAL 3.1 0.4 + - - -
206B LEU* 1.3 74.1 - - - +
208B THR* 1.3 59.6 + - - +
209B THR 3.1 0.4 - - - -
210B PHE* 3.2 16.5 - - - +
246B HIS* 2.9 65.5 + - + +
249B LEU* 3.3 30.6 - - + +
250B ARG* 3.3 19.2 + - - +
259B TYR* 2.7 21.8 + - - +
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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
------------------------------------------------------------
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