Contacts of the helix formed by residues 186 - 208 (chain D) in PDB entry 1XVP
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D SER 4.9 0.4 - - - +
185D LEU* 1.3 88.4 - - + +
187D ILE* 1.3 66.6 + - - +
188D GLU* 3.1 12.6 - - + +
189D ASP* 2.9 50.8 + - - +
190D GLN* 3.1 8.8 + - - +
276D THR* 3.2 11.4 - - - +
277D GLN* 3.6 21.5 - - + +
280D GLU* 5.1 0.7 - - - +
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D ARG* 5.3 2.7 - - - +
185D LEU 3.3 2.3 + - - +
186D PRO* 1.3 71.9 - - - +
188D GLU* 1.3 57.8 + - - +
190D GLN* 3.3 24.4 + - - +
191D ILE* 3.2 31.4 + - - +
691H HIS* 4.5 19.1 - - + +
694H LEU* 4.1 34.3 - - + +
695H GLN* 4.4 17.3 - - - +
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Residues in contact with GLU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D PRO* 4.3 14.9 - - + +
187D ILE* 1.3 76.8 - - + +
189D ASP* 1.3 62.1 + - - +
191D ILE* 4.1 13.2 - - + +
192D SER* 3.0 23.4 + - - -
274D GLY 4.3 3.5 - - - +
276D THR* 3.5 24.8 - - + +
691H HIS* 5.9 2.0 - - - +
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Residues in contact with ASP 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LEU* 3.8 10.5 - - + +
186D PRO* 2.9 26.1 + - + +
188D GLU* 1.3 75.4 - - - +
190D GLN* 1.3 69.4 + - - +
191D ILE 3.1 1.1 - - - -
192D SER* 3.0 14.7 + - - -
193D LEU* 3.1 19.1 + - - +
275D VAL* 3.5 1.7 - - - +
276D THR* 2.5 54.8 + - - +
277D GLN* 2.9 20.8 + - - +
281D ILE* 3.7 12.9 - - + +
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Residues in contact with GLN 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D PHE* 2.8 73.4 - - + +
183D ARG* 3.4 33.4 + - - +
185D LEU* 2.9 23.4 + - + +
186D PRO 3.1 9.0 - - - +
187D ILE* 3.3 36.8 - - - +
189D ASP* 1.3 78.2 - - - +
191D ILE* 1.3 61.3 + - - +
193D LEU* 3.3 1.3 + - - -
194D LEU* 3.2 15.5 + - - +
694H LEU* 4.3 9.8 - - + +
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Residues in contact with ILE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ILE* 3.2 19.0 + - + +
188D GLU* 4.2 8.7 - - - +
190D GLN* 1.3 77.1 - - - +
192D SER* 1.3 52.3 + - - +
194D LEU* 3.3 7.0 + - - +
195D LYS* 2.8 45.5 + - + +
687H HIS* 4.5 7.9 - - + +
690H LEU* 3.8 33.3 - - + +
691H HIS* 3.2 39.5 - - + +
694H LEU* 3.3 22.9 - - + -
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D GLU 3.0 16.4 + - - -
189D ASP 3.0 8.3 + - - -
191D ILE* 1.3 76.6 - - - +
193D LEU* 1.3 66.5 + - - +
195D LYS* 3.3 19.0 + - - +
196D GLY 3.5 7.3 + - - -
272D ARG* 3.6 13.1 - - - +
273D PRO 4.3 6.4 + - - +
274D GLY* 3.3 36.3 + - - -
275D VAL* 3.7 8.5 - - - -
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PHE* 3.4 23.3 - - + -
185D LEU* 3.8 22.2 - - + -
189D ASP 3.1 16.3 + - - +
190D GLN 3.5 4.0 - - - +
192D SER* 1.3 75.4 - - - +
194D LEU* 1.3 57.4 + - - +
196D GLY* 3.5 1.6 + - - -
197D ALA* 2.9 32.4 + - - +
267D LEU* 3.5 27.0 - - + +
268D PHE* 4.4 8.7 - - + -
269D SER 3.5 28.0 - - - +
272D ARG* 4.1 6.0 + - + -
275D VAL* 3.6 17.3 - - + -
281D ILE* 4.2 13.5 - - + -
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D VAL* 6.2 0.2 - - + -
172D VAL* 4.2 33.0 - - + +
173D ILE* 4.8 15.9 - - + -
176D THR* 4.2 15.7 - - + +
182D PHE* 4.0 22.2 - - + -
190D GLN 3.2 15.9 + - - +
191D ILE* 3.6 8.1 - - - +
193D LEU* 1.3 75.9 - - - +
195D LYS* 1.3 58.1 + - - +
196D GLY 3.1 5.6 - - - -
197D ALA* 4.5 0.7 - - - -
198D ALA* 2.9 43.4 + - + +
201D ILE* 4.9 3.6 - - + -
267D LEU* 4.7 2.2 - - + -
346D ILE* 3.8 7.6 - - + +
690H LEU* 6.0 7.6 - - + -
694H LEU* 4.3 21.1 - - + -
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D ILE* 2.8 34.1 + - + +
192D SER* 3.3 12.7 + - - +
194D LEU* 1.3 75.7 - - - +
196D GLY* 1.3 55.9 + - - +
273D PRO 5.3 7.4 - - - -
323D ASN* 4.9 4.7 - - - +
345D GLU 4.1 9.4 - - - +
346D ILE* 3.1 39.3 + - + +
348D SER* 2.7 36.5 + - - -
685H GLU* 5.2 5.4 - - - -
687H HIS* 3.4 29.6 - - + -
690H LEU* 4.5 6.7 - - + -
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Residues in contact with GLY 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D SER 3.5 4.0 + - - -
193D LEU 3.5 2.8 + - - -
195D LYS* 1.3 79.0 - - - +
197D ALA* 1.3 58.8 + - - +
198D ALA 3.8 0.2 - - - -
199D VAL 5.3 0.2 - - - -
200D GLU* 2.5 29.6 - - - +
272D ARG* 3.4 24.5 + - - -
273D PRO* 6.4 0.9 - - - -
323D ASN* 3.0 16.4 + - - -
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Residues in contact with ALA 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU 2.9 20.3 + - - +
194D LEU* 4.5 0.2 - - - -
196D GLY* 1.3 78.4 - - - +
198D ALA* 1.3 55.9 + - - +
199D VAL 3.3 2.2 - - - -
200D GLU* 2.9 7.2 + - - +
201D ILE* 2.7 53.1 + - + +
266D ALA 3.1 28.7 - - - +
267D LEU* 3.4 7.0 - - + -
272D ARG* 4.0 2.0 - - - +
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Residues in contact with ALA 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 4.3 20.0 - - + -
172D VAL* 4.1 9.7 - - + +
194D LEU* 2.9 28.4 + - + +
196D GLY 3.8 0.2 - - - -
197D ALA* 1.3 76.0 - - - +
199D VAL* 1.3 63.2 + - - +
201D ILE* 3.3 12.7 + - - +
202D CYS* 3.0 29.7 + - - -
346D ILE* 3.6 18.8 - - + -
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Residues in contact with VAL 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D VAL* 5.5 0.7 - - + -
197D ALA 3.3 0.6 - - - -
198D ALA* 1.3 75.9 - - - +
200D GLU* 1.3 67.2 + - - +
202D CYS* 3.1 18.3 + - - +
203D HIS* 3.1 25.9 + - + -
322D ILE* 5.3 0.4 - - + -
323D ASN* 3.2 27.4 - - - +
326D TYR* 3.9 27.6 - - + -
343D LEU* 4.2 6.3 - - + -
346D ILE* 4.1 13.2 - - + +
347D CYS* 4.0 14.6 - - - -
1003D CID 3.6 28.9 - - - -
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D GLY 2.5 23.3 - - - +
197D ALA* 2.9 8.1 + - - +
199D VAL* 1.3 77.0 - - - +
201D ILE* 1.3 61.8 + - - +
203D HIS* 3.1 2.8 + - - -
204D ILE* 3.0 28.6 + - - +
266D ALA* 4.3 12.0 - - + +
272D ARG* 3.2 27.2 + - - -
316D LEU* 4.1 4.3 - - - +
319D LEU* 2.8 63.5 - - + +
320D ARG* 4.0 11.6 + - - +
322D ILE* 6.0 0.4 - - + -
323D ASN* 3.4 12.5 + - + +
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Residues in contact with ILE 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D MET* 4.8 6.3 - - + -
172D VAL* 4.0 23.6 - - + -
175D PHE* 5.4 8.3 - - + -
176D THR* 5.7 1.6 - - + -
194D LEU* 4.9 4.0 - - + -
197D ALA* 2.7 57.0 + - + +
198D ALA* 3.5 10.3 - - - +
200D GLU* 1.3 69.6 - - - +
202D CYS* 1.3 63.4 + - - +
204D ILE* 3.8 7.7 - - - +
205D VAL* 2.8 46.8 + - + +
263D ALA* 4.2 16.4 - - + +
266D ALA* 4.0 13.2 - - + -
267D LEU* 4.4 17.5 - - + -
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Residues in contact with CYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D MET* 6.0 0.2 - - - -
168D MET* 3.8 25.4 - - - +
169D VAL* 3.8 25.4 - - - -
172D VAL* 3.4 23.3 - - - -
198D ALA 3.0 21.5 + - - -
199D VAL 3.1 9.6 + - - +
201D ILE* 1.3 75.5 - - - +
203D HIS* 1.3 57.5 + - - +
205D VAL* 3.9 2.5 - - - -
206D LEU* 2.8 32.8 + - - +
1003D CID 4.0 20.4 - - + -
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Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D VAL* 3.1 32.9 + - + +
200D GLU 3.1 9.6 + - - +
202D CYS* 1.3 75.8 - - + +
204D ILE* 1.3 63.3 + - - +
206D LEU* 4.1 5.6 - - + +
207D ASN* 3.0 18.4 + - - +
238D PHE* 5.3 1.4 - - - -
242D LEU* 3.7 25.4 - - + +
245D PHE* 4.6 3.1 - + + -
246D HIS* 3.1 34.7 + - + +
249D LEU* 4.9 0.5 - - - +
319D LEU* 3.6 15.0 - - + -
322D ILE* 4.2 19.0 - - + +
326D TYR* 5.2 2.8 - - - -
1003D CID 3.5 47.8 + + - -
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Residues in contact with ILE 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D GLU 3.0 17.0 + - - +
201D ILE* 3.8 5.2 - - - +
202D CYS 3.4 0.2 - - - -
203D HIS* 1.3 74.3 - - - +
205D VAL* 1.3 60.4 + - + +
207D ASN* 2.9 27.5 + - - +
208D THR* 3.9 2.8 + - - +
249D LEU* 4.7 9.6 - - + -
259D TYR* 3.8 41.6 - - + +
262D LEU* 4.0 14.8 - - + +
263D ALA* 3.3 35.2 - - + +
266D ALA* 3.8 17.0 - - + -
316D LEU* 4.8 1.6 - - + -
319D LEU* 3.6 22.7 - - + -
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D HIS* 4.8 6.5 - - + +
125D MET* 3.3 42.8 - - + -
126D GLY* 4.2 4.0 - - - +
128D MET* 3.8 27.4 - - + -
129D PHE* 3.1 12.8 - - + -
201D ILE* 2.8 29.8 + - + +
202D CYS* 4.1 4.0 - - - +
204D ILE* 1.3 77.9 - - + +
206D LEU* 1.3 56.2 + - - +
207D ASN 3.4 0.2 - - - -
208D THR* 3.0 27.7 + - + +
259D TYR* 6.2 0.2 - - - -
263D ALA* 4.9 5.2 - - + -
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D PHE* 3.2 30.5 - - + -
168D MET* 4.3 4.5 - - + -
202D CYS 2.8 20.1 + - - +
203D HIS* 3.7 20.6 - - - +
204D ILE 3.1 0.4 - - - -
205D VAL* 1.3 75.2 - - - +
207D ASN* 1.3 61.2 + - - +
208D THR 3.1 2.7 - - - -
209D THR* 3.0 25.3 + - - +
217D PHE* 3.4 35.2 - - + -
219D CYS* 4.6 2.7 - - - -
1003D CID 3.5 48.2 - - + +
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Residues in contact with ASN 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D HIS 3.0 11.5 + - - +
204D ILE 2.9 13.7 + - - +
206D LEU* 1.3 74.1 - - - +
208D THR* 1.3 64.8 + - - +
209D THR 3.0 4.1 + - - -
210D PHE* 3.1 15.6 + - - +
246D HIS* 3.0 51.5 + - - +
249D LEU* 3.0 28.4 - - + +
250D ARG* 3.2 20.2 + - - +
259D TYR* 2.9 27.0 + - + -
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Residues in contact with THR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D HIS* 6.3 0.9 - - - +
126D GLY* 5.6 3.6 - - - -
129D PHE* 4.7 2.8 - - - -
204D ILE 4.4 2.7 - - - +
205D VAL* 3.0 24.4 + - + +
207D ASN* 1.3 78.2 - - - +
209D THR* 1.3 65.2 + - - +
250D ARG* 3.0 32.1 + - - +
256D GLU* 6.3 2.5 - - + -
259D TYR* 4.3 32.3 - - + -
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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