Contacts of the helix formed by residues 195 - 220 (chain D) in PDB entry 4P9O
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 195 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D TYR* 3.4 23.8 - - + +
185D VAL* 5.0 1.1 - - + +
188D VAL* 3.9 23.3 - - + -
189D MET* 3.8 12.1 - - + -
192D HIS* 3.1 19.2 + - + +
193D PRO 3.2 1.6 - - - -
194D ASN* 1.4 74.1 - - - +
196D TRP* 1.4 56.0 + - - +
197D VAL 3.2 0.2 - - - -
198D PHE* 3.2 18.0 + - - +
199D PHE* 3.2 23.6 - - + -
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Residues in contact with TRP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D VAL* 4.8 7.9 - - + -
189D MET* 3.9 22.8 - - - +
193D PRO 3.3 22.4 + - - -
194D ASN* 2.9 9.9 + - - +
195D ALA* 1.4 71.1 - - - +
197D VAL* 1.3 83.0 + - + +
198D PHE 3.2 1.8 - - - -
199D PHE 4.0 2.0 - - - +
200D ILE* 3.0 54.6 + - + +
201D PRO* 3.6 1.0 - - + +
302D 2CV 3.4 81.0 + - + -
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ASN* 2.9 24.3 + - + +
196D TRP* 1.3 112.9 - - + +
198D PHE* 1.3 56.7 + - - +
201D PRO* 3.0 26.4 - - + +
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Residues in contact with PHE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ALA* 3.4 41.1 - - + -
148D MET* 3.9 20.6 - - + -
149D ALA* 4.0 12.8 - - + -
152D LEU* 4.9 9.6 - - + -
153D TYR* 3.4 26.5 - + - +
171D LEU* 3.9 11.4 - - + -
194D ASN 4.4 0.4 + - - -
195D ALA 3.2 2.5 + - - +
196D TRP 3.2 0.2 - - - -
197D VAL* 1.3 79.1 - - - +
199D PHE* 1.3 101.5 + + - +
201D PRO* 3.3 11.1 - - - +
202D PHE* 3.3 20.1 + + + +
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Residues in contact with PHE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D TYR* 3.6 35.2 - + - -
161D PHE* 3.7 33.4 - + - -
171D LEU* 4.1 9.2 - - + -
174D VAL* 4.5 18.2 - - + -
180D TRP* 5.4 0.2 - - + -
184D ILE* 4.9 4.0 - - + -
185D VAL* 3.7 38.6 - - + -
188D VAL* 4.3 15.0 - - + -
195D ALA 3.2 24.4 + - - +
196D TRP* 4.8 0.4 - - - +
198D PHE* 1.3 96.2 - + - +
200D ILE* 1.4 64.9 + - + +
202D PHE* 3.3 6.6 + - + +
203D ILE* 3.1 31.4 + - + +
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Residues in contact with ILE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D TRP* 4.3 27.1 - - + -
185D VAL* 6.0 1.3 - - + -
196D TRP* 3.0 49.4 + - + +
199D PHE* 1.4 69.3 - - + +
201D PRO* 1.4 64.9 - - + +
203D ILE* 3.2 9.6 + - + +
204D MET* 3.0 50.3 + - + +
302D 2CV 4.3 35.0 - - + -
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Residues in contact with PRO 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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196D TRP* 3.6 6.1 - - + +
197D VAL* 3.0 31.4 - - + +
198D PHE 3.3 7.6 - - - +
200D ILE* 1.4 89.3 - - + +
202D PHE* 1.4 50.6 + - - +
204D MET* 3.2 20.2 + - + +
205D LEU* 2.7 38.4 + - - +
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Residues in contact with PHE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D VAL* 5.0 6.5 - - + -
142D PHE* 3.7 20.6 - + - -
145D ALA* 3.7 32.3 - - + -
171D LEU* 3.3 50.7 - - + -
174D VAL* 4.1 15.5 - - + -
175D MET* 4.3 5.4 - - + -
198D PHE* 3.3 18.2 + + + +
199D PHE* 3.3 13.1 + + + +
201D PRO* 1.4 76.8 - - - +
203D ILE* 1.4 52.4 + - - +
205D LEU* 3.8 7.5 - - + +
206D THR* 2.8 72.1 + - + +
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Residues in contact with ILE 203 (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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174D VAL* 3.8 31.2 - - + +
175D MET* 5.8 0.4 - - - +
177D LEU* 3.8 20.2 - - + -
180D TRP* 3.6 49.1 - - + +
199D PHE* 3.1 22.4 + - + +
200D ILE* 3.5 9.6 - - + +
202D PHE* 1.4 71.4 - - - +
204D MET* 1.3 63.8 + - + +
206D THR* 3.5 5.3 + - - -
207D THR* 2.7 42.0 + - + +
303D BR 4.4 14.6 - - + -
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Residues in contact with MET 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 ILE* 3.0 30.6 + - + +
201D PRO* 3.6 28.7 - - + +
203D ILE* 1.3 78.8 - - + +
205D LEU* 1.3 61.5 + - - +
207D THR* 4.1 7.1 + - - -
208D PHE* 3.6 16.1 - - - +
302D 2CV 5.7 6.5 - - - -
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Residues in contact with LEU 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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137D LEU* 6.1 2.9 - - + -
141D VAL* 3.7 38.4 - - + -
201D PRO 2.7 21.1 + - - +
202D PHE* 3.8 9.4 - - + +
204D MET* 1.3 71.2 - - - +
206D THR* 1.4 57.2 + - + +
208D PHE* 3.4 8.8 - - + +
209D THR* 2.6 47.6 + - - +
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Residues in contact with THR 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 4.5 12.6 - - + -
141D VAL* 4.8 8.7 - - + -
142D PHE* 4.6 2.5 - - + -
175D MET* 3.5 34.8 - - - +
202D PHE* 2.8 60.8 + - + +
203D ILE* 3.5 6.4 + - - -
205D LEU* 1.4 66.9 - - + +
207D THR* 1.3 54.7 + - - +
208D PHE 2.6 17.4 + - - -
209D THR* 4.2 6.1 - - - +
210D VAL* 3.0 29.6 + - - +
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Residues in contact with THR 207 (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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175D MET* 3.4 27.8 - - + +
177D LEU* 4.6 19.5 - - + -
203D ILE* 2.7 31.7 + - + +
204D MET* 4.1 4.2 + - - +
206D THR* 1.3 74.4 - - - +
208D PHE* 1.3 59.0 + - - +
210D VAL* 5.7 0.7 - - - -
211D LEU* 4.2 18.8 - - - +
303D BR 4.3 13.2 - - - +
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Residues in contact with PHE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D MET 3.6 11.4 - - - +
205D LEU* 3.4 12.6 - - + +
206D THR 2.6 6.7 + - - -
207D THR* 1.3 74.7 - - - +
209D THR* 1.4 62.6 + - - +
210D VAL 3.3 0.9 - - - -
211D LEU* 3.5 10.0 - - + +
212D ASN* 2.9 57.9 + - - -
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Residues in contact with THR 209 (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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134D VAL* 4.0 11.8 - - + +
137D LEU* 3.8 28.3 - - + +
138D LEU* 3.9 34.8 - - + +
141D VAL* 6.0 2.0 - - + -
205D LEU* 2.6 40.3 + - - +
206D THR* 4.0 2.0 - - - -
208D PHE* 1.4 81.3 - - - +
210D VAL* 1.3 56.2 + - - +
212D ASN* 3.7 3.2 + - - +
213D LEU* 3.2 26.0 + - - +
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Residues in contact with VAL 210 (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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138D LEU* 3.8 30.3 - - + -
175D MET* 3.7 33.4 - - + -
206D THR 3.0 15.1 + - - +
207D THR* 5.5 0.9 - - - -
209D THR* 1.3 73.1 - - - +
211D LEU* 1.4 60.2 + - - +
212D ASN 3.2 0.9 - - - -
213D LEU* 4.1 7.2 - - + -
214D PHE* 2.9 62.5 + - + +
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Residues in contact with LEU 211 (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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206D THR 4.3 0.2 + - - -
207D THR* 4.4 11.8 - - - +
208D PHE* 3.2 25.0 + - + +
210D VAL* 1.4 77.1 - - - +
212D ASN* 1.3 60.5 + - - +
214D PHE* 5.1 3.1 - - + +
215D ILE* 3.4 43.5 + - + +
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Residues in contact with ASN 212 (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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134D VAL* 4.9 9.0 - - + -
208D PHE* 2.9 49.5 + - - +
209D THR* 4.0 5.6 - - - +
211D LEU* 1.3 83.5 - - - +
213D LEU* 1.4 59.0 + - - +
215D ILE* 3.6 6.4 + - - +
216D GLY* 2.9 27.2 + - - -
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Residues in contact with LEU 213 (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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131D VAL* 4.2 9.7 - - + +
134D VAL* 3.8 23.0 - - + +
135D ALA* 5.4 4.7 - - + +
138D LEU* 5.7 5.8 - - + -
209D THR 3.2 18.9 + - - +
210D VAL* 3.4 12.3 + - + +
212D ASN* 1.4 76.5 - - - +
214D PHE* 1.4 62.1 + - + +
216D GLY* 3.3 3.5 + - - -
217D ILE* 3.3 30.5 + - + +
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Residues in contact with PHE 214 (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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204C MET* 4.2 24.9 - - + -
207C THR* 4.5 16.4 - - - -
208C PHE* 3.5 35.8 - + + -
211C LEU* 5.3 13.2 - - + -
210D VAL* 2.9 45.8 + - + +
211D LEU* 5.1 2.7 - - + +
213D LEU* 1.4 73.7 - - + +
215D ILE* 1.4 61.5 + - + +
217D ILE* 3.4 24.2 + - + +
218D ILE* 3.5 19.2 + - + +
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Residues in contact with ILE 215 (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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211C LEU* 6.2 3.1 - - + -
215C ILE* 6.5 0.7 - - + -
211D LEU* 3.4 40.8 + - + +
212D ASN* 3.6 6.3 + - - +
213D LEU 3.4 0.2 - - - -
214D PHE* 1.4 75.7 - - + +
216D GLY* 1.3 64.8 + - - +
218D ILE* 3.3 28.9 + - + +
219D VAL* 3.3 23.0 + - + +
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Residues in contact with GLY 216 (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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131D VAL* 3.8 15.5 - - - -
212D ASN 2.9 17.8 + - - -
213D LEU 3.7 2.9 - - - -
214D PHE 3.3 0.4 - - - -
215D ILE* 1.3 77.2 - - - +
217D ILE* 1.4 55.6 + - - +
219D VAL* 3.5 5.2 + - - +
220D ASP* 3.0 36.9 + - - +
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Residues in contact with ILE 217 (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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208C PHE* 4.0 24.9 - - + -
131D VAL* 3.8 21.5 - - + -
213D LEU* 3.3 20.1 + - + +
214D PHE* 3.6 28.9 - - + +
215D ILE 3.3 0.2 - - - -
216D GLY* 1.4 74.4 - - - +
218D ILE* 1.4 58.8 + - - +
220D ASP* 2.9 26.3 - - - +
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Residues in contact with ILE 218 (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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208C PHE* 5.1 7.9 - - + -
211C LEU* 5.1 15.3 - - + -
212C ASN* 3.6 26.2 - - - +
215C ILE* 5.4 20.0 - - + -
214D PHE* 3.5 19.1 - - + +
215D ILE* 3.4 26.7 - - + +
217D ILE* 1.4 76.2 - - - +
219D VAL* 1.3 64.3 + - + +
220D ASP 4.4 1.7 - - - +
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Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D ILE* 3.3 23.3 + - + +
216D GLY* 3.5 7.2 + - - +
218D ILE* 1.3 80.4 - - + +
220D ASP* 1.4 65.1 + - - +
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Residues in contact with ASP 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLY* 5.9 0.9 - - - -
131D VAL* 3.4 21.4 + - + +
216D GLY* 3.0 26.1 + - - +
217D ILE* 2.9 21.6 - - - +
218D ILE 4.4 1.7 - - - +
219D VAL* 1.4 82.8 - - - +
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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