Contacts of the helix formed by residues 178 - 202 (chain D) in PDB entry 2XH2
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 THR 178 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ALA* 3.8 2.9 - - - +
177D LYS* 1.3 85.6 - - + +
179D PHE* 1.3 63.7 + - - +
180D ALA* 3.6 7.1 + - - +
181D GLU* 3.0 26.5 + - - +
182D ALA* 3.0 22.2 + - - +
416D GLU* 3.5 14.4 - - - +
425D PHE* 3.7 10.8 - - - -
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Residues in contact with PHE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D LEU* 4.3 12.8 - - + -
147D PRO* 3.2 31.4 - - + -
149D PRO* 3.9 21.1 - - + -
178D THR* 1.3 69.2 - - - +
180D ALA* 1.3 66.5 + - - +
182D ALA* 3.2 1.2 + - - +
183D LEU* 2.9 38.0 + - + +
409D LEU* 3.4 35.7 - - + -
412D LEU* 3.5 35.0 - - + -
413D LEU* 3.8 19.3 - - + -
416D GLU* 2.8 22.9 + - - +
425D PHE* 3.7 17.0 - + + -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 4.5 1.7 + - - -
56C TRP* 5.7 0.9 - - - -
178D THR* 3.3 6.0 - - - +
179D PHE* 1.3 77.6 - - - +
181D GLU* 1.3 61.4 + - - +
183D LEU* 3.5 2.3 + - - +
184D ARG* 3.1 22.7 + - - +
413D LEU* 3.7 23.4 - - + +
416D GLU* 2.9 16.4 + - - +
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Residues in contact with GLU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLY 4.7 0.5 - - - +
176D ALA* 3.6 18.5 - - + +
177D LYS* 2.8 35.1 + - - +
178D THR* 3.0 20.2 + - - +
180D ALA* 1.3 73.8 - - - +
182D ALA* 1.3 66.2 + - - +
184D ARG* 3.2 26.2 + - - +
185D ILE* 2.9 36.4 + - + +
240D LYS* 4.6 10.6 - - - +
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Residues in contact with ALA 182 (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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149D PRO* 4.3 9.4 - - + -
151D LEU* 4.8 0.3 - - - +
173D PRO* 3.3 25.9 - - + +
176D ALA* 3.5 12.4 - - + +
178D THR 3.0 14.7 + - - +
179D PHE* 3.2 9.2 + - - +
181D GLU* 1.3 75.6 - - - +
183D LEU* 1.3 57.0 + - - +
185D ILE* 3.6 1.0 - - - +
186D GLY* 2.9 24.8 + - - -
425D PHE* 3.5 28.0 - - + -
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.4 37.4 + - + +
149D PRO* 5.1 3.1 - - + +
151D LEU* 4.4 17.3 - - + -
179D PHE* 2.9 38.8 + - + +
180D ALA 3.9 4.0 - - - +
182D ALA* 1.3 74.6 - - - +
184D ARG* 1.3 61.4 + - - +
186D GLY* 5.0 0.7 - - - -
187D SER* 2.9 31.8 + - - +
400D PRO* 4.8 9.6 - - + -
406D LEU* 5.4 0.9 - - + -
409D LEU* 3.9 45.8 - - + +
413D LEU* 4.0 8.5 - - + -
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Residues in contact with ARG 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.2 14.9 + - - +
54C SER 3.8 12.9 + - - -
55C LYS* 4.1 29.5 - - - +
56C TRP* 3.5 39.0 - - + +
180D ALA 3.1 17.4 + - - +
181D GLU* 3.7 19.5 + - - +
183D LEU* 1.3 76.7 - - - +
185D ILE* 1.3 77.7 + - - +
187D SER* 2.7 21.2 + - - -
188D GLU* 2.8 62.1 + - - +
237D HIS* 4.6 3.2 - - - -
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Residues in contact with ILE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PRO* 3.9 9.6 - - + -
176D ALA* 4.1 17.0 - - + +
181D GLU* 2.9 30.5 + - + +
182D ALA 3.6 5.6 - - - +
184D ARG* 1.3 97.5 - - - +
186D GLY* 1.3 64.1 + - - +
188D GLU* 3.2 4.5 + - - +
189D VAL* 3.0 28.7 + - - +
237D HIS* 3.2 38.1 - - + +
240D LYS* 4.3 17.9 - - + -
241D ILE* 3.6 24.2 - - + -
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Residues in contact with GLY 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 3.8 22.2 - - - +
171D ILE* 3.6 18.7 - - - +
173D PRO* 4.2 4.9 - - - -
182D ALA 2.9 17.9 + - - -
185D ILE* 1.3 77.3 - - - +
187D SER* 1.3 57.2 + - - +
189D VAL* 3.2 1.9 + - - -
190D TYR* 2.9 28.7 + - - +
241D ILE* 5.0 0.4 - - - -
400D PRO* 4.9 0.2 - - - -
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Residues in contact with SER 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C TYR* 3.8 21.1 - - - -
15C GLY 4.1 12.8 + - - -
56C TRP* 3.9 9.5 - - - -
151D LEU* 4.7 1.2 - - - +
183D LEU 2.9 17.0 + - - -
184D ARG* 2.7 20.8 + - - -
186D GLY* 1.3 74.9 - - - +
188D GLU* 1.3 57.8 + - - +
190D TYR* 3.3 8.3 + - - +
191D HIS* 3.0 37.5 + - - -
400D PRO* 4.2 16.1 - - - +
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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
----------------------------------------------------------
54C SER 4.4 4.8 - - - +
55C LYS* 3.5 3.1 - - - -
56C TRP* 2.8 36.2 + - - +
57C MET* 3.3 20.9 - - - +
184D ARG* 2.8 49.9 + - - +
185D ILE 3.2 6.9 + - - +
187D SER* 1.3 79.0 + - - +
189D VAL* 1.3 61.4 + - - +
191D HIS* 4.7 0.4 - - - -
192D ASN* 3.0 31.0 + - - +
235D ALA* 4.2 7.7 - - + +
237D HIS* 2.8 28.3 + - + +
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Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D VAL* 5.4 2.0 - - + -
171D ILE* 3.7 28.7 - - + -
185D ILE 3.0 19.0 + - - +
186D GLY 3.7 0.4 - - - +
188D GLU* 1.3 74.3 - - - +
190D TYR* 1.3 58.1 + - - +
192D ASN* 3.3 2.4 + - - +
193D LEU* 2.8 32.3 + - + +
228D ILE* 4.9 1.8 - - + +
231D ALA* 4.2 5.7 - - + +
232D ILE* 3.8 34.3 - - + +
235D ALA* 4.0 12.1 - - + -
237D HIS* 3.8 18.4 - - + -
241D ILE* 4.1 20.0 - - + -
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Residues in contact with TYR 190 (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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14C ARG 4.7 2.7 - - - -
152D ASN 4.0 9.2 - - - -
153D VAL* 4.3 19.7 - - + -
171D ILE* 4.6 0.6 - - - +
186D GLY 2.9 13.7 + - - +
187D SER 3.4 7.9 - - - +
188D GLU 3.3 0.2 - - - -
189D VAL* 1.3 77.3 - - - +
191D HIS* 1.3 80.2 + + - +
193D LEU* 3.3 8.5 + - + +
194D LYS* 2.9 45.8 + - + +
208D VAL* 3.7 12.8 - - - +
212D GLY 2.6 29.8 + - - -
213D GLY* 4.5 5.1 - - - -
214D VAL* 5.1 3.9 - - + +
399D ALA* 3.8 9.2 - - + -
400D PRO* 3.6 30.3 - - + -
401D ALA* 3.4 21.7 - - + +
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Residues in contact with HIS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ARG 3.0 23.4 + - - -
15C GLY* 2.9 28.9 - - - -
16C ASN* 3.2 19.9 + - - -
57C MET* 3.1 34.3 - - + +
59C LYS* 6.2 1.1 - - - -
187D SER* 3.0 29.4 + - - +
190D TYR* 1.3 86.8 - + - +
192D ASN* 1.3 60.0 + - - +
194D LYS* 3.3 8.5 + - + +
195D SER* 3.0 30.8 + - - -
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Residues in contact with ASN 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C MET* 3.3 19.8 - - - +
188D GLU* 3.0 26.3 + - - +
189D VAL 3.7 4.0 - - - +
191D HIS* 1.3 74.5 - - - +
193D LEU* 1.3 62.1 - - - +
195D SER* 3.1 9.9 + - - -
196D LEU* 3.0 28.5 - - + -
231D ALA* 4.2 17.9 - - + +
234D ALA* 4.6 11.3 + - + +
235D ALA* 3.3 29.0 + - - +
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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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153D VAL* 3.4 43.7 - - + +
154D LEU* 4.7 3.1 - - + -
189D VAL* 2.8 22.8 + - + +
190D TYR* 3.5 9.0 - - + +
192D ASN* 1.3 71.6 + - - +
194D LYS* 1.3 58.4 + - - +
196D LEU* 3.4 3.9 + - - +
197D THR* 2.8 35.9 + - - +
214D VAL* 4.0 14.6 - - + -
227D LEU* 3.9 29.4 - - + -
228D ILE* 4.0 29.6 - - + -
231D ALA* 3.8 14.9 - - + +
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Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ASP* 4.5 13.9 + - - -
190D TYR* 2.9 40.1 + - + +
191D HIS* 3.7 10.5 - - + +
193D LEU* 1.3 77.8 - - + +
195D SER* 1.3 64.8 + - - +
197D THR* 3.3 6.7 + - - -
198D LYS* 3.0 44.2 + - + +
206D GLY* 2.8 30.0 + - - +
207D ASN* 5.1 0.2 - - - +
208D VAL* 3.9 14.6 - - - +
214D VAL* 4.3 16.6 - - + -
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D HIS 3.0 14.7 + - - -
192D ASN* 3.1 15.4 + - - -
194D LYS* 1.3 75.8 - - - +
196D LEU* 1.3 60.7 + - - +
198D LYS* 3.4 9.6 + - - +
199D LYS* 3.0 29.5 + - - +
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Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ASN* 3.0 20.6 - - + -
193D LEU 3.7 3.8 - - - +
195D SER* 1.3 78.1 + - - +
197D THR* 1.3 56.8 + - - +
199D LYS* 3.4 6.9 + - + +
200D ARG* 3.0 65.5 + - + +
227D LEU* 4.0 19.1 - - + +
230D ASP* 4.7 6.5 - - + +
231D ALA* 4.2 29.8 - - + +
234D ALA* 5.2 7.2 - - + -
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Residues in contact with THR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D LEU* 2.8 25.8 + - - +
194D LYS* 3.5 8.7 - - - +
195D SER 3.3 0.2 - - - -
196D LEU* 1.3 76.5 - - - +
198D LYS* 1.3 54.5 + - - +
201D TYR* 2.7 47.5 + - + +
202D GLY 4.1 0.2 - - - +
205D ALA* 3.6 34.5 - - + +
214D VAL* 3.9 14.6 - - + +
216D PRO* 3.9 22.0 - - + -
227D LEU* 3.9 17.9 - - - +
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Residues in contact with LYS 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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158C SER 5.3 6.5 + - - -
159C HIS 6.3 0.6 - - - -
194D LYS* 3.0 31.4 + - + +
195D SER* 3.9 7.0 - - - +
197D THR* 1.3 74.6 - - - +
199D LYS* 1.3 59.9 + - - +
202D GLY* 2.9 37.5 + - - +
203D ALA* 3.5 32.9 + - - +
206D GLY* 3.8 24.0 - - - +
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Residues in contact with LYS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D SER 3.0 17.5 + - - +
196D LEU* 3.6 11.7 - - + +
197D THR 3.3 0.2 - - - -
198D LYS* 1.3 79.4 - - - +
200D ARG* 1.3 62.6 + - + +
202D GLY 4.5 0.9 + - - -
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 3.0 46.8 + - + +
199D LYS* 1.3 80.6 - - + +
201D TYR* 1.3 82.8 + - + +
202D GLY 3.7 0.2 - - - -
227D LEU* 3.7 33.5 - - - +
230D ASP* 4.6 17.0 + - - +
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Residues in contact with TYR 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D THR* 2.7 29.3 + - + +
200D ARG* 1.3 95.7 + - + +
202D GLY* 1.3 58.7 + - - +
204D SER* 5.2 2.1 + - - -
205D ALA* 3.6 19.4 + - + +
216D PRO* 3.6 20.0 - - + -
217D ASN* 4.5 13.7 - - + +
218D ILE* 3.8 14.5 - - + +
223D GLU* 2.5 40.1 + - - +
227D LEU* 4.1 23.9 - - + +
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Residues in contact with GLY 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LYS* 2.9 25.5 + - - -
199D LYS 4.5 0.8 + - - -
200D ARG 3.7 0.8 - - - -
201D TYR* 1.3 78.9 - - - +
203D ALA* 1.3 66.4 + - - +
204D SER* 3.3 3.6 - - - -
205D ALA* 3.1 18.1 + - - +
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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