Contacts of the helix formed by residues 183 - 204 (chain D) in PDB entry 2AXZ
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 GLY 183 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C PHE 6.2 0.4 - - - -
60C GLU* 5.8 0.2 - - - -
63C ASN* 3.0 21.8 - - - +
181D SER* 3.6 4.6 + - - -
182D PHE* 1.3 76.2 - - - +
184D LYS* 1.3 65.2 + - - -
185D ASP* 3.3 3.6 - - - -
186D TYR* 3.2 4.0 + - - +
187D ASP* 2.6 32.3 + - - +
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LYS* 3.4 37.5 - - + +
185C ASP* 4.2 21.6 + - - +
181D SER* 5.8 0.2 - - - -
183D GLY* 1.3 74.0 - - - -
185D ASP* 1.3 60.9 + - - +
187D ASP* 3.2 10.5 + - - +
188D LEU* 2.9 28.6 + - - +
225D ASN 4.8 5.8 - - - -
227D SER* 3.9 32.5 + - - +
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Residues in contact with ASP 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASN* 4.4 16.4 + - - +
59C PHE* 5.5 6.8 - - - +
184C LYS* 3.7 20.7 - - - +
70D LYS* 4.9 4.7 + - - -
150D GLY* 5.5 0.7 - - - -
183D GLY* 3.3 0.8 - - - -
184D LYS* 1.3 77.7 - - - +
186D TYR* 1.3 59.5 - - - +
188D LEU* 3.6 8.9 + - - +
189D THR* 3.4 26.7 + - - +
299D TYR 5.2 1.0 - - - +
300D GLU* 3.8 11.9 - - - +
7H VAL* 3.3 35.1 - - - +
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Residues in contact with TYR 186 (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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60C GLU* 4.2 11.4 - - + +
64C ARG* 4.2 7.2 - - - -
148D PHE 4.1 5.2 + - - -
149D PHE 3.9 1.8 - - - -
150D GLY* 3.4 35.2 - - - -
153D TYR* 3.7 32.1 + + - -
178D ILE* 4.1 10.0 - - + +
180D ASP 3.6 13.2 - - - -
182D PHE* 3.4 58.5 - + + +
183D GLY* 3.2 9.1 + - - +
184D LYS 3.1 0.4 - - - -
185D ASP* 1.3 78.6 - - - +
187D ASP* 1.3 69.6 + - - +
188D LEU 3.1 0.2 - - - -
189D THR* 3.0 17.7 + - - -
190D ILE* 3.1 33.4 + - + +
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Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D SER* 2.8 32.3 + - - -
183D GLY 2.6 21.5 + - - +
184D LYS* 3.2 13.6 + - - +
186D TYR* 1.3 77.6 - - - +
188D LEU* 1.3 61.8 + - - +
190D ILE* 3.2 22.7 - - - +
191D GLN* 3.2 20.9 + - - +
225D ASN 3.7 1.6 - - - +
226D ILE* 2.6 42.8 - - + +
227D SER 3.9 7.2 - - - +
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C LYS* 5.7 8.1 - - - +
184D LYS 2.9 16.4 + - - +
185D ASP* 3.6 13.2 - - - +
186D TYR 3.1 0.2 - - - -
187D ASP* 1.3 78.4 - - - +
189D THR* 1.3 62.2 + - + +
191D GLN* 3.4 6.9 + - - +
192D THR* 2.8 28.1 + - - +
229D ASN* 4.3 12.6 - - + +
232D TYR* 3.7 7.6 - - + -
298D TYR* 3.6 47.8 - - + +
299D TYR 5.5 4.5 - - - +
5H VAL* 3.2 32.1 - - + -
7H VAL 5.2 3.8 - - - +
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Residues in contact with THR 189 (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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150D GLY* 3.4 23.0 + - - +
153D TYR* 3.8 9.7 - - - +
154D GLU* 3.9 23.3 - - + +
157D SER* 3.6 5.0 + - - -
185D ASP 3.4 13.6 + - - +
186D TYR* 3.0 16.3 + - - -
188D LEU* 1.3 73.0 - - + +
190D ILE* 1.3 62.0 + - - +
191D GLN 3.1 1.6 - - - -
192D THR* 3.1 18.2 + - - -
193D VAL* 3.2 13.7 + - - +
5H VAL* 3.7 21.3 - - + -
7H VAL 4.3 11.7 - - - +
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Residues in contact with ILE 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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153D TYR* 3.6 42.8 - - + -
176D TYR* 2.9 21.2 + - + -
178D ILE* 4.0 26.2 - - + -
186D TYR* 3.1 36.1 - - + +
187D ASP* 3.2 37.9 - - + +
189D THR* 1.3 76.9 + - - +
191D GLN* 1.3 62.0 + - + +
194D LEU* 3.7 11.8 + - - +
220D LEU* 4.6 7.6 - - + +
226D ILE* 4.5 11.7 - - + -
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Residues in contact with GLN 191 (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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187D ASP* 3.2 24.7 + - - +
188D LEU* 3.4 3.7 + - - +
189D THR 3.1 0.6 - - - -
190D ILE* 1.3 81.8 - - + +
192D THR* 1.3 58.8 + - - +
194D LEU* 3.3 6.1 + - - +
195D LYS* 3.0 27.7 + - - +
217D PHE* 4.1 7.9 - - + -
220D LEU* 3.9 24.2 - - + -
226D ILE* 4.4 5.1 - - - +
227D SER 3.3 10.5 + - - -
228D ILE* 3.2 36.7 - - - +
229D ASN* 2.8 32.0 + - - +
232D TYR* 3.5 20.8 - - + +
236D ILE* 4.5 2.8 - - - +
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Residues in contact with THR 192 (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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157D SER* 3.6 5.2 - - - +
188D LEU 2.8 17.5 + - - -
189D THR 3.1 8.6 + - - -
191D GLN* 1.3 75.3 - - - +
193D VAL* 1.3 60.0 + - - +
195D LYS* 3.2 2.1 + - - +
196D ASN* 2.8 35.7 + - - +
232D TYR* 2.7 31.5 + - + +
3H THR* 3.6 18.6 - - - +
5H VAL* 3.1 39.3 - - + +
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D TYR* 3.1 21.3 - - + +
156D VAL* 3.3 24.7 - - + -
157D SER* 2.9 27.3 + - - +
160D LEU* 4.0 4.3 - - + +
172D ILE* 4.1 19.3 - - + -
176D TYR* 2.9 39.0 - - + +
189D THR 3.2 7.7 + - - +
191D GLN 3.3 0.2 - - - -
192D THR* 1.3 75.8 - - - +
194D LEU* 1.3 56.3 + - + +
196D ASN* 3.9 1.3 - - - -
197D ALA* 2.9 33.5 + - + +
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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
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176D TYR* 3.6 38.4 - - + -
190D ILE 3.7 3.8 + - - +
191D GLN* 3.3 7.1 + - - +
192D THR 3.2 0.4 - - - -
193D VAL* 1.3 73.8 - - - +
195D LYS* 1.3 60.8 + - - +
197D ALA* 3.9 2.6 - - - +
198D LEU* 2.8 34.5 + - - +
213D TYR* 3.6 33.4 - - + +
216D GLN* 3.6 21.8 - - + +
217D PHE* 3.4 39.3 - - + +
220D LEU* 3.9 14.8 - - + -
236D ILE* 4.8 3.1 - - + -
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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 GLN 3.0 17.9 + - - +
192D THR* 3.2 5.6 + - - +
194D LEU* 1.3 77.3 - - - +
196D ASN* 1.3 67.1 + - - +
198D LEU* 3.6 2.8 + - - +
199D THR* 2.8 28.3 + - - +
232D TYR* 3.7 26.4 + - + -
235D GLU* 3.2 28.0 + - + +
236D ILE* 3.7 30.9 - - + +
239D LEU* 4.0 2.7 - - + +
302D TYR* 2.5 26.3 + - - -
1H LEU 2.9 27.4 + - - -
3H THR* 2.6 25.9 + - - -
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Residues in contact with ASN 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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157D SER* 3.4 10.5 - - - +
160D LEU* 3.9 17.3 - - + -
192D THR* 2.8 24.2 + - - +
193D VAL* 4.8 0.4 - - - -
195D LYS* 1.3 81.0 - - - +
197D ALA* 1.3 65.5 + - - +
199D THR* 3.3 3.3 + - - -
200D ILE* 3.1 27.7 + - - +
1H LEU 2.8 14.8 + - - -
2H VAL* 3.3 19.9 - - + +
3H THR* 2.6 49.0 + - - +
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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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160D LEU* 3.8 13.7 - - + +
165D TYR* 4.9 4.1 - - + -
172D ILE* 4.7 4.0 - - + -
193D VAL* 2.9 20.2 + - + +
194D LEU 3.9 0.4 - - - +
196D ASN* 1.3 76.0 - - - +
198D LEU* 1.3 60.2 + - - +
199D THR 3.2 0.2 + - - -
200D ILE* 3.2 6.2 + - - +
201D SER* 2.8 32.6 + - - -
213D TYR* 3.3 41.7 - - + +
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Residues in contact with LEU 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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194D LEU 2.8 23.0 + - - +
195D LYS 3.9 4.3 - - - +
197D ALA* 1.3 74.1 - - - +
199D THR* 1.3 57.0 + - - +
201D SER* 4.3 0.9 - - - -
202D ILE* 3.0 36.1 + - + +
210D ALA* 3.5 36.6 - - + +
213D TYR* 3.8 13.6 - - + -
214D ILE* 3.6 27.6 - - + -
236D ILE* 3.8 26.5 - - + +
239D LEU* 3.6 30.1 - - + -
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Residues in contact with THR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LYS 2.8 19.0 + - - -
196D ASN 3.4 9.4 - - - -
197D ALA 3.1 0.4 - - - -
198D LEU* 1.3 75.6 - - - +
200D ILE* 1.3 59.3 + - - +
202D ILE* 3.8 1.6 - - - +
203D MSE 2.9 57.9 + - + +
235D GLU* 4.2 0.3 + - - -
239D LEU* 3.3 17.7 - - + +
279D GLU* 3.4 13.0 - - - +
1H LEU* 2.8 42.3 + - - +
2H VAL* 4.4 3.8 - - + +
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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
----------------------------------------------------------
160D LEU* 3.5 42.6 - - + +
163D LEU 5.7 0.2 - - - +
165D TYR* 4.0 27.8 - - + +
196D ASN 3.1 15.3 + - - +
197D ALA* 3.8 4.5 - - - +
199D THR* 1.3 76.5 - - - +
201D SER* 1.3 57.9 + - - +
204D ASN* 3.0 50.0 + - - +
206D ASN* 5.5 0.7 - - - +
289D PHE* 3.6 31.9 - - + -
2H VAL* 3.6 17.5 - - + -
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Residues in contact with SER 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 4.7 6.5 - - - -
197D ALA 2.8 20.1 + - - -
198D LEU* 3.7 5.2 - - - -
200D ILE* 1.3 78.3 - - - +
202D ILE* 1.3 60.2 + - - +
204D ASN 3.7 0.3 - - - -
205D ARG 3.1 4.0 + - - -
206D ASN* 2.7 40.1 + - - +
209D GLU* 3.3 21.3 - - - +
210D ALA* 3.6 26.9 - - - -
213D TYR* 3.4 10.4 - - - -
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Residues in contact with ILE 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU* 3.0 29.2 + - + +
199D THR 3.9 1.6 - - - +
201D SER* 1.3 76.3 - - - +
203D MSE 1.3 63.5 + - - +
205D ARG* 3.2 26.0 + - - +
206D ASN 5.0 0.2 - - - +
207D LEU* 4.0 4.7 - - + -
210D ALA* 3.9 13.7 - - + -
239D LEU* 4.3 18.2 - - + +
242D ILE* 3.9 14.4 - - + -
243D TYR* 3.6 43.5 - - + -
246D LEU* 3.9 13.9 - - + +
283D ILE* 3.8 27.1 - - + -
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Residues in contact with MSE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D THR* 2.9 40.4 + - + +
200D ILE 3.8 4.3 - - - +
202D ILE* 1.3 78.1 - - - +
204D ASN* 1.3 58.9 + - - +
205D ARG* 3.0 20.7 + - - +
279D GLU* 3.4 22.2 - - + +
282D LYS* 4.6 20.2 - - + -
283D ILE* 4.0 21.8 - - + +
286D LYS 5.4 1.4 - - - -
287D GLU 4.0 21.9 - - - +
288D LYS* 4.4 4.1 - - - +
289D PHE* 3.3 55.2 - - + +
290D THR 5.0 2.0 - - - +
1H LEU* 5.4 0.4 - - - -
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Residues in contact with ASN 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D TYR* 5.2 3.8 - - - +
166D GLU* 5.6 3.0 + - - -
200D ILE* 3.0 40.0 + - - +
203D MSE 1.3 74.0 - - - +
205D ARG* 1.3 70.4 + - - +
206D ASN* 3.2 26.3 - - - +
288D LYS* 3.0 48.9 - - + +
289D PHE* 3.3 10.4 + - - +
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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) + - + + + + + -
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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