Contacts of the helix formed by residues 186 - 207 (chain D) in PDB entry 1CCW
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 186 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D ASN* 3.3 4.2 + - - -
184D ASN 4.0 2.4 + - - +
185D VAL* 1.3 77.7 - - - +
187D ILE* 1.3 65.3 + - - +
188D GLU* 3.7 8.4 + - - +
189D LYS* 2.9 27.8 + - - +
190D SER 3.1 16.6 + - - -
413D TYR* 3.5 32.8 - - + +
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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
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174D GLY 5.1 3.1 - - - +
175D ILE* 5.2 2.0 - - + -
178D ASN* 3.9 13.5 - - + +
179D VAL* 3.7 29.6 - - + -
185D VAL 3.7 0.2 + - - -
186D THR* 1.3 70.7 - - - +
188D GLU* 1.3 66.4 + - - +
190D SER* 3.2 6.1 + - - +
191D LEU* 2.9 50.9 + - + +
395D THR* 4.1 16.2 - - + -
396D VAL* 4.2 16.6 - - + +
399D PHE* 3.9 30.7 - - + -
411D SER* 4.9 0.4 - - - +
413D TYR* 4.0 20.4 - - + -
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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
----------------------------------------------------------
1D MET 4.6 3.5 - - - +
2D GLU* 5.1 1.0 - - - -
3D LEU* 3.8 38.3 + - + +
186D THR* 3.2 7.9 + - - +
187D ILE* 1.3 80.1 - - - +
189D LYS* 1.3 56.1 + - - +
191D LEU* 3.4 1.9 + - - +
192D LEU* 3.0 38.8 + - + +
396D VAL* 3.9 26.8 - - + +
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Residues in contact with LYS 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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154D ASP* 5.0 2.9 - - - -
156D ARG* 3.9 16.6 - - - +
185D VAL* 4.3 13.9 - - + -
186D THR* 2.9 23.7 + - + +
188D GLU* 1.3 77.3 - - - +
190D SER* 1.3 57.9 + - - +
192D LEU* 3.3 12.0 + - + +
193D ASP* 2.9 59.4 + - - +
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Residues in contact with SER 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 PRO* 4.1 19.7 - - - -
174D GLY* 2.7 29.3 + - - -
178D ASN* 3.0 32.1 + - - -
185D VAL* 4.2 7.4 - - - +
186D THR 3.1 5.2 + - - -
187D ILE* 3.2 8.8 + - - -
189D LYS* 1.3 78.1 - - - +
191D LEU* 1.3 58.7 + - - +
193D ASP* 3.3 0.6 + - - -
194D TRP* 2.8 36.4 + - - +
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.0 13.7 - - + -
174D GLY* 4.0 24.0 - - - +
175D ILE* 4.3 12.1 - - + -
187D ILE* 2.9 38.6 + - + +
188D GLU 3.7 4.0 - - - +
190D SER* 1.3 77.5 + - - +
192D LEU* 1.3 57.2 + - - +
194D TRP* 3.3 1.8 + - - +
195D GLN* 2.9 35.4 + - + +
236D GLU* 6.2 0.2 - - + -
239D LEU* 3.8 25.8 - - + -
392D ALA* 3.7 27.6 - - + +
395D THR* 4.0 9.0 - - + -
396D VAL* 3.9 8.7 - - + -
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Residues in contact with LEU 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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1D MET* 3.6 40.8 - - + +
2D GLU 3.9 20.6 - - - +
3D LEU* 3.9 12.1 - - + +
8D TRP* 3.5 11.6 - - + -
188D GLU* 3.0 38.1 + - + +
189D LYS* 3.5 12.6 - - + +
191D LEU* 1.3 77.3 - - - +
193D ASP* 1.3 67.9 + - - +
195D GLN* 3.3 31.1 + - - +
196D TYR 3.3 8.7 + - - -
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Residues in contact with ASP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D PRO 4.0 15.9 - - - +
154D ASP* 3.4 21.0 - - - +
155D SER 5.1 0.7 - - - +
156D ARG* 3.5 37.5 + - + +
189D LYS* 2.9 60.0 + - - +
190D SER 4.0 0.2 - - - +
192D LEU* 1.3 80.2 - - - +
194D TRP* 1.3 64.3 + - + +
196D TYR* 3.3 18.0 + - - +
197D CYS* 3.4 8.2 + - - -
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Residues in contact with TRP 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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150D HIS* 4.0 0.9 - + - -
152D THR 3.1 28.2 + - - -
153D PRO* 3.3 15.3 + - + +
155D SER* 3.5 19.9 - - - -
170D ASN* 3.8 20.0 - - - -
171D GLU 3.3 21.1 - - - -
172D GLY* 3.6 13.2 - - - -
173D GLY* 3.6 14.9 + - - -
174D GLY* 3.5 27.4 - - - +
177D TYR* 3.6 16.0 - + - +
190D SER* 2.8 28.3 + - - +
191D LEU* 4.1 2.5 - - + +
193D ASP* 1.3 75.5 - - - +
195D GLN* 1.3 64.9 + - - +
196D TYR 3.2 0.7 - - - -
197D CYS* 3.2 19.6 + - + +
198D ASP* 2.9 32.3 + - - +
213D ARG* 3.6 29.4 - - - -
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Residues in contact with GLN 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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2D GLU 5.3 0.7 - - - +
3D LEU* 3.8 15.7 - - + +
4D LYS 2.9 28.7 + - - +
5D ASN* 4.2 8.7 - - - +
8D TRP* 3.0 29.6 + - - +
191D LEU* 2.9 17.1 + - + +
192D LEU* 3.3 25.9 + - - +
194D TRP* 1.3 75.0 - - - +
196D TYR* 1.3 57.3 + - - +
198D ASP* 3.4 3.3 + - - +
199D ARG* 2.7 33.6 + - - +
239D LEU* 5.5 11.1 + - + +
243D GLN* 3.6 29.0 - - + +
392D ALA* 4.8 3.2 - - - +
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Residues in contact with TYR 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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8D TRP* 3.7 23.6 - + + -
13D PHE* 3.9 11.0 - + - -
16D GLN* 3.9 15.5 - - + -
17D ARG* 3.3 33.9 + - + -
20D VAL* 3.7 24.3 - - + +
21D LEU* 5.2 0.2 - - - +
156D ARG* 3.6 46.7 - - + -
159D ALA* 5.6 0.2 - - + -
160D GLU* 2.5 36.4 + - + +
192D LEU 3.3 3.2 + - - +
193D ASP 3.3 12.4 + - - +
194D TRP 3.2 0.4 - - - -
195D GLN* 1.3 78.6 - - - +
197D CYS* 1.3 61.3 + - - +
199D ARG* 3.1 3.6 + - - +
200D LEU* 2.9 31.8 + - + +
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Residues in contact with CYS 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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155D SER* 3.7 44.0 - - - -
156D ARG* 4.0 4.7 - - - -
159D ALA* 4.0 11.5 - - + +
163D HIS* 5.2 1.4 + - - -
170D ASN* 4.5 6.9 + - - +
193D ASP 3.4 12.8 + - - -
194D TRP* 3.2 33.0 + - + +
196D TYR* 1.3 82.4 - - - +
198D ASP* 1.3 62.3 + - - +
200D LEU* 3.6 6.7 + - - +
201D VAL* 3.4 24.4 + - - +
213D ARG* 4.7 2.4 - - - +
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Residues in contact with ASP 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 TRP* 2.9 23.4 + - - +
195D GLN* 3.8 2.4 - - - +
197D CYS* 1.3 75.0 - - - +
199D ARG* 1.3 59.4 + - - +
201D VAL* 3.2 2.6 + - - -
202D GLY* 2.8 23.7 + - - -
213D ARG* 2.8 37.1 + - - +
236D GLU 4.8 1.2 - - - +
239D LEU* 4.1 4.9 - - - +
240D ALA* 3.3 32.9 + - - +
243D GLN* 3.7 20.3 - - + +
245D VAL* 3.4 18.5 - - + +
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Residues in contact with ARG 199 (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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7D LYS* 3.8 17.3 - - - +
8D TRP* 2.8 36.5 + - + +
9D THR* 3.8 0.4 - - - +
10D ASP* 2.7 37.6 + - - +
13D PHE* 3.7 33.9 - - + -
195D GLN 2.7 23.0 + - - +
196D TYR* 3.1 4.7 + - - +
198D ASP* 1.3 70.2 - - - +
200D LEU* 1.3 59.3 + - - +
202D GLY 3.2 0.5 + - - -
203D PHE* 2.8 47.5 + - - +
206D GLU* 4.1 7.7 + - - -
243D GLN* 3.4 36.7 - - - +
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Residues in contact with LEU 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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13D PHE* 3.5 21.5 - - + -
17D ARG* 4.6 0.4 - - - +
32D LEU* 4.3 11.9 - - + -
159D ALA* 3.9 14.4 - - + +
160D GLU* 3.7 58.3 - - + +
163D HIS* 3.9 11.2 - - + -
196D TYR* 2.9 18.8 + - + +
197D CYS 3.6 5.4 - - - +
198D ASP 3.2 0.2 - - - -
199D ARG* 1.3 71.9 - - - +
201D VAL* 1.3 68.0 + - - +
203D PHE* 3.2 6.0 + - + +
204D TYR* 3.0 49.9 + - + -
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Residues in contact with VAL 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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163D HIS* 3.8 17.7 - - + +
197D CYS 3.4 12.1 + - - +
198D ASP 3.2 8.4 + - - +
200D LEU* 1.3 79.1 - - - +
202D GLY* 1.3 53.6 + - - +
204D TYR* 3.2 8.0 + - - +
205D GLU* 2.9 33.9 + - + +
211D ILE* 3.6 46.7 - - + +
213D ARG* 4.0 15.5 - - + -
245D VAL* 3.8 27.4 - - + -
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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
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198D ASP 2.8 11.9 + - - -
199D ARG* 3.2 8.3 + - - -
200D LEU 3.2 0.4 - - - -
201D VAL* 1.3 75.7 - - - +
203D PHE* 1.3 61.6 + - - +
205D GLU* 3.4 2.5 + - - +
206D GLU* 3.0 31.8 + - - +
243D GLN 3.6 18.8 - - - -
244D GLY* 3.6 19.4 - - - +
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Residues in contact with PHE 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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10D ASP* 5.6 4.9 - - - -
13D PHE* 4.1 16.4 - + + -
32D LEU* 3.3 46.0 - - + -
36D VAL* 4.2 11.7 - - + -
199D ARG* 2.8 27.3 + - - +
200D LEU* 3.2 10.3 + - + +
202D GLY* 1.3 76.1 - - - +
204D TYR* 1.3 71.1 + + - +
206D GLU* 3.1 11.7 + - - +
207D GLN* 3.0 59.6 + - + +
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Residues in contact with TYR 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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30D VAL* 5.5 0.3 - - - +
32D LEU* 3.4 23.4 - - + +
35D ALA* 3.6 15.4 - - - +
36D VAL* 3.9 29.4 - - + -
39D LEU* 3.4 26.0 - - + -
160D GLU* 5.0 2.6 + - - -
163D HIS* 3.9 17.7 - - + -
164D ALA* 4.0 12.6 + - - +
200D LEU* 3.0 43.8 + - + +
201D VAL* 3.2 6.7 + - - +
203D PHE* 1.3 78.9 - + - +
205D GLU* 1.3 58.1 + - - +
207D GLN* 2.9 15.8 + - - +
208D GLY 3.3 0.2 + - - -
209D VAL* 2.9 35.3 + - + +
211D ILE* 3.6 26.2 - - + -
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Residues in contact with GLU 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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201D VAL* 2.9 26.6 + - + +
202D GLY 3.8 4.0 - - - +
204D TYR* 1.3 75.8 - - + +
206D GLU* 1.3 58.7 + - - +
208D GLY* 2.9 19.8 + - - -
209D VAL 3.2 15.3 - - - +
210D HIS* 2.7 32.7 + - - +
211D ILE 3.2 27.8 + - - +
244D GLY 4.1 11.4 - - - +
246D LYS* 4.1 35.5 + - + +
247D ASN* 4.6 4.9 + - - +
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Residues in contact with GLU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LYS* 2.7 35.9 + - - +
10D ASP* 4.7 9.7 - - - +
199D ARG* 4.1 10.7 + - - -
202D GLY 3.0 19.8 + - - +
203D PHE* 3.1 14.0 + - - +
205D GLU* 1.3 75.4 - - + +
207D GLN* 1.3 71.3 + - - +
208D GLY 3.3 1.0 + - - -
244D GLY* 6.6 0.4 - - - -
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Residues in contact with GLN 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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36D VAL* 4.1 27.1 - - + -
40D LYS* 2.8 27.4 + - - -
203D PHE* 3.0 61.2 + - + +
204D TYR* 2.9 8.0 + - - +
206D GLU* 1.3 93.5 + - - +
208D GLY* 1.3 57.8 + - - +
209D VAL* 3.3 0.7 - - + +
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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