Contacts of the helix formed by residues 186 - 207 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B ASN* 3.3 3.5 + - - -
184B ASN 4.0 1.5 + - - +
185B VAL* 1.3 77.9 - - - +
187B ILE* 1.3 65.5 + - - +
188B GLU* 4.0 9.5 + - - +
189B LYS* 3.4 22.0 + - - +
190B SER 3.1 18.0 + - - -
413B TYR* 3.2 38.3 - - + +
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B GLY 5.2 3.1 - - - +
175B ILE* 5.2 2.0 - - + -
178B ASN* 3.9 12.6 - - + +
179B VAL* 3.7 29.2 - - + -
185B VAL 3.6 0.2 + - - -
186B THR* 1.3 73.9 - - - +
188B GLU* 1.3 63.5 + - - +
190B SER* 3.3 5.5 + - - +
191B LEU* 2.9 49.7 + - + +
395B THR* 4.0 16.6 - - + -
396B VAL* 4.1 17.9 - - + -
399B PHE* 3.9 33.0 - - + -
411B SER* 4.8 0.4 - - - +
413B TYR* 4.0 22.2 - - + -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.4 4.3 - - - +
2B GLU* 4.5 8.8 - - - +
3B LEU* 3.9 37.6 + - + +
186B THR* 3.2 9.4 + - - +
187B ILE* 1.3 80.4 - - - +
189B LYS* 1.3 55.0 + - - +
191B LEU* 3.4 2.4 + - - +
192B LEU* 2.9 39.7 + - + +
396B VAL* 3.9 28.3 - - + +
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Residues in contact with LYS 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP* 5.0 2.5 - - - -
156B ARG* 3.9 18.5 - - - +
185B VAL* 4.5 12.8 - - + -
186B THR* 3.4 21.0 + - - +
187B ILE 3.3 0.2 - - - -
188B GLU* 1.3 73.3 - - - +
190B SER* 1.3 67.1 + - - +
192B LEU* 3.2 13.4 + - + +
193B ASP* 2.9 58.9 + - - +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO* 4.1 18.4 - - - -
174B GLY* 2.6 28.9 + - - -
178B ASN* 3.0 32.1 + - - -
185B VAL* 4.1 9.1 - - - +
186B THR 3.1 5.6 + - - -
187B ILE* 3.3 8.0 + - - -
189B LYS* 1.3 78.3 - - - +
191B LEU* 1.3 57.3 + - - +
193B ASP* 3.8 0.8 - - - -
194B TRP* 2.9 35.2 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 4.0 13.2 - - + -
174B GLY* 4.0 24.7 - - - +
175B ILE* 4.3 11.9 - - + +
187B ILE* 2.9 40.4 + - + +
188B GLU 3.7 4.3 - - - +
190B SER* 1.3 75.4 + - - +
192B LEU* 1.3 57.0 + - - +
194B TRP* 3.3 2.2 + - - +
195B GLN* 2.8 36.2 + - + +
236B GLU* 6.2 0.2 - - + -
239B LEU* 3.8 25.8 - - + -
392B ALA* 3.6 28.7 - - + +
395B THR* 3.9 9.4 - - + -
396B VAL* 3.9 7.9 - - + -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 3.5 40.4 - - + +
2B GLU 3.8 20.6 - - - +
3B LEU* 3.9 13.2 - - + +
8B TRP* 3.4 11.5 - - + -
188B GLU* 2.9 38.0 + - + +
189B LYS* 3.6 13.0 - - + +
191B LEU* 1.3 76.4 - - - +
193B ASP* 1.4 66.3 + - - +
195B GLN* 3.3 25.2 + - - +
196B TYR 3.2 15.6 + - - -
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Residues in contact with ASP 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B PRO 3.9 16.5 - - - +
154B ASP* 3.5 20.6 - - - +
156B ARG* 3.4 32.4 + - + +
189B LYS* 2.9 61.5 + - - +
190B SER 4.1 0.2 - - - +
192B LEU* 1.4 80.0 - - - +
194B TRP* 1.3 63.3 + - - +
196B TYR* 3.3 17.7 - - - +
197B CYS* 3.3 12.4 + - - -
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Residues in contact with TRP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B HIS* 4.1 0.2 - + - -
152B THR 3.0 29.7 + - - -
153B PRO* 3.3 16.0 + - - +
155B SER* 3.5 19.0 - - - -
170B ASN* 3.8 19.5 - - - -
171B GLU 3.2 21.5 - - - -
172B GLY* 3.6 6.7 - - - -
173B GLY* 3.6 14.4 + - - -
174B GLY* 3.5 26.9 - - - +
177B TYR* 3.6 16.7 + + - +
190B SER* 2.9 28.5 + - - +
191B LEU* 4.0 2.7 - - + +
193B ASP* 1.3 76.2 - - - +
195B GLN* 1.3 63.7 + - - +
197B CYS* 3.1 19.1 + - + +
198B ASP* 2.9 32.5 + - - +
213B ARG* 3.5 35.0 - - - -
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Residues in contact with GLN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLU 5.3 0.3 - - - +
3B LEU* 3.9 16.9 - - + +
4B LYS 2.9 28.5 + - - +
5B ASN* 4.2 8.3 - - - +
8B TRP* 2.9 30.5 + - - +
191B LEU* 2.8 17.4 + - + +
192B LEU* 3.3 25.5 + - - +
194B TRP* 1.3 76.4 - - - +
196B TYR* 1.3 57.0 + - - +
198B ASP* 4.5 2.7 - - - +
199B ARG* 2.7 32.8 + - - +
239B LEU* 5.4 11.5 + - + +
243B GLN* 3.7 28.8 - - + +
392B ALA* 4.8 3.8 - - - +
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Residues in contact with TYR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B TRP* 3.7 32.6 - + + -
13B PHE* 3.9 15.0 - + - -
16B GLN* 3.9 6.3 - - + -
17B ARG* 3.6 29.0 + - + +
20B VAL* 3.6 25.1 - - + +
156B ARG* 3.5 48.0 - - + -
159B ALA* 5.5 0.2 - - + -
160B GLU* 2.4 38.1 + - + +
192B LEU 3.2 3.8 + - - -
193B ASP 3.3 11.7 - - - +
194B TRP 3.2 0.4 - - - -
195B GLN* 1.3 79.7 - - - +
197B CYS* 1.3 61.0 + - - +
199B ARG* 3.1 3.0 + - - +
200B LEU* 2.9 32.1 + - + +
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Residues in contact with CYS 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B SER* 3.7 43.5 - - - -
156B ARG* 3.9 6.1 - - - -
159B ALA* 4.1 9.5 - - + +
163B HIS* 5.2 1.6 + - - -
170B ASN* 4.4 7.6 + - - +
193B ASP 3.3 13.4 + - - -
194B TRP* 3.1 34.5 + - + +
196B TYR* 1.3 83.2 - - - +
198B ASP* 1.3 60.8 + - - +
200B LEU* 3.5 6.6 + - - +
201B VAL* 3.4 24.4 + - - +
213B ARG* 4.7 2.9 - - - +
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B TRP* 2.9 23.1 + - - +
195B GLN* 3.8 3.4 - - - +
197B CYS* 1.3 72.4 - - - +
199B ARG* 1.3 61.5 + - - +
201B VAL* 3.2 2.5 + - - -
202B GLY* 2.8 23.6 + - - -
213B ARG* 2.8 42.7 + - - +
236B GLU 4.7 1.0 - - - +
239B LEU* 4.1 4.9 - - - +
240B ALA* 3.3 33.4 + - - +
243B GLN* 3.7 20.5 - - + +
245B VAL* 3.4 18.3 - - + +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 3.7 22.4 - - - +
8B TRP* 2.8 36.6 + - + +
9B THR* 4.5 0.2 - - - +
10B ASP* 2.7 38.2 + - - +
13B PHE* 3.7 31.5 - - + -
195B GLN 2.7 23.1 + - - +
196B TYR* 3.6 5.2 - - - +
198B ASP* 1.3 70.4 - - - +
200B LEU* 1.3 56.3 + - - +
202B GLY* 3.1 1.1 + - - -
203B PHE* 2.8 52.3 + - - +
206B GLU* 4.3 4.9 + - - -
243B GLN* 3.4 36.9 - - - +
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Residues in contact with LEU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE* 3.5 21.0 - - + -
17B ARG* 4.6 0.2 - - - +
32B LEU* 4.2 11.2 - - + -
159B ALA* 3.8 15.7 - - + +
160B GLU* 3.8 58.6 - - + +
163B HIS* 3.9 11.0 - - + -
196B TYR* 2.9 18.8 + - + +
197B CYS* 3.7 5.8 - - - +
198B ASP 3.2 0.2 - - - -
199B ARG* 1.3 73.0 - - - +
201B VAL* 1.3 65.8 + - - +
203B PHE* 3.2 6.1 + - + +
204B TYR* 3.0 49.5 + - + -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B HIS* 3.8 25.4 - - + +
197B CYS 3.4 12.3 + - - +
198B ASP 3.2 7.9 + - - +
200B LEU* 1.3 77.4 - - - +
202B GLY* 1.3 57.0 + - - +
204B TYR* 3.1 8.6 + - - +
205B GLU* 2.9 36.1 + - + +
211B ILE* 3.6 40.4 - - + +
213B ARG* 4.0 15.5 - - + -
245B VAL* 4.0 23.6 - - + -
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ASP 2.8 11.5 + - - -
199B ARG* 3.1 8.2 + - - -
201B VAL* 1.3 76.7 - - - +
203B PHE* 1.3 60.4 + - - +
205B GLU* 3.3 2.8 + - - +
206B GLU* 3.0 29.1 + - - +
243B GLN 3.5 18.8 - - - -
244B GLY* 3.6 20.9 - - - +
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 5.8 3.4 - - - -
13B PHE* 4.1 15.0 - + + -
32B LEU* 3.5 43.7 - - + -
36B VAL* 4.2 16.8 - - + -
199B ARG* 2.8 30.0 + - - +
200B LEU* 3.5 10.1 - - + +
202B GLY* 1.3 73.8 - - - +
204B TYR* 1.3 71.0 + + - +
206B GLU* 3.1 14.0 + - - -
207B GLN* 3.0 62.0 + - + +
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.5 24.4 - - + +
35B ALA* 3.6 15.2 - - - +
36B VAL* 3.9 27.6 - - + -
39B LEU* 3.4 26.5 - - + -
160B GLU* 5.0 1.9 + - - -
163B HIS* 3.8 19.7 - + + +
164B ALA* 4.1 12.5 + - - +
200B LEU* 3.0 43.6 + - + -
201B VAL* 3.1 6.5 + - - +
203B PHE* 1.3 79.0 - + - +
205B GLU* 1.3 61.5 + - - +
207B GLN* 3.0 11.6 + - - +
208B GLY 3.3 0.2 + - - -
209B VAL* 2.9 34.4 + - + +
211B ILE* 3.6 26.0 - - + -
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B VAL* 2.9 27.3 + - + +
202B GLY 3.7 4.9 - - - +
204B TYR* 1.3 75.8 - - - +
206B GLU* 1.3 59.5 + - + +
208B GLY* 2.9 19.2 + - - -
209B VAL 3.3 10.3 - - - +
210B HIS* 2.7 33.1 + - - +
211B ILE 3.2 27.6 + - - +
244B GLY 4.1 11.7 - - - +
246B LYS* 4.0 36.5 + - + +
247B ASN* 4.6 4.7 + - - +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LYS* 2.5 37.0 + - - +
10B ASP* 4.3 13.0 - - - +
199B ARG* 4.3 4.7 + - - -
202B GLY 3.0 17.4 + - - +
203B PHE* 3.1 11.6 + - - +
205B GLU* 1.3 79.0 - - - +
207B GLN* 1.3 78.3 + - - +
208B GLY 3.3 0.8 + - - -
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.1 26.0 - - + -
40B LYS* 2.8 26.7 + - - -
203B PHE* 3.0 63.4 + - + +
204B TYR* 3.0 7.2 + - - +
206B GLU* 1.3 94.0 + - - +
208B GLY* 1.3 57.8 - - - +
209B VAL* 3.4 0.9 - - + -
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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