Contacts of the helix formed by residues 203 - 223 (chain D) in PDB entry 3RIK
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 ASP 203 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D LYS 3.8 0.2 - - - +
199D GLY* 3.2 11.8 - - - -
200D GLN* 2.7 43.3 + - + +
201D PRO 3.2 0.4 + - - -
202D GLY* 1.3 80.1 - - - +
204D ILE* 1.3 55.5 + - + +
205D TYR* 3.0 22.7 + - - +
206D HIS* 3.0 19.1 + - - -
207D GLN* 2.7 34.9 + - - +
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Residues in contact with ILE 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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142D PHE* 3.8 38.1 - - + -
203D ASP* 1.3 74.4 - - + +
205D TYR* 1.3 79.4 + - + +
207D GLN* 4.3 6.5 - - + -
208D THR* 2.6 42.2 + - - +
211D ARG* 4.5 8.5 - - - +
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Residues in contact with TYR 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D PHE* 3.7 33.4 - + - -
184D TRP 4.1 5.8 - - - -
185D LEU* 3.9 26.0 - - + +
197D LEU* 4.6 4.1 - - + +
198D LYS* 3.4 68.6 - - + +
199D GLY* 4.8 2.2 - - - -
203D ASP* 3.0 16.7 + - - +
204D ILE* 1.3 87.7 - - + +
206D HIS* 1.3 59.2 - - + +
208D THR* 3.7 1.9 - - - -
209D TRP* 3.0 30.2 + - - +
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Residues in contact with HIS 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 3.5 31.7 - - + +
198D LYS 3.0 22.8 + - - -
199D GLY 3.8 4.0 - - - -
200D GLN 3.5 16.2 + - - -
201D PRO* 3.5 20.4 - - + +
202D GLY 3.9 3.1 - - - +
203D ASP* 3.0 20.0 + - - +
205D TYR* 1.3 77.2 - - - +
207D GLN* 1.3 56.3 + - - +
209D TRP* 3.5 2.6 + - - +
210D ALA* 3.0 28.2 + - - +
255D HIS* 2.6 33.9 + - - -
259D PHE* 3.7 16.7 - + + -
263D ASP* 3.2 19.5 - - - +
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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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202D GLY* 3.9 11.6 - - - +
203D ASP 2.7 23.2 + - - +
204D ILE* 4.0 6.5 - - - +
206D HIS* 1.3 71.5 - - - +
208D THR* 1.3 59.7 + - - +
210D ALA* 3.3 3.5 + - - +
211D ARG* 2.9 46.7 + - - +
262D ARG 3.9 5.5 + - - -
263D ASP* 2.7 41.9 + - - +
266D PRO* 6.3 0.2 - - - +
267D THR* 4.0 13.1 + - - -
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Residues in contact with THR 208 (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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142D PHE* 3.4 38.9 + - - +
144D LEU* 3.7 22.9 - - + +
184D TRP* 4.1 10.3 - - + -
185D LEU* 4.2 10.8 - - + -
204D ILE* 2.6 25.5 + - - +
205D TYR 3.3 3.8 + - - -
207D GLN* 1.3 75.6 - - - +
209D TRP* 1.3 64.3 + - - +
211D ARG* 3.1 24.7 + - - +
212D TYR* 3.0 20.5 + - - +
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Residues in contact with TRP 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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178D PRO* 3.7 31.2 - - + -
180D THR 3.7 8.5 - - - -
181D SER* 3.5 39.5 - - - -
182D PRO* 3.6 3.4 - - + -
185D LEU* 4.0 8.4 - - + +
197D LEU* 3.8 26.7 - - + -
205D TYR 3.0 17.3 + - - +
206D HIS 3.6 4.7 - - - +
208D THR* 1.3 77.4 - - - +
210D ALA* 1.3 62.1 + - - +
212D TYR* 3.0 59.7 + + - +
213D PHE* 3.4 20.9 + + - -
232D ALA 4.8 3.0 + - - -
233D GLU* 4.6 0.9 + - - -
249D LEU* 3.8 17.4 - - + +
251D PHE* 4.6 2.8 - + - -
259D PHE* 3.5 29.4 - + - -
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Residues in contact with ALA 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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206D HIS 3.0 17.2 + - - +
207D GLN 3.7 3.8 - - - +
209D TRP* 1.3 74.8 - - - +
211D ARG* 1.3 63.5 + - - +
212D TYR 3.1 0.5 + - - -
213D PHE* 3.2 19.5 + - - +
214D VAL* 3.5 3.1 + - - +
259D PHE* 4.4 3.3 - - + -
263D ASP* 3.8 19.5 - - + +
264D LEU* 4.0 18.3 - - - +
267D THR* 3.4 33.6 - - - +
268D LEU* 5.7 0.2 - - - +
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Residues in contact with ARG 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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142D PHE* 2.6 27.5 + - - +
143D GLN* 4.1 22.4 + - - +
144D LEU* 4.1 10.0 - - + +
204D ILE* 4.5 9.9 - - - +
207D GLN* 2.9 27.0 + - - +
208D THR* 3.1 40.9 + - - +
210D ALA* 1.3 75.5 - - - +
212D TYR* 1.3 56.6 + - - +
214D VAL* 2.9 8.4 + - + +
215D LYS* 2.9 32.3 + - + +
267D THR* 4.2 15.9 - - + -
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Residues in contact with TYR 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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123D MET* 4.0 18.6 + - + -
124D ALA* 4.1 5.4 - - - +
134D THR* 3.5 10.0 - - - +
135D TYR* 3.0 49.4 + + + -
136D ALA* 4.1 8.3 - - + -
144D LEU* 3.9 14.1 - - + +
147D PHE* 3.8 18.7 - + - -
180D THR 4.7 2.4 + - - -
182D PRO* 3.5 28.9 - - + +
185D LEU* 5.6 0.7 - - + -
208D THR 3.0 11.2 + - - +
209D TRP* 3.0 46.6 + + + +
211D ARG* 1.3 74.4 - - - +
213D PHE* 1.3 67.0 + + - +
215D LYS* 3.2 4.3 + - - +
216D PHE* 2.9 20.8 + - + +
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Residues in contact with PHE 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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123D MET* 4.1 22.0 - - + -
178D PRO* 3.5 24.5 - - + -
209D TRP* 3.5 44.2 - + - -
210D ALA 3.4 7.4 - - - +
212D TYR* 1.3 75.1 - + - +
214D VAL* 1.3 62.0 + - - +
216D PHE* 3.2 4.0 + + - +
217D LEU* 3.0 29.5 + - + +
230D VAL* 4.1 25.1 - - + -
231D THR 3.4 22.9 - - - -
232D ALA 3.8 10.8 - - - -
259D PHE* 4.8 0.4 - + - -
264D LEU* 3.6 34.8 - - + -
268D LEU* 4.5 9.9 - - + -
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Residues in contact with VAL 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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210D ALA 3.5 2.6 + - - +
211D ARG* 2.9 12.6 + - + +
213D PHE* 1.3 75.8 - - - +
215D LYS* 1.3 58.0 + - + +
217D LEU* 3.2 8.2 + - - +
218D ASP* 2.8 52.1 + - - +
267D THR* 3.8 29.6 - - + +
268D LEU* 4.5 11.4 - - + -
271D SER* 4.0 32.5 - - - +
273D HIS* 4.2 3.6 - - + -
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Residues in contact with LYS 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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143D GLN 4.8 3.0 + - - -
144D LEU* 3.3 49.3 + - + -
145D HIS* 5.4 1.0 + - - +
147D PHE* 3.6 36.5 + - + +
211D ARG* 2.9 20.0 + - + +
212D TYR 3.2 0.6 + - - +
214D VAL* 1.3 78.7 - - + +
216D PHE* 1.3 57.3 + - - +
218D ASP* 3.4 14.2 + - + +
219D ALA* 2.8 32.7 + - - +
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Residues in contact with PHE 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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121D VAL* 4.5 5.6 - - + -
122D PRO 4.7 0.9 - - - -
123D MET* 3.7 37.5 - - + -
135D TYR* 3.3 39.9 - + + -
147D PHE* 3.4 12.7 - - + -
149D LEU* 4.9 1.3 - - + -
176D ALA* 3.5 23.3 - - + -
212D TYR 2.9 14.0 + - - +
213D PHE 3.3 7.9 - - - +
215D LYS* 1.3 77.4 - - - +
217D LEU* 1.3 76.6 + - + +
219D ALA* 3.2 3.1 + - - +
220D TYR* 3.0 43.8 + + - +
227D PHE* 3.7 32.8 - + - -
230D VAL* 5.7 0.7 - - + -
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Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213D PHE* 3.0 22.8 + - + +
214D VAL* 3.7 0.4 - - - +
216D PHE* 1.3 86.2 - - + +
218D ASP* 1.3 55.4 + - - +
220D TYR* 3.3 5.6 + - - +
221D ALA* 2.9 30.1 + - - +
225D LEU 4.7 0.9 - - - +
227D PHE* 3.6 40.1 - - + +
230D VAL* 4.1 20.2 - - + -
268D LEU* 3.8 27.1 - - + -
273D HIS* 3.6 38.8 - - + +
276D VAL* 4.6 8.7 - - + -
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Residues in contact with ASP 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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214D VAL* 2.8 37.2 + - - +
215D LYS* 3.5 14.4 - - + +
217D LEU* 1.3 68.7 - - - +
219D ALA* 1.3 62.3 + - - +
221D ALA* 3.2 6.1 + - - +
222D GLU* 2.9 39.5 + - - +
272D THR* 4.2 5.0 + - - -
273D HIS* 2.7 29.3 + - - -
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Residues in contact with ALA 219 (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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147D PHE* 4.2 9.2 - - + -
148D SER* 6.3 0.2 - - - -
149D LEU* 3.9 29.8 - - + +
215D LYS 2.8 21.2 + - - +
216D PHE 3.2 4.0 + - - +
218D ASP* 1.3 72.8 - - - +
220D TYR* 1.3 65.3 + - - +
222D GLU* 3.3 20.3 + - - +
223D HIS* 3.1 23.8 - - + -
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Residues in contact with TYR 220 (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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121D VAL* 3.9 6.9 - - + +
149D LEU* 3.8 14.1 - - + -
153D ASP* 2.8 29.3 + - - +
157D LYS* 3.6 18.7 - - - +
158D ILE* 3.5 33.5 - - + +
161D ILE* 4.6 5.2 - - + -
216D PHE* 3.0 38.5 + + - +
217D LEU 3.8 4.0 - - - +
219D ALA* 1.3 78.5 - - - +
221D ALA* 1.3 56.0 + - - +
223D HIS* 2.9 22.6 + - - +
224D LYS 3.3 0.3 + - - -
225D LEU* 3.2 44.4 + - + +
227D PHE* 3.5 39.0 - + + -
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Residues in contact with ALA 221 (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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217D LEU 2.9 17.3 + - - +
218D ASP* 3.6 8.1 - - - +
220D TYR* 1.3 71.5 - - - +
222D GLU* 1.3 65.4 + - - +
223D HIS 3.1 1.8 - - - -
224D LYS* 3.1 16.7 + - - +
225D LEU 3.3 13.4 + - - +
226D GLN* 5.6 4.3 - - + -
273D HIS* 4.4 12.8 - - + -
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Residues in contact with GLU 222 (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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218D ASP* 2.9 27.7 + - - +
219D ALA* 3.5 17.1 - - - +
220D TYR 3.2 0.4 - - - -
221D ALA* 1.3 75.8 - - - +
223D HIS* 1.3 64.6 + - + +
224D LYS* 3.2 6.6 + - - +
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Residues in contact with HIS 223 (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 LEU* 4.3 6.1 - - + +
154D THR* 3.9 33.8 - - + +
158D ILE* 3.9 39.3 - - + +
162D HIS* 2.7 32.9 + - - -
219D ALA* 3.1 23.6 - - + -
220D TYR 2.9 8.2 + - - +
222D GLU* 1.3 84.1 + - + +
224D LYS* 1.3 60.9 + - - +
225D LEU* 3.4 3.3 + - + +
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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