Contacts of the helix formed by residues 189 - 208 (chain D) in PDB entry 3NJ4
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 PHE 189 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C ILE* 4.0 23.8 - - + -
250C LEU* 3.3 49.8 - - + -
251C GLN* 3.8 21.8 - - + -
254C MET* 4.1 7.2 - - + -
184D VAL 3.5 19.5 - - - -
185D THR* 3.6 22.4 - - + +
186D LYS 2.8 4.2 + - - +
187D SER 3.2 0.2 - - - -
188D LYS* 1.3 92.5 - - + +
190D ASP* 1.3 59.8 + - - +
191D ASN 3.6 0.4 - - - -
193D TYR* 2.7 51.9 + + + +
194D GLY 2.9 7.6 + - - -
357D VAL* 3.5 14.0 - - + +
360D ASN* 3.9 7.9 - - + +
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Residues in contact with ASP 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D LYS* 2.6 22.9 + - - +
189D PHE* 1.3 72.1 - - - +
191D ASN* 1.3 79.3 + - - +
194D GLY* 2.8 25.3 + - - -
353D HIS* 3.0 19.2 - - - -
357D VAL* 3.5 13.1 + - + +
358D MET* 3.1 15.4 - - + +
360D ASN* 5.9 0.4 - - + +
361D SER* 2.9 24.8 + - - +
504D NAD 3.5 9.0 - - - -
604D AFX 2.7 27.0 + - - +
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Residues in contact with ASN 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D THR* 3.5 8.1 + - - -
181D ASN* 3.2 19.9 + - - -
186D LYS* 2.7 27.9 + - - +
187D SER* 3.3 28.4 - - - +
189D PHE 3.6 0.2 - - - -
190D ASP* 1.3 83.1 + - - +
192D LEU* 1.3 56.2 + - - +
195D CYS* 3.3 27.7 - - - +
223D ASP* 3.3 21.2 - - + +
224D VAL* 3.5 8.0 - - + -
504D NAD 3.4 26.3 + - + -
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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
----------------------------------------------------------
255C GLU* 5.1 2.5 - - - +
187D SER 3.7 4.7 + - - +
188D LYS* 3.6 39.9 - - - +
189D PHE 3.6 0.4 + - - -
190D ASP 3.2 0.8 - - - -
191D ASN* 1.3 78.0 - - - +
193D TYR* 1.3 84.8 + - + +
196D ARG* 3.1 25.8 + - - +
223D ASP* 3.1 25.4 - - + +
226D LYS* 3.4 32.1 - - + -
227D GLY* 3.4 18.5 - - - +
230D GLN* 5.4 6.5 - - - +
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Residues in contact with TYR 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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210B MET* 3.5 14.3 - - + +
212B ALA* 5.0 0.9 - - + -
251C GLN* 3.6 25.1 + - - +
254C MET* 3.7 37.7 - - + -
255C GLU* 3.5 33.6 + - - +
188D LYS 3.2 16.0 + - - -
189D PHE* 2.7 53.5 + + + +
192D LEU* 1.3 89.4 - - + +
194D GLY* 1.3 66.0 + - - +
196D ARG* 3.0 44.2 + - - +
197D GLU* 3.3 6.2 + - - +
230D GLN* 5.5 0.2 - - - -
357D VAL* 4.7 0.4 - - + -
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Residues in contact with GLY 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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210B MET* 4.3 2.9 - - - -
189D PHE 2.9 5.1 + - - -
190D ASP 2.8 17.2 + - - -
193D TYR* 1.3 77.5 - - - +
195D CYS* 1.3 55.5 + - - -
197D GLU* 3.4 2.3 + - - +
198D SER* 2.8 27.5 + - - -
353D HIS* 3.1 26.0 - - - +
354D PRO* 4.4 0.3 - - - +
357D VAL* 4.0 14.2 - - - +
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Residues in contact with CYS 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D ASP 3.4 2.8 + - - -
191D ASN 3.3 21.5 - - - +
192D LEU 3.6 1.5 + - - +
193D TYR 3.3 0.4 - - - -
194D GLY* 1.3 71.1 - - - +
196D ARG* 1.3 63.7 + - - +
197D GLU 3.1 3.3 + - - -
198D SER* 3.4 7.2 - - - -
199D LEU* 3.4 24.9 + - - +
224D VAL* 3.8 27.1 - - - +
227D GLY 4.4 5.1 - - - +
228D CYS* 4.4 3.3 + - - -
231D ALA* 4.7 0.2 - - - +
299D ILE* 3.6 26.5 - - + -
353D HIS* 3.3 19.3 + - - -
504D NAD 3.9 14.8 - - - -
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Residues in contact with ARG 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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212B ALA* 3.9 3.2 - - - +
234B GLY 4.4 7.0 + - - +
235B PHE* 3.0 56.5 + - + +
236B GLY* 3.6 2.7 - - - -
254C MET 2.9 27.1 + - - -
255C GLU* 2.8 25.1 + - - -
192D LEU* 3.1 15.0 + - - +
193D TYR* 3.0 32.3 + - - +
195D CYS* 1.3 80.0 - - - +
197D GLU* 1.3 59.1 + - + +
199D LEU 5.1 0.2 - - - -
200D ILE* 4.7 1.4 - - - +
227D GLY* 3.6 20.4 - - - +
230D GLN* 2.8 48.6 + - - +
231D ALA* 3.2 20.1 - - + +
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Residues in contact with GLU 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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204B LYS* 2.5 43.6 + - - +
210B MET* 3.2 31.1 - - + +
211B ILE* 2.7 23.2 + - - -
212B ALA* 3.0 28.5 + - - +
235B PHE* 3.3 34.0 - - + +
193D TYR 3.3 3.8 + - - +
194D GLY 4.3 0.7 - - - +
196D ARG* 1.3 81.5 + - + +
198D SER* 1.3 60.3 + - - +
199D LEU 3.7 0.4 - - - -
200D ILE* 4.5 4.1 + - - +
201D ASP* 3.7 17.2 + - - +
354D PRO* 4.4 4.0 - - + -
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Residues in contact with SER 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D GLY 2.8 12.5 + - - -
195D CYS* 3.4 3.8 - - - -
197D GLU* 1.3 77.8 - - - +
199D LEU* 1.3 67.9 + - - +
201D ASP* 3.1 8.9 + - - +
202D GLY 3.0 17.7 + - - -
346D ASN* 3.2 23.8 + - - +
350D ALA* 4.7 1.1 - - - +
352D GLY 3.7 20.4 - - - -
353D HIS* 2.7 35.5 + - - -
354D PRO* 4.9 1.1 - - - -
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Residues in contact with LEU 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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195D CYS 3.4 15.8 + - - +
198D SER* 1.3 77.9 + - - +
200D ILE* 1.3 65.2 + - + +
202D GLY* 2.8 19.8 + - - -
203D ILE* 3.1 27.4 + - + +
228D CYS* 3.5 39.0 - - + +
231D ALA* 5.1 0.7 - - + -
232D LEU* 4.3 10.8 - - + -
273D VAL* 3.7 34.1 - - + -
297D CYS* 4.4 0.4 - - - -
299D ILE* 3.9 18.6 - - + +
345D VAL* 3.8 22.6 - - + +
346D ASN* 4.1 4.0 - - - +
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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
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235B PHE* 5.0 4.5 - - + -
196D ARG 4.7 2.5 - - - +
197D GLU 4.5 5.9 + - - +
198D SER 3.4 0.6 - - - -
199D LEU* 1.3 80.5 - - + +
201D ASP* 1.3 57.4 + - - +
203D ILE* 3.4 6.4 + - + +
204D LYS* 2.8 57.9 + - + +
211D ILE* 4.2 15.3 - - + -
231D ALA* 3.8 24.7 - - + -
232D LEU* 3.3 40.8 - - + +
235D PHE* 3.8 29.2 - - + -
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Residues in contact with ASP 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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201B ASP* 4.6 8.5 - - - +
204B LYS* 4.2 21.4 - - + +
205B ARG* 4.6 0.7 - - - +
208B ASP* 4.2 3.8 - - - +
197D GLU 3.7 14.3 + - - +
198D SER* 3.1 13.8 + - - +
199D LEU 3.1 0.4 - - - -
200D ILE* 1.3 78.6 - - - +
202D GLY* 1.3 63.3 + - - +
204D LYS* 4.3 3.8 - - - +
205D ARG* 2.8 77.8 + - - +
350D ALA* 3.9 8.8 - - + +
351D MET 4.7 1.2 + - - -
352D GLY 5.2 4.2 - - - +
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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 SER 3.0 8.5 + - - -
199D LEU 2.8 7.9 + - - -
201D ASP* 1.3 77.7 - - - +
203D ILE* 1.3 61.4 + - - +
206D ALA* 3.1 24.9 + - - +
345D VAL* 4.0 15.1 - - - +
346D ASN* 4.5 0.9 - - - -
349D CYS* 3.3 16.3 - - - +
350D ALA* 3.7 16.5 - - - +
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Residues in contact with ILE 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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199D LEU* 3.1 38.5 + - + +
200D ILE* 3.9 13.9 - - + +
202D GLY* 1.3 77.9 - - - +
204D LYS* 1.3 52.6 + - + +
206D ALA 3.7 0.2 - - - -
207D THR* 2.7 54.0 + - - +
209D VAL* 3.7 16.6 - - + -
211D ILE* 4.9 7.0 - - + -
232D LEU* 4.8 2.9 - - + -
271D ILE* 4.3 23.3 - - + -
273D VAL* 4.4 3.1 - - + -
295D ILE* 4.3 15.3 - - + -
297D CYS* 4.3 16.8 - - - -
339D LEU* 4.2 9.4 - - + -
345D VAL* 4.9 1.6 - - + -
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Residues in contact with LYS 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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197B GLU* 2.7 53.1 + - - +
198B SER* 5.9 0.2 - - - +
201B ASP* 3.9 28.5 + - + +
205B ARG* 3.7 2.5 - - - -
354B PRO* 3.5 14.1 - - - +
200D ILE* 2.8 45.1 + - + +
201D ASP* 3.6 7.2 - - - +
203D ILE* 1.3 73.1 - - + +
205D ARG* 1.3 64.8 + - - +
206D ALA 3.1 1.8 - - - -
208D ASP* 2.6 40.8 + - - +
209D VAL* 3.3 20.8 + - + +
211D ILE* 4.4 6.5 - - + -
235D PHE* 5.7 1.6 - - - -
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Residues in contact with ARG 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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204B LYS 3.6 11.1 + - - -
205B ARG* 3.6 58.2 + - - +
208B ASP* 2.9 24.5 + - - -
201D ASP* 2.8 47.4 + - - +
204D LYS* 1.3 75.9 - - + +
206D ALA* 1.3 61.4 + - - +
208D ASP* 4.4 5.5 - - - +
322D LYS* 3.5 18.1 + - - -
349D CYS 3.5 22.9 - - - +
350D ALA* 3.9 6.4 - - - +
351D MET* 3.9 19.8 - - - +
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Residues in contact with ALA 206 (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 3.1 20.0 + - - +
203D ILE 3.9 1.6 - - - +
204D LYS 3.1 0.6 - - - -
205D ARG* 1.3 81.0 - - - +
207D THR* 1.3 61.3 + - - +
208D ASP* 5.2 0.6 - - - +
321D ILE* 5.7 1.2 - - - +
322D LYS* 3.5 23.6 + - - +
325D VAL* 3.7 21.5 - - + +
339D LEU* 4.1 12.8 - - + -
349D CYS* 3.8 24.8 + - + -
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Residues in contact with THR 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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24B ILE* 5.0 14.0 - - - +
203D ILE* 2.7 27.2 + - - +
206D ALA* 1.3 79.1 - - - +
208D ASP* 1.3 65.7 + - - +
209D VAL* 2.9 30.8 + - - +
295D ILE* 3.5 23.0 - - + +
325D VAL* 5.0 1.8 - - + -
337D ILE* 4.2 12.6 - - + -
339D LEU* 3.6 30.1 - - + -
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Residues in contact with ASP 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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59B GLU* 5.6 4.7 - - - +
201B ASP* 4.6 2.3 - - - +
205B ARG* 2.8 28.6 + - - -
351B MET* 3.1 39.2 - - + +
354B PRO* 3.2 25.7 - - + +
355B SER* 4.5 3.4 + - - +
203D ILE 3.6 0.8 + - - -
204D LYS* 2.6 28.7 + - - +
205D ARG 4.4 6.6 - - - +
206D ALA 5.2 0.3 - - - +
207D THR* 1.3 75.1 + - - +
209D VAL* 1.3 65.3 + - - +
322D LYS* 5.3 3.8 + - - -
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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