Contacts of the helix formed by residues 176 - 199 (chain D) in PDB entry 2ONK
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 VAL 176 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 4.6 8.7 - - + -
84B HIS* 4.4 6.5 - - + -
93B TYR* 3.8 16.4 - - + +
154D VAL* 4.7 0.9 - - + -
158D LEU* 3.9 29.2 - - + +
159D GLU* 4.2 7.2 - - + -
162D ALA* 3.5 28.9 - - + -
172D VAL* 2.6 21.4 + - + +
175D THR* 1.3 78.9 - - - +
177D SER* 1.3 70.7 + - - +
179D PRO* 3.3 1.3 - - - +
180D LEU* 3.1 43.4 + - + +
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D TYR* 3.6 22.7 + - - -
151D PHE* 4.3 7.0 - - - -
154D VAL* 4.0 7.2 - - - +
159D GLU* 3.0 34.7 + - - +
172D VAL* 3.2 2.3 + - - +
173D PHE* 3.3 22.0 - - - -
176D VAL* 1.3 82.0 - - - +
178D LEU* 1.3 66.9 + - - +
180D LEU* 3.1 7.4 + - - +
181D SER* 3.0 18.5 + - - -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D THR* 4.4 4.3 - - + -
151D PHE* 3.4 20.0 - - + -
173D PHE* 2.7 58.9 + - + +
174D PHE* 3.9 28.5 - - + +
177D SER* 1.3 70.6 - - - +
179D PRO* 1.3 63.5 - - + +
181D SER* 2.7 27.9 + - - -
182D VAL* 2.9 16.4 + - + +
185D ILE* 4.2 15.2 - - + +
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Residues in contact with PRO 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B HIS* 4.3 17.8 - - + +
174D PHE 3.1 25.1 - - - +
175D THR* 3.0 29.4 - - - +
176D VAL 3.3 9.2 - - - +
178D LEU* 1.3 89.9 - - + +
180D LEU* 1.3 58.7 + - - +
182D VAL* 3.5 24.8 - - + +
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Residues in contact with LEU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 4.0 16.6 - - + -
84B HIS* 3.5 40.6 - - + +
153D SER* 4.9 4.2 + - - -
154D VAL* 3.4 38.2 - - + +
158D LEU* 3.9 15.3 - - + -
176D VAL* 3.1 34.9 + - + +
177D SER 3.1 0.4 + - - -
178D LEU 2.8 1.8 + - - -
179D PRO* 1.3 82.3 - - - +
181D SER* 1.3 57.1 + - - +
182D VAL 3.3 1.5 + - - -
183D ARG* 4.9 2.8 + - - +
184D HIS* 5.0 2.4 - - - -
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D ALA 5.2 0.2 - - - -
150D GLY* 3.4 34.8 - - - -
151D PHE* 3.5 25.3 - - - -
154D VAL* 4.5 1.3 - - - -
177D SER 3.0 14.9 + - - -
178D LEU* 2.7 8.1 + - - -
180D LEU* 1.3 71.9 - - - +
182D VAL* 1.3 66.5 + - - +
183D ARG 3.3 2.7 - - - -
184D HIS* 2.7 22.2 + - - +
185D ILE* 3.0 16.7 + - - +
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Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 2.9 21.5 + - + +
179D PRO* 3.5 22.9 - - + +
180D LEU 3.3 1.6 - - - -
181D SER* 1.3 76.8 - - - +
183D ARG* 1.3 54.4 + - - +
184D HIS 2.6 12.5 + - - -
185D ILE* 2.9 12.2 + - + -
186D VAL* 2.8 40.4 + - + +
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Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LEU 4.9 2.9 + - - +
181D SER 3.2 1.6 + - - -
182D VAL* 1.3 78.7 - - - +
184D HIS* 1.3 64.8 + - + +
186D VAL* 4.5 7.4 - - + +
187D ALA* 3.6 19.8 + - - +
251D VAL* 4.5 32.0 + - + -
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Residues in contact with HIS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN* 3.7 32.7 + - - +
147D ALA* 5.0 0.9 - - - -
149D GLU* 4.3 13.5 - - + +
150D GLY* 3.2 35.4 + - - -
153D SER* 3.7 22.4 + - - -
180D LEU 5.0 2.0 - - - -
181D SER* 2.7 20.0 + - - +
182D VAL 2.6 4.9 + - - -
183D ARG* 1.3 79.2 + - + +
185D ILE* 1.3 56.1 + - - +
186D VAL 3.2 1.1 - - - -
187D ALA* 3.7 0.6 - - - +
188D GLY* 2.7 32.7 + - - -
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Residues in contact with ILE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D VAL* 4.7 11.7 - - + -
70D THR* 4.5 7.6 - - + +
143D TYR* 3.1 32.3 - - + +
147D ALA* 4.9 12.1 - - + +
151D PHE* 4.4 11.0 - - + -
178D LEU* 4.2 29.4 - - + +
181D SER* 3.0 21.5 + - - +
182D VAL* 2.9 13.2 + - + +
184D HIS* 1.3 78.4 - - + +
186D VAL* 1.3 59.0 + - + +
189D ALA* 2.8 29.9 + - + +
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 2.8 33.6 + - + +
183D ARG* 4.5 7.0 - - + +
185D ILE* 1.3 79.8 - - + +
187D ALA* 1.3 66.1 + - - +
189D ALA* 3.2 6.9 + - - +
190D ILE* 2.9 38.5 + - + +
251D VAL* 4.7 20.6 - - + -
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN* 4.1 11.9 - - - +
183D ARG 3.6 17.7 + - - +
184D HIS* 3.3 5.4 + - - +
186D VAL* 1.3 82.4 - - + +
188D GLY* 1.3 65.6 + - - +
190D ILE* 3.1 8.8 + - - +
191D MET* 2.8 35.7 + - + +
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Residues in contact with GLY 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE 4.9 0.2 - - - -
143D TYR* 3.4 17.5 - - - -
146D GLN* 3.5 26.2 - - - +
184D HIS 2.7 21.0 + - - -
185D ILE 3.7 1.1 - - - -
187D ALA* 1.3 75.0 - - - +
189D ALA* 1.3 61.8 + - - +
191D MET* 3.2 4.1 + - - +
192D SER* 3.0 23.9 + - - -
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D THR* 3.9 22.9 + - + -
66D VAL* 4.1 13.5 - - + -
143D TYR* 3.4 8.6 - - - -
185D ILE* 2.8 20.6 + - + +
186D VAL* 3.2 6.7 + - - +
188D GLY* 1.3 72.0 - - - +
190D ILE* 1.3 66.0 + - + +
192D SER* 2.9 16.3 + - - -
193D TRP* 2.9 12.9 + - - +
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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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186D VAL* 2.9 31.7 + - + +
187D ALA* 3.5 10.1 - - - +
189D ALA* 1.3 76.8 - - + +
191D MET* 1.3 60.6 + - + +
193D TRP* 3.2 9.6 + - + +
194D ALA* 3.0 26.0 + - - +
244D PHE* 4.0 23.5 - - + -
247D LEU* 3.6 46.2 - - + +
251D VAL* 5.3 5.2 - - + -
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Residues in contact with MET 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 5.2 10.8 - - + +
145C ASN* 5.6 7.6 - - - +
142D ILE* 3.9 19.0 - - + +
146D GLN* 3.3 37.9 - - + +
187D ALA* 2.8 30.0 + - + +
188D GLY 3.5 4.5 - - - +
190D ILE* 1.3 81.4 - - + +
192D SER* 1.3 61.1 + - - +
194D ALA* 3.3 8.3 + - - +
195D ARG* 3.1 20.6 + - - +
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Residues in contact with SER 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D SER* 4.7 1.6 + - - -
62D THR* 2.8 30.8 + - - +
65D ALA* 4.7 3.7 - - - +
139D SER* 3.4 38.6 + - - -
142D ILE* 3.8 5.6 - - - +
143D TYR* 4.1 13.5 - - - +
188D GLY 3.0 12.0 + - - -
189D ALA* 2.9 8.0 + - - -
191D MET* 1.3 73.0 - - - +
193D TRP* 1.3 64.3 + - - +
195D ARG* 3.3 1.2 + - - -
196D GLY* 3.1 18.9 + - - -
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Residues in contact with TRP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D TYR* 3.2 49.8 + + + -
58D ALA* 3.5 9.7 - - + +
59D LEU* 3.4 41.6 - - + +
62D THR* 3.4 13.0 - - + +
189D ALA 2.9 9.5 + - - +
190D ILE* 3.4 11.9 - - - +
192D SER* 1.3 75.9 + - - +
194D ALA* 1.3 64.4 + - - +
195D ARG 3.0 0.3 + - - -
196D GLY* 3.2 1.8 + - - +
197D ILE* 3.0 56.1 + - + +
243D VAL* 3.7 24.2 - - + -
244D PHE* 3.7 31.4 - + - -
247D LEU* 5.2 7.0 - - + -
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Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.6 26.8 - - + +
96C VAL* 4.8 1.7 - - + -
190D ILE 3.0 8.2 + - - +
191D MET* 3.3 11.9 + - - +
193D TRP* 1.3 76.8 - - - +
195D ARG* 1.3 60.8 + - - +
197D ILE* 3.8 6.4 - - - +
198D SER* 3.0 29.3 + - - -
244D PHE* 3.6 35.2 - - + -
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Residues in contact with ARG 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 5.1 4.7 - - + +
99C HIS* 3.9 12.3 + - - -
195C ARG* 4.9 7.7 - - - +
99D HIS* 3.3 24.5 - - - -
138D VAL* 2.7 45.0 + - + +
139D SER* 3.6 21.3 - - - -
142D ILE* 4.0 21.0 - - + +
191D MET 3.1 12.2 + - - +
192D SER 3.4 9.4 - - - +
193D TRP 3.0 0.4 - - - -
194D ALA* 1.3 75.6 - - - +
196D GLY* 1.3 67.2 + - - +
198D SER* 3.1 13.1 + - - -
199D GLU* 2.7 42.8 + - - +
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Residues in contact with GLY 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ALA* 4.1 4.9 - - - -
61D SER* 5.0 1.1 - - - -
135D MET* 2.9 50.9 - - - +
139D SER* 4.4 0.8 - - - -
192D SER 3.1 10.8 + - - -
193D TRP 3.7 1.6 - - - -
195D ARG* 1.3 78.5 - - - +
197D ILE* 1.3 64.1 + - - +
199D GLU* 3.0 16.4 + - - +
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Residues in contact with ILE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C VAL 4.3 10.3 - - - +
98C PRO* 4.1 7.0 - - + +
54D THR* 3.8 19.1 - - + +
55D TYR* 3.2 44.0 - - + -
58D ALA* 3.6 13.2 - - + +
135D MET* 4.2 0.9 - - - -
193D TRP* 3.0 51.5 + - + +
194D ALA* 3.8 7.4 - - - +
196D GLY* 1.3 76.2 - - - +
198D SER* 1.3 67.1 + - - +
199D GLU 3.4 0.9 + - - +
212D ILE* 4.4 0.7 - - - +
213D ALA* 5.6 0.2 - - - +
214D PRO* 3.5 17.8 - - - +
240D SER* 5.1 4.7 - - - +
244D PHE* 4.9 6.7 - - + -
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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
----------------------------------------------------------
94C PRO 5.6 0.7 - - - -
95C VAL 3.6 10.0 + - - -
96C VAL 3.5 19.9 + - - -
97C ILE 3.6 4.5 - - - -
98C PRO* 3.4 23.5 - - - +
99C HIS* 3.2 37.6 + - - +
194D ALA 3.0 16.9 + - - -
195D ARG* 3.1 8.7 + - - -
197D ILE* 1.3 76.9 - - - +
199D GLU* 1.3 63.8 - - - +
214D PRO* 4.1 0.7 - - - +
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Residues in contact with GLU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C HIS* 3.0 11.4 + - - -
99D HIS* 3.5 11.5 + - - +
135D MET* 4.8 3.4 - - + -
138D VAL* 4.2 9.2 - - + -
195D ARG* 2.7 44.8 + - - +
196D GLY* 3.0 18.3 + - - +
197D ILE 4.1 1.0 - - - +
198D SER* 1.3 77.2 - - - +
200D PHE* 1.3 62.6 + - - +
201D GLY 3.6 0.7 + - - -
202D ALA* 2.6 41.7 + - + +
203D VAL* 3.6 28.9 - - + +
212D ILE* 4.2 7.8 - - - +
214D PRO* 3.3 19.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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