Contacts of the helix formed by residues 190 - 212 (chain B) in PDB entry 2OQ4
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 ASN 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B LEU* 1.3 79.5 - - - +
191B ALA* 1.3 61.8 + - - +
192B ALA* 2.8 18.2 + - - +
193B GLN* 2.5 66.6 + - - +
194B LEU 3.0 16.6 + - - -
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Residues in contact with ALA 191 (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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140B LYS* 5.4 2.8 + - - +
189B LEU 4.0 0.2 + - - -
190B ASN* 1.3 74.0 - - - +
192B ALA* 1.3 57.9 + - - +
194B LEU* 3.5 11.3 + - + +
195B ASP* 3.0 24.6 + - - -
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Residues in contact with ALA 192 (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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190B ASN* 2.8 17.1 + - - +
191B ALA* 1.3 71.7 - - - +
193B GLN* 1.3 64.7 + - + +
195B ASP* 3.2 3.2 + - - +
196B ALA* 3.0 20.8 + - - +
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Residues in contact with GLN 193 (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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178B VAL* 5.2 9.6 + - + +
180B LEU* 3.7 32.9 - - + +
189B LEU* 3.5 19.7 - - + +
190B ASN* 2.5 58.2 + - - +
192B ALA* 1.3 69.5 - - + +
194B LEU* 1.3 57.3 + - - +
196B ALA* 2.8 9.5 + - - +
197B LEU* 2.6 36.6 + - - +
262B HIS 6.0 0.2 - - - -
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Residues in contact with LEU 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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140B LYS* 3.3 31.4 - - + -
143B LEU* 4.2 23.3 - - + -
144B LEU* 3.5 37.7 - - + -
186B ALA* 4.2 4.7 - - + +
189B LEU* 3.4 38.5 - - + +
190B ASN 3.0 7.5 + - - +
191B ALA* 3.6 10.1 - - + +
192B ALA 3.3 0.2 - - - -
193B GLN* 1.3 79.1 - - - +
195B ASP* 1.3 57.2 + - - +
197B LEU* 3.7 4.1 - - + +
198B ALA* 2.9 32.7 + - - +
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Residues in contact with ASP 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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140B LYS* 4.0 17.4 - - - +
191B ALA 3.0 16.1 + - - -
192B ALA* 3.6 3.8 - - - +
193B GLN 3.1 0.4 - - - -
194B LEU* 1.3 77.0 - - - +
196B ALA* 1.3 59.6 + - - +
198B ALA* 3.8 0.5 - - - +
199B HIS* 2.3 43.7 + - - -
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Residues in contact with ALA 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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177B GLN 5.7 0.2 - - - +
178B VAL* 3.7 22.1 - - + +
192B ALA 3.0 12.1 + - - +
193B GLN* 2.8 10.4 + - - +
195B ASP* 1.3 74.6 - - - +
197B LEU* 1.3 53.1 + - - +
199B HIS* 3.2 6.5 + - - +
200B ALA* 2.7 36.7 + - - +
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Residues in contact with LEU 197 (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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143B LEU* 4.3 16.8 - - + -
153B PHE* 3.8 41.5 - - + -
157B LEU* 5.2 2.7 - - + -
174B ILE* 4.2 13.2 - - + -
175B LEU* 5.7 3.4 - - + -
178B VAL* 3.8 19.9 - - + +
180B LEU* 4.6 4.3 - - + -
186B ALA* 5.5 0.2 - - + -
189B LEU* 4.3 9.4 - - + -
193B GLN 2.6 19.0 + - - +
194B LEU* 3.7 7.0 - - + +
196B ALA* 1.3 71.8 - - - +
198B ALA* 1.3 54.5 + - - +
200B ALA* 2.8 2.3 + - + +
201B LEU* 2.7 62.0 + - + +
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Residues in contact with ALA 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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136B PRO* 3.7 25.1 - - - +
139B VAL* 4.2 8.8 - - + +
140B LYS* 4.1 13.5 - - + +
143B LEU* 3.9 21.6 - - + +
194B LEU 2.9 20.7 + - - +
195B ASP 3.8 3.1 - - - +
197B LEU* 1.3 74.4 - - - +
199B HIS* 1.3 63.4 + - - +
200B ALA 3.3 0.2 + - - -
201B LEU* 3.4 9.2 + - - +
202B LEU* 3.6 19.1 + - - +
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Residues in contact with HIS 199 (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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136B PRO* 3.9 34.7 - - + +
140B LYS* 4.7 11.4 - - - -
195B ASP* 2.3 45.1 + - - +
196B ALA* 3.6 6.3 - - - +
198B ALA* 1.3 75.9 - - - +
200B ALA* 1.3 52.4 + - - +
202B LEU* 3.5 2.2 + - - +
203B GLU* 2.8 63.6 + - + +
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Residues in contact with ALA 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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174B ILE* 3.6 30.1 - - + +
177B GLN* 4.9 9.9 - - + -
178B VAL* 3.7 19.7 - - + -
196B ALA 2.7 21.2 + - - +
197B LEU* 2.8 5.5 + - - +
199B HIS* 1.3 70.5 - - - +
201B LEU* 1.3 56.5 + - - +
202B LEU 2.8 11.9 + - - -
203B GLU* 3.4 12.8 + - - +
204B ILE* 3.4 14.9 + - + +
205B PRO* 3.6 1.0 - - - +
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Residues in contact with LEU 201 (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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129B VAL* 3.5 23.9 - - - +
139B VAL* 3.8 15.3 - - + -
143B LEU* 3.4 30.5 - - + -
157B LEU* 3.4 32.5 - - + -
162B PHE* 4.3 2.5 - - + -
163B LEU* 3.9 17.7 - - + -
166B LEU* 4.3 12.9 - - + +
174B ILE* 3.8 13.0 - - + -
197B LEU* 2.7 43.0 + - + +
198B ALA 3.4 5.1 + - - +
200B ALA* 1.3 71.3 - - - +
202B LEU* 1.3 58.2 + - - +
205B PRO* 3.9 8.6 - - - +
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Residues in contact with LEU 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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129B VAL* 4.1 16.2 - - + +
134B LEU* 3.5 39.0 - - + +
135B THR 3.6 23.3 - - - +
136B PRO* 3.7 15.7 - - + -
139B VAL* 3.6 13.0 - - + -
163B LEU* 5.1 0.7 - - + -
198B ALA 3.7 12.1 - - - +
199B HIS* 3.5 3.2 + - - +
200B ALA 2.9 0.4 - - - -
201B LEU* 1.3 90.3 - - + +
203B GLU* 1.3 63.8 + - + +
204B ILE 3.6 0.4 - - - -
205B PRO* 3.7 4.9 - - - +
206B ARG* 2.8 59.2 + - - +
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Residues in contact with GLU 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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199B HIS* 2.8 59.0 + - + +
200B ALA* 3.9 4.1 + - - +
202B LEU* 1.3 72.8 - - + +
204B ILE* 1.3 68.8 + - + +
206B ARG* 3.3 7.4 + - - +
207B PHE* 2.9 24.1 + - - +
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Residues in contact with ILE 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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170B LEU* 3.5 17.5 - - + -
173B GLU* 3.8 23.3 - - + +
174B ILE* 3.2 27.6 - - + -
177B GLN* 4.1 20.9 - - + +
200B ALA* 3.4 8.8 + - + +
203B GLU* 1.3 75.0 - - + +
205B PRO* 1.3 61.9 - - + +
207B PHE* 2.8 9.6 + - + +
208B SER* 2.6 34.5 + - - -
225B PHE* 3.4 30.5 - - + -
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Residues in contact with PRO 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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4B PRO* 3.7 9.5 - - + +
129B VAL* 3.8 21.5 - - + -
130B LEU* 3.9 5.4 - - + -
166B LEU* 3.8 23.3 - - + -
170B LEU* 3.7 17.5 - - + -
174B ILE* 4.3 1.6 - - + -
200B ALA 3.6 10.8 - - - +
201B LEU 3.9 8.3 - - - +
202B LEU 3.7 7.6 - - - +
203B GLU 3.6 2.0 - - - -
204B ILE* 1.3 95.2 - - + +
206B ARG* 1.3 52.8 + - - +
208B SER* 2.7 10.5 + - - +
209B TYR* 2.6 36.4 + - - +
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Residues in contact with ARG 206 (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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129B VAL 3.2 17.6 + - - +
130B LEU* 3.6 25.3 - - + +
131B ASP 3.5 14.7 + - - -
132B PRO* 4.4 14.1 + - - +
134B LEU* 2.6 30.1 + - - +
136B PRO* 5.7 0.4 - - - +
202B LEU* 2.8 45.2 + - - +
203B GLU* 3.3 6.5 + - - +
204B ILE 3.3 0.6 - - - -
205B PRO* 1.3 75.3 - - - +
207B PHE* 1.3 57.9 + - - +
209B TYR* 3.4 6.0 + - + +
210B ALA* 3.0 30.0 + - - +
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Residues in contact with PHE 207 (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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203B GLU 2.9 14.3 + - - +
204B ILE* 2.8 12.7 + - + +
206B ARG* 1.3 75.7 - - - +
208B SER* 1.3 65.3 + - - +
210B ALA* 2.9 14.9 + - + +
211B THR* 3.0 26.7 + - + -
223B ALA* 3.2 42.0 - - - -
224B LEU 3.5 2.0 - - - -
225B PHE* 3.1 46.2 - + + -
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Residues in contact with SER 208 (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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4B PRO* 3.2 12.0 - - - +
8B ARG* 3.6 7.4 + - - -
169B TYR* 3.6 21.3 + - - -
170B LEU* 3.9 2.6 - - - +
204B ILE 2.6 17.8 + - - -
205B PRO* 2.7 26.0 + - - +
207B PHE* 1.3 73.5 - - - +
209B TYR* 1.3 60.2 + - - +
210B ALA 3.2 0.5 + - - -
212B ARG* 3.3 26.5 + - - +
225B PHE* 3.9 32.8 - - - +
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Residues in contact with TYR 209 (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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4B PRO* 3.7 17.9 - - + +
7B ARG* 3.2 40.1 + - + +
8B ARG* 4.0 18.7 - - + +
11B ASP* 2.9 26.6 + - - -
130B LEU* 3.7 26.0 - - + -
205B PRO 2.6 21.7 + - - +
206B ARG* 3.6 9.0 - - + +
207B PHE 3.1 0.2 - - - -
208B SER* 1.3 74.4 + - - +
210B ALA* 1.3 64.6 + - + +
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Residues in contact with ALA 210 (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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206B ARG 3.0 15.3 + - - +
207B PHE* 2.9 7.1 + - + +
209B TYR* 1.3 86.3 - - + +
211B THR* 1.3 68.7 + - + +
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Residues in contact with THR 211 (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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207B PHE* 3.0 24.3 + - + +
208B SER 3.5 0.8 + - - -
209B TYR 3.7 0.2 - - - -
210B ALA* 1.3 89.9 - - + +
212B ARG* 1.3 71.6 + - - +
223B ALA 3.4 23.8 - - - +
224B LEU* 3.8 12.3 - - - +
225B PHE* 2.8 28.4 + - - +
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Residues in contact with ARG 212 (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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1B PRO* 5.9 0.8 - - - +
5B GLU* 3.1 27.7 + - - +
8B ARG* 3.9 36.2 + - - +
169B TYR* 3.2 27.1 - - - -
208B SER* 3.3 21.9 + - - +
211B THR* 1.3 87.7 + - - +
224B LEU* 6.2 0.2 - - - -
225B PHE* 4.3 28.3 - - + +
227B PHE* 3.6 26.9 - - - -
230B PHE* 5.8 1.6 - - - -
603B SO4 5.3 5.2 + - - -
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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
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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