Contacts of the helix formed by residues 181 - 202 (chain B) in PDB entry 3RK6
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 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B GLY* 1.3 75.3 - - - +
182B GLU* 1.3 63.5 + - - +
183B VAL* 3.0 14.7 + - - +
184B THR* 2.6 42.9 + - - -
185B ARG* 2.9 21.0 + - - +
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 1.3 74.8 - - - +
183B VAL* 1.3 61.9 + - + +
185B ARG* 3.4 31.6 + - - +
186B LYS* 2.9 39.5 + - + +
235B ASP* 4.6 5.4 - - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 3.0 9.8 + - - +
182B GLU* 1.3 78.6 - - + +
184B THR* 1.3 66.9 + - - +
186B LYS* 3.4 12.5 + - + +
187B ARG* 3.1 34.9 + - + +
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Residues in contact with THR 184 (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 ALA* 3.8 30.9 - - + +
180B GLY* 4.2 6.1 - - - -
181B ASP* 2.6 34.8 + - - -
183B VAL* 1.3 77.5 - - - +
185B ARG* 1.3 57.7 + - - +
187B ARG* 3.3 9.7 + - - +
188B PHE* 3.0 25.1 + - - +
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Residues in contact with ARG 185 (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 ALA 3.6 18.4 - - - +
178B ALA 3.5 18.4 - - - +
179B LYS* 5.0 1.1 - - - +
180B GLY 3.0 33.1 + - - +
181B ASP* 2.9 7.3 + - - +
182B GLU* 3.5 38.6 + - - +
184B THR* 1.3 72.9 - - - +
186B LYS* 1.3 64.8 + - - +
188B PHE* 3.1 5.1 + - - +
189B HIS* 2.9 34.8 + - + -
233B MET* 3.5 37.7 - - - +
235B ASP* 3.1 37.3 + - - +
236B ASN* 3.6 15.5 - - - +
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Residues in contact with LYS 186 (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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182B GLU* 2.9 36.6 + - + +
183B VAL* 3.7 13.0 - - + +
185B ARG* 1.3 71.7 - - - +
187B ARG* 1.3 62.7 + - + +
189B HIS* 3.3 23.2 + - - +
190B ALA* 3.3 13.2 + - - +
235B ASP* 5.1 3.8 - - + +
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Residues in contact with ARG 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLN* 5.0 7.5 + - - +
130B THR* 4.1 21.3 + - - +
131B SER* 3.4 26.7 + - - +
170B GLU* 3.3 35.6 + - - +
183B VAL* 3.1 27.3 + - + +
184B THR* 3.7 10.3 - - - +
186B LYS* 1.3 74.9 - - + +
188B PHE* 1.3 65.1 + - - +
190B ALA* 3.3 7.8 + - - +
191B PHE* 3.0 22.2 + - - +
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Residues in contact with PHE 188 (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 GLU* 5.2 3.8 - - - -
174B LYS* 3.7 32.8 - - + -
177B ALA* 3.8 21.5 - - + -
178B ALA* 3.9 24.0 - - + -
184B THR 3.0 13.6 + - - +
185B ARG* 3.3 11.0 - - - +
187B ARG* 1.3 76.7 - - - +
189B HIS* 1.3 54.9 + + - +
191B PHE* 3.1 19.2 + + - +
192B VAL* 2.7 54.7 + - + +
224B LEU* 3.7 22.4 - - + -
227B ALA* 4.5 6.3 - - + -
228B LEU* 3.6 33.0 - - + -
236B ASN* 4.8 0.9 - - - -
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Residues in contact with HIS 189 (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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185B ARG 2.9 26.1 + - - -
186B LYS* 3.6 14.9 - - - +
187B ARG 3.2 0.2 - - - -
188B PHE* 1.3 79.2 - + - +
190B ALA* 1.3 58.3 + - - +
192B VAL* 3.3 1.2 + - - +
193B LEU* 2.9 39.1 + - + +
228B LEU* 4.0 6.5 - - + -
235B ASP* 3.3 45.9 + - + +
236B ASN* 2.6 32.1 + - - -
239B CYS* 3.5 34.3 - - + -
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Residues in contact with ALA 190 (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 ALA 4.4 5.6 - - - +
130B THR* 3.4 28.2 - - - +
131B SER 6.0 0.4 - - - -
132B ILE 6.1 0.7 - - - +
136B SER* 4.7 4.5 + - - +
186B LYS 3.3 9.4 + - - +
187B ARG* 3.8 5.6 - - - +
188B PHE 3.3 0.2 - - - -
189B HIS* 1.3 76.2 - - - +
191B PHE* 1.3 61.0 + - - +
193B LEU* 3.9 6.3 - - - +
194B PHE* 3.0 30.7 + - - +
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Residues in contact with PHE 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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126B TYR* 3.4 29.2 - + - -
130B THR* 4.3 13.7 - - + +
167B CYS* 3.4 29.4 - - - -
170B GLU* 3.7 24.2 - - + +
171B TYR* 3.6 23.6 - - - -
187B ARG 3.0 11.0 + - - +
188B PHE* 3.4 25.6 - + + +
190B ALA* 1.3 73.1 - - - +
192B VAL* 1.3 69.7 + - + +
194B PHE* 3.3 1.9 + - - +
195B LEU* 2.9 65.1 + - + +
224B LEU* 4.2 12.3 - - + -
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Residues in contact with VAL 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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188B PHE* 2.7 58.7 + - + +
189B HIS 3.6 4.7 - - - +
191B PHE* 1.3 73.0 - - + +
193B LEU* 1.3 59.3 + - - +
195B LEU* 3.1 5.2 + - - +
196B GLY* 2.9 24.4 + - - -
221B LEU* 4.5 0.9 - - - +
224B LEU* 4.2 22.7 - - + -
228B LEU* 4.1 9.0 - - + -
239B CYS* 3.9 18.2 - - - -
243B LEU* 3.6 34.7 - - + +
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Residues in contact with LEU 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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136B SER* 4.2 14.4 - - - +
189B HIS* 2.9 25.2 + - + +
190B ALA* 4.3 4.0 - - - +
192B VAL* 1.3 73.4 - - - +
194B PHE* 1.3 65.4 + - - +
196B GLY* 3.4 2.6 + - - +
197B GLU* 3.0 27.8 + - + +
239B CYS* 4.3 13.0 - - - +
242B LYS* 3.9 32.1 - - + +
243B LEU* 3.9 38.1 - - + +
246B LEU* 4.2 8.1 - - + +
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Residues in contact with PHE 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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125B ILE* 5.4 0.4 - - + -
126B TYR* 4.2 22.4 - + - -
129B ALA* 3.5 40.2 - - + +
130B THR* 4.2 11.4 - - + -
136B SER* 3.7 23.0 - - - -
139B GLY 3.8 1.8 - - - -
140B ALA* 3.5 28.9 - - + -
143B CYS* 4.1 19.3 - - - -
163B LEU* 4.5 4.5 - - + -
167B CYS* 4.5 4.3 - - - -
190B ALA 3.0 19.3 + - - +
191B PHE* 3.7 3.8 - - - +
193B LEU* 1.3 77.9 - - - +
195B LEU* 1.3 69.0 + - + +
197B GLU* 3.1 2.6 + - - +
198B LEU* 2.9 44.6 + - + +
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Residues in contact with LEU 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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167B CYS* 3.8 21.1 - - + -
168B ARG* 3.9 24.0 - - - +
171B TYR* 4.6 1.8 - - + -
191B PHE* 2.9 56.8 + - + +
192B VAL 3.6 7.4 - - - +
194B PHE* 1.3 79.2 - - + +
196B GLY* 1.3 61.1 + - - +
198B LEU* 3.6 7.0 - - + +
199B TYR* 2.9 30.7 + - - +
217B LEU* 4.1 19.5 - - + +
220B GLY* 5.5 1.8 - - - -
221B LEU* 4.0 12.7 - - + +
224B LEU* 3.7 21.5 - - + -
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Residues in contact with GLY 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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192B VAL 2.9 10.9 + - - -
193B LEU 3.4 4.0 + - - -
194B PHE 3.2 0.2 - - - -
195B LEU* 1.3 78.2 - - - +
197B GLU* 1.3 60.5 + - - +
199B TYR* 3.4 3.6 + - - +
200B LEU* 3.2 17.8 + - - +
221B LEU* 3.9 6.1 - - - +
243B LEU* 3.7 26.5 - - - -
246B LEU* 3.8 7.4 - - - -
247B THR* 3.6 15.7 - - - +
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Residues in contact with GLU 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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92A GLU 4.8 2.6 - - - +
93A GLN* 4.7 2.9 - - - -
94A PRO* 4.7 8.3 - - - +
95A GLY* 5.1 1.7 + - - -
136B SER* 3.7 11.7 - - - +
137B TYR* 3.5 41.4 + - - +
140B ALA* 3.5 16.8 - - + -
193B LEU 3.0 17.3 + - - +
194B PHE 3.1 4.5 + - - +
196B GLY* 1.3 73.1 - - - +
198B LEU* 1.3 61.4 + - - +
200B LEU* 3.3 5.9 + - - +
201B ASN* 2.8 54.2 + - - +
246B LEU* 3.5 30.7 - - + +
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Residues in contact with LEU 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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140B ALA* 3.7 15.9 - - + +
143B CYS* 3.9 17.0 - - + -
163B LEU* 3.8 31.9 - - + -
164B LEU* 4.6 6.1 - - + -
167B CYS* 4.1 22.4 - - - -
194B PHE* 2.9 29.4 + - + +
195B LEU* 3.6 7.9 - - - +
197B GLU* 1.3 74.2 - - - +
199B TYR* 1.3 60.6 + - - +
202B LEU* 2.7 52.4 + - + +
217B LEU* 3.8 21.1 - - + -
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Residues in contact with TYR 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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195B LEU 2.9 17.6 + - - +
196B GLY 3.5 3.4 - - - +
198B LEU* 1.3 78.1 - - - +
200B LEU* 1.3 64.1 + - + +
202B LEU* 4.2 3.7 - - - +
213B ARG* 3.3 46.2 + - + +
214B ALA 3.9 16.3 + - - +
217B LEU* 3.5 19.4 - - + +
218B GLN* 3.8 25.9 + - + +
221B LEU* 3.5 22.7 - - + -
247B THR* 4.2 10.8 - - + -
250B VAL* 3.6 28.8 + - + +
251B LEU* 3.6 31.1 - - + +
254B ALA* 3.9 13.7 - - - +
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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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196B GLY 3.2 14.9 + - - +
197B GLU* 3.7 10.3 - - - +
198B LEU 3.2 0.2 - - - -
199B TYR* 1.3 79.7 - - + +
201B ASN* 1.3 66.7 + - - +
202B LEU 5.0 0.5 - - - +
203B GLU* 5.8 1.2 - - - +
213B ARG* 3.3 24.8 + - - +
246B LEU* 3.3 47.1 - - + +
247B THR* 4.0 9.9 - - + -
250B VAL* 3.7 38.1 - - + -
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Residues in contact with ASN 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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137B TYR* 3.8 23.5 + - - -
140B ALA* 4.0 24.7 - - + +
141B ARG* 4.3 13.3 - - - +
144B ASN* 3.1 25.4 + - + +
197B GLU* 2.8 44.2 + - - +
200B LEU* 1.3 81.8 - - - +
202B LEU* 1.3 64.3 + - - +
203B GLU* 3.2 7.6 + - - +
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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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143B CYS* 4.2 7.2 - - + +
144B ASN* 3.6 33.4 - - - +
147B SER* 4.2 10.5 - - - +
160B ARG* 3.9 26.7 - - + -
163B LEU* 5.0 5.4 - - + -
164B LEU* 4.4 15.9 - - + -
198B LEU* 2.7 48.0 + - + +
199B TYR 4.2 5.9 - - - +
200B LEU 5.0 0.5 - - - +
201B ASN* 1.3 71.5 - - - +
203B GLU* 1.3 60.7 + - - +
204B ILE* 4.1 5.8 + - + -
212B THR 4.0 0.2 - - - +
213B ARG* 4.0 21.8 - - - +
214B ALA* 4.4 17.1 + - + +
217B LEU* 4.6 2.0 - - + -
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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