Contacts of the helix formed by residues 173 - 197 (chain B) in PDB entry 1RQD
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 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B ARG* 4.6 11.9 + - - +
162B GLY* 3.0 35.3 + - - +
164B ASN* 2.9 35.9 + - - +
171B VAL 3.8 0.2 + - - -
172B PRO* 1.3 71.7 - - - +
174B GLU* 1.3 70.3 + - - +
176B TYR* 2.9 22.3 + - - +
177B CYS* 3.3 15.5 + - - -
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Residues in contact with GLU 174 (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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161B ASN 5.6 0.7 - - - +
162B GLY* 4.2 6.6 - - - +
172B PRO* 3.0 16.1 + - + +
173B ASN* 1.3 87.9 + - - +
175B ASN* 1.3 62.3 + - - +
177B CYS* 3.5 14.1 - - + +
178B LYS* 3.0 40.2 + - + +
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Residues in contact with ASN 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 3.9 20.8 - - + +
143B LEU* 5.2 0.7 - - - +
144B ALA* 3.5 36.9 + - - +
145B PRO 3.2 24.0 + - - +
146B THR* 4.9 2.0 + - - -
147B TYR* 5.4 0.3 - - - -
171B VAL* 3.8 20.7 - - + +
172B PRO* 2.8 39.2 + - - +
174B GLU* 1.3 79.0 - - - +
176B TYR* 1.3 56.0 + - + +
178B LYS* 3.5 4.8 + - - +
179B PHE* 3.0 24.8 + - - +
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLU* 5.0 4.0 + - - -
137B GLU* 4.4 19.2 + - + +
140B ILE* 3.4 27.1 - - + -
164B ASN* 3.8 21.5 - - + -
166B ILE* 4.9 5.2 - - - +
171B VAL* 3.6 29.4 - - + +
172B PRO 4.1 8.1 - - - -
173B ASN* 2.9 11.2 + - - +
175B ASN* 1.3 77.0 - - + +
177B CYS* 1.3 59.7 + - - +
179B PHE* 3.3 6.2 + + - +
180B GLU* 2.9 28.1 + - - +
240B SER* 3.2 35.7 - - - +
244B MET* 4.3 10.2 - - + +
370B NAD 5.8 2.6 - - - -
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Residues in contact with CYS 177 (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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173B ASN* 3.3 16.2 + - - -
174B GLU* 3.2 17.9 + - + +
176B TYR* 1.3 77.2 - - - +
178B LYS* 1.3 65.6 + - + +
180B GLU* 3.1 13.7 + - - +
181B ASP* 3.0 28.1 + - - +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.7 40.4 + - + +
144B ALA* 4.3 14.0 - - + +
174B GLU* 3.0 23.1 + - + +
175B ASN 3.5 7.2 - - - +
177B CYS* 1.3 79.1 - - + +
179B PHE* 1.3 62.2 + - - +
181B ASP* 3.1 13.9 + - - +
182B TRP* 3.0 23.9 + - - +
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Residues in contact with PHE 179 (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 GLU* 4.0 21.5 - - + -
139B LEU* 4.3 14.1 - - + -
140B ILE* 3.6 28.9 - - + -
143B LEU* 3.8 12.3 - - + +
175B ASN 3.0 15.2 + - - +
176B TYR* 3.3 11.9 - + - +
178B LYS* 1.3 76.4 - - - +
180B GLU* 1.3 56.1 + - - +
182B TRP* 3.3 28.5 + + - +
183B LEU* 2.8 46.5 + - + +
240B SER* 3.6 25.6 - - - -
241B LEU* 4.1 16.2 - - + -
244B MET* 3.9 21.1 - - + -
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Residues in contact with GLU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TYR 2.9 13.7 + - - +
177B CYS* 3.4 14.6 - - - +
179B PHE* 1.3 76.5 - - - +
181B ASP* 1.3 70.0 + - - +
183B LEU* 3.2 2.0 + - - +
184B MET* 2.9 62.3 + - + +
244B MET* 3.6 21.8 - - + +
247B PHE* 4.8 11.1 - - - +
251B LYS* 4.6 9.2 + - - -
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Residues in contact with ASP 181 (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 CYS* 3.0 18.3 + - - +
178B LYS* 3.3 15.0 - - - +
180B GLU* 1.3 82.6 - - - +
182B TRP* 1.3 63.4 + - - +
184B MET* 5.2 1.3 - - - -
185B PRO* 3.3 18.7 - - - +
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Residues in contact with TRP 182 (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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139B LEU* 4.1 12.8 - - + -
143B LEU* 3.9 24.5 - - + -
178B LYS 3.0 11.6 + - - +
179B PHE* 3.6 29.4 - + - +
181B ASP* 1.3 80.1 - - - +
183B LEU* 1.3 81.1 + - + +
185B PRO* 3.5 12.9 - - - +
186B ILE* 3.4 37.0 - - + +
210B LEU* 3.6 33.9 - - + -
213B GLU* 3.7 10.4 + - - -
214B ILE* 3.4 41.0 - - + +
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Residues in contact with LEU 183 (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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179B PHE* 2.8 29.0 + - + +
180B GLU* 4.0 2.7 - - - +
182B TRP* 1.3 87.1 - - + +
184B MET* 1.3 67.6 + - - +
186B ILE* 2.8 17.7 + - + +
187B LEU* 3.1 34.3 + - + -
210B LEU* 3.6 31.4 - - + -
241B LEU* 3.6 25.4 - - + -
244B MET* 3.4 35.4 - - + -
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Residues in contact with MET 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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180B GLU* 2.9 57.2 + - + +
181B ASP* 4.5 1.1 - - - +
183B LEU* 1.3 71.3 - - - +
185B PRO* 1.3 71.0 - - + +
187B LEU* 2.9 19.1 + - + +
188B ASP* 3.0 15.8 + - - +
244B MET* 3.8 37.5 - - + +
247B PHE* 4.7 3.1 - - + -
248B HIS* 3.6 35.1 - - + +
251B LYS* 4.4 17.5 - - - +
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Residues in contact with PRO 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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181B ASP 3.3 16.6 - - - +
182B TRP 3.5 13.7 - - - +
183B LEU 3.6 1.3 - - - -
184B MET* 1.3 96.4 - - + +
186B ILE* 1.3 61.0 + - + +
188B ASP* 3.3 16.7 + - + +
189B GLN* 3.2 28.9 + - - +
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Residues in contact with ILE 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 TRP* 3.4 63.9 - - + +
183B LEU* 2.8 12.6 + - + +
185B PRO* 1.3 71.8 - - + +
187B LEU* 1.3 61.3 + - - +
189B GLN* 3.2 14.1 + - - +
190B MET* 2.9 42.3 + - + +
209B ARG* 4.4 10.1 - - + +
210B LEU* 4.0 16.6 - - + -
213B GLU* 3.8 35.9 - - + +
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Residues in contact with LEU 187 (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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183B LEU* 3.1 37.6 + - + +
184B MET* 2.9 14.1 + - - +
186B ILE* 1.3 74.0 - - - +
188B ASP* 1.3 65.2 + - - +
190B MET* 3.0 29.3 + - + +
191B VAL* 2.9 26.2 + - - +
206B MET* 3.8 15.0 - - + -
244B MET 4.0 10.8 - - - +
245B ILE* 4.3 11.7 - - + -
248B HIS* 3.4 42.6 - - + +
255B LEU* 4.3 11.4 - - + -
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Residues in contact with ASP 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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184B MET* 3.0 17.7 + - - +
185B PRO* 3.4 17.7 - - + +
186B ILE 3.2 0.2 - - - -
187B LEU* 1.3 77.5 - - - +
189B GLN* 1.3 57.8 + - + +
191B VAL* 3.3 3.1 + - - +
192B MET* 2.9 27.6 + - - +
248B HIS* 2.9 17.5 + - - -
252B ASN* 2.9 29.4 + - - +
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Residues in contact with GLN 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 PRO* 3.5 17.5 + - - +
186B ILE* 3.2 16.9 + - - +
188B ASP* 1.3 74.4 - - + +
190B MET* 1.3 61.7 + - - +
192B MET* 3.1 7.5 + - - +
193B GLU* 2.7 49.3 + - + +
209B ARG* 3.5 18.4 + - - +
213B GLU* 4.7 9.8 + - - +
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Residues in contact with MET 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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186B ILE* 2.9 32.4 + - + +
187B LEU* 3.4 28.9 - - + +
189B GLN* 1.3 76.7 - - - +
191B VAL* 1.3 61.9 + - - +
193B GLU* 3.6 1.0 + - - -
194B GLN* 3.0 11.5 + - - +
201B TRP* 2.9 68.8 + - + -
206B MET* 3.4 42.6 - - + +
209B ARG* 4.2 13.9 - - - +
210B LEU* 4.3 5.6 - - + -
255B LEU* 4.5 11.9 - - + -
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Residues in contact with VAL 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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187B LEU 2.9 15.7 + - - +
188B ASP 3.7 7.0 - - - +
190B MET* 1.3 76.1 - - - +
192B MET* 1.3 65.5 + - - +
194B GLN* 3.0 10.1 + - - +
195B ASN* 3.0 38.9 + - - +
248B HIS* 4.1 16.2 - - + -
252B ASN* 3.6 27.6 - - - +
253B PRO 4.0 8.3 - - - +
254B GLY* 5.0 1.1 - - - -
255B LEU* 3.9 38.6 - - + +
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Residues in contact with MET 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 ASP 2.9 14.5 + - - +
189B GLN* 3.3 12.3 - - - +
191B VAL* 1.3 77.0 - - - +
193B GLU* 1.3 56.3 + - + +
195B ASN* 2.9 8.5 + - - +
196B THR* 2.8 67.1 + - + +
197B GLU* 5.6 1.6 - - - +
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Residues in contact with GLU 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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189B GLN* 2.7 33.4 + - - +
190B MET 4.0 3.4 - - - +
192B MET* 1.3 76.0 - - + +
194B GLN* 1.3 57.3 + - - +
196B THR* 4.2 2.9 - - - -
197B GLU* 3.0 54.9 + - - +
198B GLY 3.2 3.1 + - - -
199B VAL* 3.3 19.7 + - + +
201B TRP* 3.7 8.0 - - + -
209B ARG* 3.0 42.1 + - - -
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Residues in contact with GLN 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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190B MET 3.0 15.3 + - - +
191B VAL* 3.0 12.4 + - - +
193B GLU* 1.3 78.3 - - - +
195B ASN* 1.3 71.3 + - - +
198B GLY* 3.5 18.0 + - - -
199B VAL* 3.5 23.6 + - - +
200B LYS* 5.4 0.4 - - - -
201B TRP* 3.3 20.0 + - - +
254B GLY 3.0 33.1 + - - -
255B LEU* 3.6 6.8 - - - +
256B VAL* 3.3 29.8 + - - +
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Residues in contact with ASN 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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191B VAL* 3.3 31.1 + - - +
192B MET* 2.9 8.8 + - - +
194B GLN* 1.3 97.5 + - - +
196B THR* 1.3 65.5 + - + +
198B GLY* 4.4 2.5 + - - -
253B PRO 5.3 2.0 + - - -
254B GLY* 5.7 3.0 - - - -
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Residues in contact with THR 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 MET* 2.8 60.3 + - + +
195B ASN* 1.3 78.4 - - + +
197B GLU* 1.3 77.8 + - - +
198B GLY 3.6 0.7 - - - -
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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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192B MET* 5.6 1.6 - - - +
193B GLU* 3.0 39.7 + - - +
196B THR* 1.3 91.6 + - - +
198B GLY* 1.3 63.0 + - - +
199B VAL* 3.3 10.5 + - + +
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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