Contacts of the helix formed by residues 195 - 218 (chain B) in PDB entry 4U1D
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 ARG 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B THR* 4.8 10.3 + - - +
155B LEU* 3.2 29.7 + - - +
156B ARG* 3.7 28.1 - - - +
189B PHE* 3.8 16.9 - - + -
190B CYS* 2.9 18.4 + - - +
193B TYR* 3.2 37.9 - - + +
194B GLN* 1.3 67.5 - - - +
196B LYS* 1.3 58.6 + - - +
197B ASN 3.4 3.1 - - - -
198B GLU* 2.8 47.1 + - + +
199B PHE* 2.9 28.6 + - - +
250B LEU* 5.0 0.2 - - - -
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Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLN* 2.7 42.8 + - - +
195B ARG* 1.3 71.9 - - - +
197B ASN* 1.3 65.0 + - - +
199B PHE* 3.3 7.6 + - - +
200B LYS* 3.1 34.2 + - - +
250B LEU* 3.3 33.5 + - + -
251B GLU* 4.8 9.1 + - - +
252B LEU* 3.7 28.8 - - + +
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Residues in contact with ASN 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ARG 3.4 0.4 - - - -
196B LYS* 1.3 79.8 - - - +
198B GLU* 1.3 64.4 + - + +
200B LYS* 3.7 23.8 + - - +
201B ARG* 3.4 37.9 + - - +
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 2.8 19.8 + - - +
159B TRP* 3.2 54.9 - - + +
189B PHE* 3.6 4.7 - - - -
190B CYS* 4.8 0.4 - - - -
195B ARG* 2.8 51.6 + - + +
196B LYS 3.3 0.2 - - - -
197B ASN* 1.3 76.8 - - + +
199B PHE* 1.3 56.1 + - - +
201B ARG* 3.0 27.7 + - - +
202B LEU 2.7 32.1 + - - -
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Residues in contact with PHE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B MET* 4.3 19.3 - - + -
190B CYS* 3.8 25.2 - - + -
195B ARG 2.9 17.0 + - - +
196B LYS 3.3 4.7 + - - +
198B GLU* 1.3 76.7 - - - +
200B LYS* 1.3 65.6 - - - +
202B LEU* 3.1 12.4 + - + +
203B ALA* 3.0 22.8 + - + +
243B GLN* 3.4 34.1 - - + -
246B VAL* 3.4 30.1 - - + -
247B SER* 3.2 24.9 - - - -
250B LEU* 4.0 9.2 - - + -
252B LEU* 3.7 17.9 - - + -
255B GLU* 4.2 11.2 - - + -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LYS* 3.1 23.7 + - - +
197B ASN* 3.8 25.6 + - - +
198B GLU 3.3 0.2 - - - -
199B PHE* 1.3 76.7 - - - +
201B ARG* 1.3 64.7 + - + +
203B ALA* 3.3 6.1 + - - +
204B GLU* 3.2 21.0 + - - +
207B ARG* 4.6 0.9 + - - -
252B LEU* 4.0 32.0 - - + +
255B GLU* 4.0 25.0 - - + +
258B ARG* 5.5 4.0 - - - +
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Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 3.4 28.3 - - - +
159B TRP* 4.0 14.9 - - + +
163B ARG* 6.2 0.2 - - - +
197B ASN* 3.4 30.2 + - - +
198B GLU* 3.0 31.5 + - - +
200B LYS* 1.3 75.1 - - + +
202B LEU* 1.3 66.1 + - - +
204B GLU* 3.2 8.8 + - - +
205B MET* 3.0 22.6 + - - +
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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
----------------------------------------------------------
159B TRP* 3.6 14.3 - - + -
166B LEU* 3.7 13.2 - - + -
183B VAL* 5.6 1.6 - - + -
186B THR* 3.8 21.5 - - + -
187B MET* 3.5 40.2 - - + -
190B CYS* 4.5 2.9 - - - -
198B GLU 2.7 16.9 + - - +
199B PHE* 3.3 19.3 - - + +
201B ARG* 1.3 74.0 - - - +
203B ALA* 1.3 62.2 + - - +
205B MET* 3.0 30.2 + - + +
206B LEU* 3.0 36.9 + - + +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 3.0 14.5 + - + +
200B LYS 3.4 10.1 - - - +
202B LEU* 1.3 79.6 - - - +
204B GLU* 1.3 63.1 + - - +
206B LEU* 3.0 6.7 + - - +
207B ARG* 3.0 36.0 + - - +
243B GLN* 3.4 36.4 + - + +
255B GLU* 3.7 13.0 - - + +
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Residues in contact with GLU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LYS 3.2 9.2 + - - +
201B ARG* 3.2 10.3 + - - +
203B ALA* 1.3 78.6 - - - +
205B MET* 1.3 62.9 + - - +
207B ARG* 3.1 34.8 + - - +
208B GLN* 3.1 39.0 + - - +
258B ARG* 6.1 0.2 - - - -
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Residues in contact with MET 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 5.0 4.3 - - + -
163B ARG* 4.1 29.8 - - + +
166B LEU* 3.5 33.4 - - + -
167B ASP* 3.7 26.2 - - - +
201B ARG 3.0 12.5 + - - +
202B LEU* 3.0 23.5 + - + +
204B GLU* 1.3 77.4 - - - +
206B LEU* 1.3 58.3 + - + +
208B GLN* 3.2 10.1 + - - +
209B HIS* 3.0 50.7 + - + +
467C LYS* 4.6 8.1 - - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.7 1.8 - - + -
179B TYR* 4.0 17.5 - - - +
183B VAL* 4.1 18.4 - - + -
187B MET* 3.6 21.1 - - + -
202B LEU* 3.0 34.1 + - + +
203B ALA 3.0 9.6 + - - +
205B MET* 1.3 85.6 - - + +
207B ARG* 1.3 61.6 - - - +
209B HIS* 3.4 6.8 + - - +
210B LEU* 3.1 17.0 + - - +
239B GLN* 4.5 2.5 - - + +
240B ARG* 3.3 38.5 + - - +
243B GLN* 3.5 24.0 - - - +
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Residues in contact with ARG 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LYS 4.6 1.0 + - - -
203B ALA* 3.0 12.9 + - - +
204B GLU* 3.1 57.4 + - - +
206B LEU* 1.3 74.7 - - + +
208B GLN* 1.3 66.5 + - + +
210B LEU* 3.1 7.3 + - - +
211B ASP* 3.0 32.6 + - - +
240B ARG* 5.2 1.8 - - - +
243B GLN* 3.6 10.4 + - - +
255B GLU* 2.6 31.7 + - - -
258B ARG* 3.7 25.2 - - - +
259B SER* 4.0 1.2 + - - -
262B ASP* 3.1 36.9 + - - +
345C TYR* 5.7 4.7 - - - -
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B GLU* 3.1 31.9 + - - +
205B MET* 3.2 10.1 + - - +
207B ARG* 1.3 75.2 - - + +
209B HIS* 1.3 67.8 + - + +
211B ASP* 3.3 10.7 + - - +
212B ALA* 3.2 22.7 + - - +
467C LYS* 3.6 28.5 - - - +
471C GLN* 4.5 24.3 + - - +
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Residues in contact with HIS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.6 26.2 - - + -
167B ASP* 2.8 29.5 + - - -
170B ARG* 3.6 26.4 - - + -
171B ASN* 3.1 25.2 + - - +
179B TYR* 2.8 29.8 + + + +
205B MET* 3.0 34.6 + - + +
206B LEU* 3.6 9.2 - - + +
207B ARG 3.2 0.2 - - - -
208B GLN* 1.3 82.3 - - + +
210B LEU* 1.3 56.4 + - - +
212B ALA* 3.3 1.5 + - - -
213B ALA 3.1 20.4 + - - -
240B ARG* 5.6 0.7 - - - +
467C LYS* 5.1 3.1 - - - -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU 3.1 7.6 + - - +
207B ARG* 3.1 7.4 + - - +
209B HIS* 1.3 75.5 - - - +
211B ASP* 1.3 63.2 + - - +
213B ALA* 3.1 16.2 + - + +
214B ASN* 3.0 41.7 + - - +
227B LEU* 4.3 11.0 - - + -
236B TYR* 4.1 28.3 - - + -
240B ARG* 3.6 28.7 - - - +
266B LEU* 3.7 31.4 - - + -
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 3.0 23.5 + - - +
208B GLN* 3.3 10.6 + - - +
210B LEU* 1.3 79.0 - - - +
212B ALA* 1.3 57.6 + - - +
214B ASN* 3.4 10.7 + - - +
215B TYR* 3.1 26.7 + - - +
343C ILE* 5.6 5.2 - - - +
474C VAL* 4.0 27.6 - - + +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASN* 3.5 19.5 - - - +
208B GLN 3.2 13.0 + - - +
209B HIS* 3.5 3.6 - - - +
210B LEU 3.2 0.2 - - - -
211B ASP* 1.3 74.1 - - - +
213B ALA* 1.3 65.2 + - - +
215B TYR* 3.3 7.4 + - - +
216B GLN* 3.1 31.6 + - - +
470C LEU* 4.0 26.9 - - + -
474C VAL* 4.5 6.5 - - + +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASN* 3.8 12.1 - - - +
209B HIS 3.1 13.0 + - - +
210B LEU* 3.1 20.3 + - + +
212B ALA* 1.3 76.7 - - - +
214B ASN* 1.3 62.1 + - - +
216B GLN* 3.1 20.0 + - - +
217B GLN* 3.1 20.4 + - - +
225B VAL* 4.7 13.2 - - + -
227B LEU* 4.0 19.5 - - + -
236B TYR* 4.9 1.3 - - - +
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Residues in contact with ASN 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASN* 4.2 5.0 - - - +
200A LYS* 4.5 15.3 - - + +
254A HIS* 6.0 3.8 - - - -
210B LEU* 3.0 31.5 + - - +
211B ASP* 3.7 12.1 - - - +
212B ALA 3.3 0.2 - - - -
213B ALA* 1.3 77.2 - - - +
215B TYR* 1.3 61.6 + - - +
216B GLN 3.3 0.3 + - - -
217B GLN* 3.3 22.7 + - - +
218B SER 4.6 0.3 + - - -
227B LEU* 3.4 18.8 - - - +
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Residues in contact with TYR 215 (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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197A ASN* 3.2 49.3 + - + +
211B ASP 3.1 17.6 + - - +
212B ALA* 3.8 4.7 - - - +
213B ALA 3.2 0.4 - - - -
214B ASN* 1.3 77.4 - - - +
216B GLN* 1.3 70.2 + - + +
217B GLN 3.3 0.7 + - - -
218B SER 4.3 1.0 + - - -
219B LYS* 3.4 25.3 + - + +
470C LEU* 5.0 9.4 - - + -
473C ALA* 3.3 41.8 - - + +
474C VAL* 3.9 18.6 - - + -
479C SER* 3.6 12.2 - - - -
480C ILE* 3.2 34.3 + - + -
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Residues in contact with GLN 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASN* 3.9 22.0 - - - +
212B ALA* 3.1 22.3 + - - +
213B ALA* 3.1 6.5 + - - +
215B TYR* 1.3 85.6 - - + +
217B GLN* 1.3 67.5 + - - +
218B SER 3.3 1.3 - - - -
219B LYS* 3.1 25.3 + - + +
224B LEU* 3.2 44.8 - - + +
225B VAL* 5.4 1.7 + - - +
470C LEU* 3.4 32.1 - - + +
484C HIS* 5.1 11.7 - - - -
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Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LYS* 5.1 9.6 - - - +
213B ALA 3.1 24.5 + - - +
214B ASN* 3.4 22.7 - - - +
215B TYR 3.3 0.8 - - - -
216B GLN* 1.3 79.7 - - - +
218B SER* 1.3 58.4 + - - +
219B LYS 3.2 4.9 + - - -
220B SER 4.3 3.6 + - - -
225B VAL* 2.7 29.5 + - - +
226B ASP* 3.9 9.4 - - - +
227B LEU* 3.1 43.4 + - + +
228B SER* 4.2 5.2 + - - -
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LYS* 3.9 36.2 - - - +
197A ASN* 3.5 27.4 + - - -
200A LYS* 4.1 11.7 - - - -
252A LEU* 5.1 2.5 - - - -
214B ASN 4.9 0.2 + - - -
215B TYR 4.3 0.2 + - - -
216B GLN 3.3 0.2 - - - -
217B GLN* 1.3 76.4 - - - +
219B LYS* 1.3 69.4 + - - +
220B SER* 5.7 0.2 - - - -
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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
------------------------------------------------------------
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