Contacts of the helix formed by residues 203 - 223 (chain B) in PDB entry 2F61
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 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASP* 4.1 27.1 - - + +
28A PRO* 6.2 1.3 - - + +
198B LYS 3.6 0.7 - - - +
199B GLY* 3.1 12.5 - - - -
200B GLN* 2.9 37.0 + - + +
201B PRO 3.3 0.4 + - - -
202B GLY* 1.3 80.7 - - - +
204B ILE* 1.3 65.5 + - + +
205B TYR* 3.1 13.6 + - + +
206B HIS* 2.9 25.5 + - - -
207B GLN* 2.9 22.0 + - - +
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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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27A ASP* 4.9 4.1 + - + +
30A THR* 3.3 37.2 - - + +
51A LEU* 5.1 9.2 - - + -
53A MET* 3.5 29.2 - - + -
142B PHE* 3.8 24.9 - - + -
203B ASP* 1.3 75.8 - - + +
205B TYR* 1.3 75.8 + - + +
207B GLN* 4.2 5.0 - - - +
208B THR* 2.6 41.9 + - - +
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Residues in contact with TYR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 6.4 1.1 - - + -
29A PRO 5.0 0.7 + - - -
30A THR* 3.1 37.7 - - + +
140B ASP* 5.5 1.2 + - - -
142B PHE* 3.8 18.5 - + - -
184B TRP 4.0 4.5 - - - -
185B LEU* 3.7 30.4 - - + +
197B LEU* 4.6 4.2 - - + +
198B LYS* 3.4 75.5 + - + +
199B GLY* 4.8 2.5 - - - -
203B ASP* 3.1 19.4 + - - +
204B ILE* 1.3 79.4 - - + +
206B HIS* 1.3 60.4 + - - +
208B THR* 3.4 3.1 + - - -
209B TRP* 3.0 27.9 + - - +
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Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 3.8 21.9 - - + +
198B LYS 2.9 25.4 + - - -
199B GLY 3.8 2.9 - - - -
200B GLN* 3.5 16.8 + - - -
201B PRO* 3.4 22.8 - - + +
202B GLY 3.9 1.8 - - - +
203B ASP* 2.9 22.9 + - - +
205B TYR* 1.3 72.7 - - - +
207B GLN* 1.3 61.8 + - - +
209B TRP* 3.4 5.2 + - - -
210B ALA* 2.9 28.6 + - - +
255B HIS* 2.9 33.8 - + - -
259B PHE* 3.7 14.8 - + + -
263B ASP* 3.1 23.3 - - - +
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Residues in contact with GLN 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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202B GLY* 3.9 11.8 - - - +
203B ASP 2.9 18.6 + - - +
204B ILE* 4.2 4.9 - - + +
206B HIS* 1.3 75.5 - - - +
208B THR* 1.3 57.6 + - - +
210B ALA* 3.3 4.3 + - - +
211B ARG* 2.9 36.5 + - + +
262B ARG 3.6 6.7 + - - -
263B ASP* 2.7 41.1 + - - +
266B PRO* 6.0 0.6 - - - +
267B THR* 3.9 14.3 + - - -
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Residues in contact with THR 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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142B PHE* 3.6 36.0 + - - +
144B LEU* 4.0 13.2 - - + +
184B TRP* 4.0 26.9 - - + -
185B LEU* 4.2 10.3 - - + -
204B ILE* 2.6 26.3 + - - +
205B TYR 3.6 4.7 - - - -
207B GLN* 1.3 75.1 - - - +
209B TRP* 1.3 65.2 + - - +
211B ARG* 3.1 12.0 + - - +
212B TYR* 3.0 20.3 + - - +
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Residues in contact with TRP 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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178B PRO* 3.9 29.2 - - + -
180B THR 3.6 9.2 - - - -
181B SER* 3.4 38.4 - - - -
182B PRO* 4.2 2.5 - - + -
185B LEU* 4.3 6.0 - - + +
197B LEU* 3.5 28.7 - - + -
205B TYR 3.0 17.4 + - - +
206B HIS 3.7 4.7 - - - +
207B GLN 3.4 0.2 - - - -
208B THR* 1.3 76.2 - - - +
210B ALA* 1.3 62.9 + - - +
212B TYR* 3.0 61.4 + + + +
213B PHE* 3.4 22.7 + + - -
232B ALA 4.9 1.4 + - - -
233B GLU* 4.4 2.3 + - - -
249B LEU* 3.5 21.8 - - + +
251B PHE* 4.4 1.4 - - - -
259B PHE* 3.4 28.5 - + - -
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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 HIS 2.9 18.1 + - - +
207B GLN* 3.5 6.5 - - - +
209B TRP* 1.3 78.6 - - - +
211B ARG* 1.3 60.4 + - - +
213B PHE* 3.2 24.8 + - - +
214B VAL* 3.5 3.6 + - - +
259B PHE* 4.5 4.0 - - + -
263B ASP* 3.9 17.9 - - + -
264B LEU* 4.0 10.8 - - - +
267B THR* 3.6 34.5 - - - +
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Residues in contact with ARG 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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142B PHE 2.6 30.9 + - - -
143B GLN* 2.9 34.7 + - - +
144B LEU* 3.7 13.6 - - + +
207B GLN* 2.9 22.1 + - + +
208B THR* 3.1 9.6 + - - +
210B ALA* 1.3 73.3 - - - +
212B TYR* 1.3 55.0 + - - +
214B VAL* 2.9 10.6 + - + +
215B LYS* 2.6 49.2 + - + +
267B THR* 4.4 12.1 - - + +
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Residues in contact with TYR 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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123B MET* 4.2 18.4 - - + -
124B ALA* 4.1 4.3 - - - +
134B THR* 3.5 9.4 - - - -
135B TYR* 2.8 55.3 + + + -
136B ALA* 4.1 7.0 - - + -
144B LEU* 4.0 13.7 - - + +
147B PHE* 3.8 17.4 - + - -
180B THR 4.8 2.4 + - - -
182B PRO* 3.7 28.3 - - + -
185B LEU* 5.8 0.9 - - + -
208B THR 3.0 10.8 + - - +
209B TRP* 3.0 50.9 - + + +
211B ARG* 1.3 77.2 - - - +
213B PHE* 1.3 61.2 + - - +
215B LYS* 3.4 4.5 + - - +
216B PHE* 2.9 20.1 + - - +
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Residues in contact with PHE 213 (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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123B MET* 3.8 27.4 - - + -
178B PRO* 3.8 16.6 - - + -
209B TRP* 3.5 44.4 - + - -
210B ALA 3.2 8.4 + - - +
211B ARG 3.1 0.4 - - - -
212B TYR* 1.3 79.6 - - + +
214B VAL* 1.3 62.6 + - - +
216B PHE* 3.1 6.6 + + - +
217B LEU* 3.0 27.6 + - + +
230B VAL* 4.3 22.9 - - + -
231B THR 3.4 25.8 - - - -
232B ALA 3.9 10.5 - - - -
259B PHE* 4.7 0.7 - + - -
264B LEU* 3.8 35.9 - - + -
268B LEU* 4.7 9.2 - - + -
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Residues in contact with VAL 214 (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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210B ALA 3.5 2.2 + - - +
211B ARG* 2.9 11.5 + - + +
213B PHE* 1.3 73.4 - - - +
215B LYS* 1.3 67.2 + - + +
217B LEU* 3.2 10.0 + - - +
218B ASP* 3.0 40.3 + - - +
267B THR* 3.6 30.7 - - + +
268B LEU* 4.5 12.3 - - + -
271B SER* 4.3 23.6 - - - +
273B HIS* 4.4 10.3 - - + -
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Residues in contact with LYS 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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143B GLN 4.3 2.5 + - - -
144B LEU* 3.0 51.3 + - + -
145B HIS* 5.1 1.8 + - - +
147B PHE* 3.6 42.3 + - + +
211B ARG* 2.6 34.1 + - - +
212B TYR 3.7 1.1 - - - +
214B VAL* 1.3 73.3 - - + +
216B PHE* 1.3 63.1 + - - +
218B ASP* 3.1 13.7 + - + +
219B ALA* 3.0 19.4 + - - +
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Residues in contact with PHE 216 (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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121B VAL* 4.6 5.2 - - + -
122B PRO 5.0 0.2 - - - -
123B MET* 3.8 33.4 - - + -
135B TYR* 3.5 31.2 - + + -
147B PHE* 3.4 12.7 - - + -
149B LEU* 4.7 1.8 - - + -
176B ALA* 3.6 23.6 - - + -
212B TYR 2.9 14.5 + - - +
213B PHE* 3.2 7.6 - + - +
215B LYS* 1.3 77.3 - - - +
217B LEU* 1.3 77.9 + - + +
218B ASP 3.1 0.5 + - - -
219B ALA* 3.2 3.7 + - - +
220B TYR* 3.1 52.9 + + - +
227B PHE* 3.6 31.6 - + - -
230B VAL* 5.7 0.9 - - + -
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Residues in contact with LEU 217 (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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213B PHE* 3.0 19.9 + - + +
214B VAL* 3.7 2.5 - - - +
216B PHE* 1.3 87.0 - - + +
218B ASP* 1.3 57.9 + - - +
220B TYR* 3.7 4.5 + - - +
221B ALA* 3.0 28.4 + - - +
225B LEU 4.7 1.0 - - - +
227B PHE* 3.8 38.5 - - + +
230B VAL* 4.3 16.4 - - + -
268B LEU* 3.9 22.7 - - + -
273B HIS* 3.5 45.6 - - + +
276B VAL* 4.3 10.1 - - + -
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Residues in contact with ASP 218 (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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214B VAL* 3.0 33.2 + - - +
215B LYS* 3.1 15.1 + - + +
217B LEU* 1.3 75.9 - - - +
219B ALA* 1.3 65.6 + - - +
221B ALA* 3.1 6.6 + - - +
222B GLU* 3.1 33.9 + - - +
272B THR* 4.5 4.2 + - - -
273B HIS* 2.8 27.3 + - - -
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Residues in contact with ALA 219 (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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147B PHE* 4.4 8.3 - - + -
148B SER* 6.3 0.2 - - - -
149B LEU* 3.5 33.9 - - + +
215B LYS 3.0 11.6 + - - +
216B PHE 3.2 6.9 + - - +
218B ASP* 1.3 76.0 - - - +
220B TYR* 1.3 61.9 + - - +
222B GLU* 3.2 23.6 + - - +
223B HIS* 3.2 22.6 - - + -
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Residues in contact with TYR 220 (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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121B VAL* 3.8 18.9 - - + +
149B LEU* 3.9 22.0 - - + -
153B ASP* 2.5 30.5 + - - +
157B LYS* 3.8 6.2 - - - +
158B ILE* 3.6 22.9 - - + +
161B ILE* 5.5 2.7 - - + -
174B LEU* 5.7 0.2 - - + -
216B PHE* 3.1 45.0 + + - +
217B LEU 4.1 3.6 - - - +
219B ALA* 1.3 77.1 - - - +
221B ALA* 1.3 60.4 + - - +
223B HIS* 3.1 13.9 + - - +
224B LYS 3.3 0.2 + - - -
225B LEU* 2.9 49.4 + - + +
227B PHE* 3.4 40.4 - + + -
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Residues in contact with ALA 221 (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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217B LEU 3.0 19.8 + - - +
218B ASP* 3.1 10.3 + - - +
220B TYR* 1.3 75.2 - - - +
222B GLU* 1.3 62.7 + - + +
224B LYS* 3.1 14.6 + - - +
225B LEU 3.6 9.2 + - - +
226B GLN* 3.7 22.2 + - - +
273B HIS* 4.4 9.9 - - + -
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Residues in contact with GLU 222 (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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218B ASP* 3.1 27.8 + - - +
219B ALA* 3.4 17.7 - - - +
220B TYR 3.1 0.4 - - - -
221B ALA* 1.3 74.1 - - - +
223B HIS* 1.3 64.7 + - + +
224B LYS* 3.0 16.1 + - - +
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Residues in contact with HIS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 4.3 5.3 - - + +
154B THR* 3.9 34.5 + - + +
158B ILE* 3.8 38.9 - - + +
162B HIS* 2.8 38.8 + - - +
219B ALA 3.2 23.3 + - - -
220B TYR 3.1 8.3 + - - +
222B GLU* 1.3 83.8 + - + +
224B LYS* 1.3 56.5 + - - +
225B LEU* 3.4 3.8 + - + +
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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