Contacts of the helix formed by residues 231 - 255 (chain B) in PDB entry 3E4E
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 SER 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.8 27.7 - - - +
212B THR* 4.6 2.6 + - - -
214B TRP* 3.7 21.8 - - - +
215B LEU* 3.7 12.4 - - - +
230B GLY* 1.3 70.1 - - - -
232B HIS* 1.3 62.0 + - - +
233B ARG 3.1 0.9 - - - -
234B LYS* 3.3 18.6 + - - +
235B VAL* 3.3 11.1 + - - +
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA* 5.7 0.2 - - - +
214B TRP* 3.0 24.0 + + - +
215B LEU* 4.1 15.0 - - + -
218B TYR* 3.8 51.6 - + + -
225B LEU 3.1 16.3 + - - -
226B HIS 3.3 14.3 + - - -
228B LEU 3.1 28.0 + - - -
229B PRO 3.5 16.2 - - - -
230B GLY* 3.3 8.6 - - - -
231B SER* 1.3 80.9 + - - +
233B ARG* 1.3 67.4 + - + +
235B VAL* 3.1 2.9 + - - +
236B ILE* 3.0 32.4 + - + +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 4.0 7.6 + - - +
227B TYR* 3.4 34.4 + - - +
228B LEU 3.3 19.9 + - - -
229B PRO* 4.3 9.5 - - - +
230B GLY 2.8 19.5 + - - +
232B HIS* 1.3 84.5 - - + +
234B LYS* 1.3 61.6 + - - +
236B ILE* 4.1 8.2 - - + +
237B LYS* 2.9 52.7 + - + +
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 5.6 5.0 - - - +
201B TYR* 6.2 1.3 - - - -
205B GLU* 3.1 37.0 - - - +
209B LEU* 3.9 9.0 - - + -
230B GLY 4.1 0.6 + - - -
231B SER* 3.3 17.4 + - - +
232B HIS 3.1 0.2 - - - -
233B ARG* 1.3 78.1 - - - +
235B VAL* 1.3 65.3 + - - +
237B LYS* 3.4 34.7 + - - +
238B ASN* 2.8 43.7 + - - +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA* 3.8 24.2 - - + +
106B PHE* 5.0 0.7 - - + -
206B ASN* 3.4 21.5 - - - +
209B LEU* 3.8 15.7 - - + -
210B LEU* 4.4 16.8 - - + -
215B LEU* 3.6 38.1 - - + -
231B SER 3.3 3.1 + - - +
232B HIS 3.1 7.6 + - - +
234B LYS* 1.3 77.0 - - - +
236B ILE* 1.3 53.4 + - - +
238B ASN* 3.1 3.1 + - - +
239B VAL* 2.8 44.1 + - + +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO 4.8 2.9 - - - +
105B ALA* 3.7 25.4 - - - +
218B TYR* 3.7 18.2 - - + +
226B HIS* 3.4 33.4 - - + +
232B HIS* 3.0 24.9 + - + +
233B ARG* 4.1 8.7 - - + +
235B VAL* 1.3 72.4 - - - +
237B LYS* 1.3 69.9 + - + +
239B VAL* 2.9 6.4 + - + +
240B ALA* 2.9 25.9 + - + +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG* 2.9 50.1 + - + +
234B LYS* 3.7 34.3 - - - +
236B ILE* 1.3 73.7 - - + +
238B ASN* 1.3 57.0 + - - +
240B ALA* 3.1 7.9 + - - +
241B GLU* 2.8 32.4 + - - +
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Residues in contact with ASN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ARG* 4.9 0.7 + - - -
202B LEU* 3.4 31.6 + - + +
205B GLU* 2.8 37.0 + - - +
206B ASN* 3.0 33.6 + - - +
209B LEU* 5.0 0.2 - - - +
234B LYS* 2.8 44.9 + - - +
235B VAL* 4.3 0.4 - - - +
237B LYS* 1.3 69.4 - - - +
239B VAL* 1.3 64.9 + - - +
241B GLU* 3.2 6.4 + - - +
242B VAL* 3.0 26.5 + - - +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 3.9 17.7 - - - +
106B PHE* 3.7 27.1 - - + -
108B ALA* 4.0 15.0 - - + -
109B HIS* 3.7 34.2 + - + +
206B ASN* 3.9 11.4 - - - +
235B VAL* 2.8 26.7 + - + +
236B ILE* 3.5 7.9 - - + +
238B ASN* 1.3 73.7 - - - +
240B ALA* 1.3 59.6 + - - +
242B VAL* 3.2 6.8 + - - +
243B LYS* 3.0 26.8 + - + +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 5.4 6.5 - - + +
236B ILE* 2.9 16.1 + - + +
237B LYS* 3.6 10.3 - - - +
239B VAL* 1.3 77.9 - - - +
241B GLU* 1.3 56.8 + - - +
243B LYS* 3.5 9.5 + - - +
244B GLU* 3.0 28.5 + - - +
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Residues in contact with GLU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 4.5 12.2 + - - +
198B ARG* 2.8 53.5 + - - +
199B LEU* 5.4 0.7 - - - +
202B LEU* 3.7 15.4 - - + +
237B LYS* 2.8 16.8 + - - +
238B ASN* 3.6 7.0 - - - +
239B VAL 3.2 0.2 - - - -
240B ALA* 1.3 74.6 - - - +
242B VAL* 1.3 63.5 + - - +
244B GLU* 3.4 8.0 + - + +
245B TYR* 3.1 23.0 + - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B HIS* 6.1 1.3 - - - +
199B LEU* 5.0 7.4 - - + -
202B LEU* 3.9 22.0 - - + +
203B PHE* 4.0 34.1 - - + -
206B ASN* 5.1 4.5 - - - +
238B ASN 3.0 15.0 + - - +
239B VAL* 3.6 8.3 - - - +
241B GLU* 1.3 73.0 - - - +
243B LYS* 1.3 60.5 + - - +
245B TYR* 3.3 6.2 + - - +
246B VAL* 3.0 34.0 + - + +
294B ALA* 4.4 21.3 - - + +
297B PHE* 4.9 2.5 - - + -
298B PHE* 5.7 1.8 - - + -
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Residues in contact with LYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA* 2.8 44.5 + - + +
109B HIS* 4.5 17.0 + - + +
112B ARG* 3.6 7.5 - - - +
239B VAL 3.0 10.6 + - - +
240B ALA* 3.7 10.3 - - - +
242B VAL* 1.3 73.9 - - - +
244B GLU* 1.3 57.9 + - - +
246B VAL* 3.0 5.3 + - - +
247B SER* 2.6 40.1 + - - -
287B ASP* 3.2 28.3 + - - -
290B THR* 4.2 12.4 - - - +
291B VAL* 3.6 14.1 - - + -
294B ALA* 4.8 8.3 - - + -
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ALA 3.0 17.7 + - - +
241B GLU* 3.5 9.9 - - + +
243B LYS* 1.3 74.7 - - - +
245B TYR* 1.3 64.1 + - - +
247B SER* 3.3 8.8 + - - -
248B GLU* 3.1 45.7 + - + +
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Residues in contact with TYR 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.8 4.9 - + - -
187B LYS* 3.8 6.2 + - - +
189B PHE* 3.3 26.7 - + - -
195B LYS* 4.0 41.5 - - + +
199B LEU* 3.7 36.6 - - + -
241B GLU 3.1 16.2 + - - +
242B VAL* 3.9 3.1 - - + +
243B LYS 3.2 0.2 - - - -
244B GLU* 1.3 75.8 - - - +
246B VAL* 1.3 76.0 + - + +
248B GLU* 4.9 2.0 - - - -
249B ARG* 2.9 72.4 + - + +
297B PHE* 4.4 9.6 - + - -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.0 9.6 - - + -
242B VAL* 3.0 20.3 + - + +
243B LYS* 3.8 4.0 - - - +
245B TYR* 1.3 80.4 - - + +
247B SER* 1.3 65.8 + - - +
249B ARG* 2.9 17.8 + - - +
250B VAL* 3.0 14.6 + - + +
290B THR* 3.6 27.4 - - - +
293B VAL* 3.5 26.0 - - + -
294B ALA* 4.1 15.7 - - - +
297B PHE* 3.9 28.3 - - + -
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LYS* 2.6 23.9 + - - -
244B GLU* 3.3 13.3 + - - -
246B VAL* 1.3 72.4 - - - +
248B GLU* 1.3 63.8 + - - +
250B VAL* 3.0 5.4 + - - +
251B LYS* 3.0 41.2 + - - +
290B THR* 3.6 23.8 - - - +
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Residues in contact with GLU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 3.1 34.1 + - + +
245B TYR* 4.7 1.1 - - - -
246B VAL 3.3 0.2 - - - -
247B SER* 1.3 77.9 + - - +
249B ARG* 1.3 78.5 + - - +
251B LYS* 2.7 35.3 + - - +
252B GLU* 2.9 34.2 + - - +
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 3.6 39.0 - - + -
187B LYS* 4.0 17.4 - - - +
245B TYR* 2.9 74.0 + - - +
246B VAL* 2.9 12.2 + - - +
248B GLU* 1.3 98.9 - - - +
250B VAL* 1.3 52.1 + - - +
252B GLU* 3.3 39.4 + - - +
253B HIS* 2.7 41.9 + - + -
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Residues in contact with VAL 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 5.4 0.9 - - + -
246B VAL* 3.0 25.6 + - + +
247B SER 3.0 7.6 + - - +
249B ARG* 1.3 75.6 - - + +
251B LYS* 1.3 60.6 + - + +
252B GLU 3.3 0.2 - - - -
253B HIS* 2.9 9.7 + - - +
254B HIS* 2.9 26.5 + - - +
266B THR* 4.1 16.6 - - - +
270B LEU* 3.9 12.3 - - + +
286B MET* 4.1 21.3 - - + +
289B ILE* 4.3 19.5 - - + +
290B THR* 3.7 29.4 - - + -
293B VAL* 5.0 2.9 - - + -
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER* 3.0 26.9 + - - +
248B GLU* 2.7 36.8 + - - +
250B VAL* 1.3 74.3 - - + +
252B GLU* 1.3 56.9 + - - +
254B HIS* 3.2 8.1 + - - +
255B GLN* 3.0 34.3 + - - +
286B MET* 3.9 20.0 - - + -
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Residues in contact with GLU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 5.6 3.1 + - - -
248B GLU* 2.9 19.1 + - - +
249B ARG* 3.3 42.8 + - - +
251B LYS* 1.3 74.0 - - - +
253B HIS* 1.3 60.8 + - - +
255B GLN* 4.5 11.7 - - - +
256B SER* 3.7 17.2 + - - -
263B ARG* 5.3 0.5 + - - -
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Residues in contact with HIS 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.0 21.1 - + + -
249B ARG* 2.7 26.5 + - + +
250B VAL 2.9 12.4 + - - +
252B GLU* 1.3 83.3 + - + +
254B HIS* 1.3 59.5 + - - +
255B GLN 3.5 0.2 - - - -
256B SER 3.5 0.6 + - - -
257B LEU* 3.0 24.8 + - - +
263B ARG* 3.2 23.6 + - - +
264B ASP* 2.8 40.5 + - - -
266B THR* 3.4 22.4 - - + +
267B ASP* 3.8 11.5 - - - +
270B LEU* 3.6 12.3 - - + -
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Residues in contact with HIS 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL 2.9 11.3 + - - +
251B LYS* 3.6 11.7 - - - +
253B HIS* 1.3 71.6 - - - +
255B GLN* 1.3 56.1 + - - +
256B SER 2.8 5.3 + - - -
257B LEU* 2.7 36.5 + - + +
270B LEU* 3.9 27.6 - - + +
273B MET* 5.6 4.7 - - - +
274B GLU* 3.4 24.1 + - - -
286B MET* 4.4 21.5 - - + +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLN* 5.8 2.1 + - - -
251B LYS 3.0 18.7 + - - +
252B GLU* 4.7 11.2 - - - +
254B HIS* 1.3 77.8 + - - +
256B SER* 1.3 56.9 + - - -
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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