Contacts of the helix formed by residues 251 - 279 (chain B) in PDB entry 1LHR
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 251 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B GLN* 4.4 0.2 - - - -
217B GLN* 4.0 5.6 + - - +
248B HIS* 3.2 25.6 + - + +
249B PRO 3.4 0.6 - - - -
250B ASN* 1.3 81.8 - - - +
252B LEU* 1.3 65.0 + - - +
253B LYS* 3.2 26.4 + - - +
254B VAL* 3.3 22.2 + - + +
255B ALA* 3.2 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.9 24.0 - - + -
183B VAL 4.7 1.1 - - - +
184B VAL* 4.6 4.0 - - + -
203B GLY* 3.7 12.3 - - - -
204B SER* 3.4 43.5 - - - +
205B GLN* 3.4 24.7 + - + +
217B GLN* 3.6 14.8 + - + +
219B ILE* 4.0 8.7 - - + -
241B LEU* 5.0 0.7 - - + -
245B THR* 4.7 15.3 - - + -
248B HIS 5.3 0.2 - - - -
250B ASN 3.9 0.2 - - - -
251B ASN* 1.3 74.1 - - - +
253B LYS* 1.3 57.5 + - - +
255B ALA* 3.3 3.7 + - + -
256B CYS* 2.9 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 3.6 14.4 + - - +
219B ILE* 4.0 17.9 - - + +
251B ASN* 3.1 12.9 + - - +
252B LEU* 1.3 79.1 - - - +
254B VAL* 1.3 64.4 + - + +
256B CYS* 3.3 2.6 + - - +
257B GLU* 2.9 63.3 + - - +
308B GLN* 4.7 8.3 + - - +
309B ALA* 3.9 28.7 + - + +
311B VAL* 4.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B HIS* 3.8 21.3 - - + +
251B ASN* 3.3 31.2 + - - +
253B LYS* 1.3 80.6 - - + +
255B ALA* 1.3 60.0 + - - +
257B GLU* 3.8 15.4 - - + +
258B LYS* 3.0 54.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 4.7 3.1 - - + -
244B TRP* 3.8 17.9 - - + +
245B THR* 3.9 41.5 - - + +
248B HIS* 4.5 3.5 - - + +
251B ASN 3.2 16.6 + - - +
252B LEU* 3.6 6.5 - - - +
254B VAL* 1.3 78.9 - - - +
256B CYS* 1.3 55.2 + - - +
259B THR* 2.7 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B VAL* 4.4 14.1 - - - -
203B GLY* 5.3 0.4 - - - -
219B ILE* 3.7 16.8 - - + -
221B MET* 3.5 32.8 - - + -
237B PHE* 5.4 2.9 - - - -
241B LEU* 4.3 12.6 - - - -
252B LEU* 2.9 35.9 + - - +
253B LYS 3.8 3.1 - - - +
255B ALA* 1.3 76.2 - - - +
257B GLU* 1.3 59.7 + - - +
259B THR* 3.7 5.0 - - - -
260B VAL* 2.8 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B MET* 5.2 2.0 - - - -
253B LYS* 2.9 50.8 + - - +
254B VAL* 3.4 15.0 + - + +
256B CYS* 1.3 76.5 - - - +
258B LYS* 1.3 57.8 + - + +
260B VAL* 4.3 3.7 - - - +
261B SER* 2.8 35.4 + - - -
305B ILE* 4.2 15.3 - - + +
307B VAL* 3.8 20.1 - - + +
308B GLN* 3.3 15.4 - - - +
309B ALA* 2.9 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TRP* 3.6 53.1 + - + -
247B LYS* 5.8 0.8 - - - +
248B HIS* 3.0 31.5 + - + +
254B VAL* 3.0 29.3 + - + +
257B GLU* 1.3 75.8 - - - +
259B THR* 1.3 62.4 + - - +
262B ALA* 3.2 19.1 + - - +
303B PRO* 3.5 19.1 - - + +
305B ILE* 3.9 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B PHE* 3.8 49.1 - - + +
240B MET* 4.1 9.2 - - + +
241B LEU* 3.6 19.3 - - - +
244B TRP* 3.3 18.6 - - - +
255B ALA 2.7 22.5 + - - -
256B CYS* 3.2 6.7 + - - -
258B LYS* 1.3 75.2 - - - +
260B VAL* 1.3 65.5 + - - +
262B ALA* 3.3 7.2 + - - +
263B MET* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ALA* 5.6 1.1 - - + -
221B MET* 3.9 20.9 - - + -
223B MET* 3.7 36.8 - - + -
237B PHE* 4.1 19.7 - - + -
256B CYS* 2.8 22.6 + - - +
257B GLU* 4.3 2.2 - - - +
259B THR* 1.3 70.3 - - - +
261B SER* 1.3 66.3 + - - +
263B MET* 3.2 9.7 + - + +
264B HIS* 3.1 21.2 + - + +
307B VAL* 3.7 33.2 - - + -
402B ATP 4.4 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU 2.8 22.6 + - - -
258B LYS 3.9 4.3 - - - -
260B VAL* 1.3 79.1 - - - +
262B ALA* 1.3 62.6 + - - +
264B HIS* 3.1 4.9 + - - +
265B HIS* 3.0 28.4 + - - -
303B PRO* 4.3 4.7 - - - -
304B GLU 3.3 21.8 - - - -
305B ILE* 3.3 10.7 - - - +
306B VAL* 3.1 30.4 + - - -
307B VAL* 3.9 5.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B MET* 3.8 23.6 - - - -
244B TRP* 5.3 1.8 - - - +
258B LYS 3.2 12.1 + - - +
259B THR* 3.5 9.4 - - - +
261B SER* 1.3 80.4 - - - +
263B MET* 1.3 61.3 + - - +
265B HIS* 3.2 5.8 + - - +
266B VAL* 3.0 29.7 + - - +
299B ASP* 4.2 8.2 - - - +
300B ILE* 4.7 7.4 - - + +
303B PRO* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B MET* 6.4 0.2 - - - -
233B THR* 4.0 23.3 - - + +
236B LEU* 3.8 21.8 - - + -
237B PHE* 4.2 11.2 - - + -
240B MET* 3.6 20.2 - - + -
259B THR 3.1 18.3 + - - +
260B VAL* 3.5 10.5 - - - +
261B SER 3.2 0.2 - - - -
262B ALA* 1.3 76.0 - - - +
264B HIS* 1.3 59.1 + - - +
266B VAL* 3.3 3.6 + - + +
267B LEU* 2.9 56.0 + - + +
402B ATP 3.3 49.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B MET* 6.3 3.4 - - + -
224B HIS* 5.3 16.2 - - + +
226B VAL* 6.3 2.5 - - + -
260B VAL* 3.1 9.8 + - + +
261B SER 3.3 9.2 - - - +
263B MET* 1.3 81.5 - - - +
265B HIS* 1.3 68.5 + + - +
267B LEU* 3.9 5.1 - - - +
268B GLN* 3.0 58.1 + - + +
306B VAL* 3.9 29.4 - - + +
307B VAL* 5.5 6.1 - - + -
402B ATP 6.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B SER 3.0 24.1 + - - -
262B ALA* 3.2 5.4 + - - +
264B HIS* 1.3 86.4 + + - +
266B VAL* 1.3 62.4 + - - +
268B GLN* 3.5 4.9 + - - +
269B ARG* 3.2 29.3 + - - +
299B ASP* 3.5 33.1 + - + +
303B PRO* 4.0 9.6 - - + -
304B GLU* 2.8 47.8 + - + -
306B VAL* 3.9 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 4.2 25.4 - - + -
240B MET* 5.6 0.9 - - + -
262B ALA* 3.0 21.9 + - + +
263B MET* 3.8 5.2 - - - +
265B HIS* 1.3 77.5 - - + +
267B LEU* 1.3 54.6 + - + +
269B ARG* 3.4 4.2 + - - +
270B THR* 2.7 42.3 + - - +
291B LEU* 4.5 16.6 - - + -
292B ARG 4.6 6.7 - - - +
293B MET* 5.2 2.7 - - + +
296B SER* 3.7 32.0 + - - +
299B ASP* 5.4 1.1 - - + -
300B ILE* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 4.4 13.0 - - + +
230B PHE* 3.9 27.2 - - + -
233B THR* 4.3 7.4 - - + -
263B MET* 2.9 35.2 + - + +
264B HIS* 4.1 4.3 - - - +
266B VAL* 1.3 75.3 - - + +
268B GLN* 1.3 60.3 + - - +
270B THR* 3.5 2.6 - - - -
271B ILE* 2.8 33.4 + - - +
291B LEU* 3.9 26.0 - - + -
402B ATP 3.5 49.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 4.0 20.1 - - + +
264B HIS* 3.0 50.8 + - + +
265B HIS* 3.9 5.2 - - - +
267B LEU* 1.3 76.7 - - - +
269B ARG* 1.3 61.7 + - - +
271B ILE* 3.5 11.6 - - - +
272B LYS* 3.2 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B HIS 3.2 16.9 + - - +
266B VAL 3.6 4.7 - - - +
268B GLN* 1.3 77.4 - - - +
270B THR* 1.3 61.6 + - - +
272B LYS* 3.9 7.4 - - - +
273B CYS* 3.2 31.9 + - - +
292B ARG* 4.2 11.3 - - + +
295B GLN* 3.4 39.2 + - + +
296B SER* 3.0 26.4 + - - +
299B ASP* 2.7 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B PHE* 3.5 17.3 - - + -
266B VAL* 2.7 24.4 + - - +
267B LEU* 3.0 8.4 + - - -
269B ARG* 1.3 74.6 - - - +
271B ILE* 1.3 59.9 + - - +
273B CYS* 3.4 2.4 + - - +
274B ALA* 3.0 27.4 + - - +
289B LEU* 3.5 28.9 - - + +
290B GLU 3.7 12.8 - - - +
291B LEU* 3.8 7.6 - - - +
292B ARG* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B VAL* 3.9 23.3 - - + -
227B ASP 4.7 4.0 - - - +
228B ALA* 4.0 26.5 - - + -
230B PHE* 4.4 3.1 - - + -
267B LEU 2.8 18.1 + - - +
268B GLN* 3.5 25.8 - - - +
270B THR* 1.3 71.8 - - - +
272B LYS* 1.3 72.5 + - + +
274B ALA* 4.3 2.5 - - + -
275B LYS* 3.2 55.8 + - + +
284B PRO* 4.8 5.4 - - + -
289B LEU* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLN* 3.2 52.8 + - - +
269B ARG* 3.9 8.2 - - - +
270B THR 3.2 0.2 - - - -
271B ILE* 1.3 85.0 - - + +
273B CYS* 1.3 63.4 + - - +
275B LYS* 4.1 4.3 - - - +
276B ALA* 3.3 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ARG* 3.2 24.9 + - - +
270B THR 4.0 0.7 - - - +
271B ILE 3.4 0.2 - - - -
272B LYS* 1.3 78.3 - - - +
274B ALA* 1.3 64.3 + - - +
276B ALA* 3.5 5.8 + - - +
277B LYS* 3.1 29.8 + - + +
292B ARG* 3.6 35.2 - - - +
295B GLN* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR 3.0 18.1 + - - +
271B ILE* 3.9 4.3 - - + +
272B LYS 3.3 0.4 - - - -
273B CYS* 1.3 74.8 - - - +
275B LYS* 1.3 62.7 + - - +
277B LYS* 3.4 3.2 + - - +
278B SER* 2.8 27.8 + - - -
284B PRO* 3.8 11.6 - - + +
288B GLN* 3.4 29.0 - - - +
289B LEU* 3.5 24.7 - - + -
292B ARG* 4.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 5.6 5.7 + - - +
271B ILE* 3.2 42.7 + - + +
272B LYS* 4.1 4.3 - - - +
274B ALA* 1.3 76.7 - - - +
276B ALA* 1.3 63.2 + - - +
278B SER* 3.4 7.9 + - - -
279B GLY 3.3 26.2 + - - +
282B VAL 5.7 0.4 - - - -
283B LYS* 6.4 2.5 - - - +
284B PRO* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B LYS 3.3 15.8 + - - +
273B CYS* 3.8 7.4 - - - +
274B ALA 3.2 0.4 - - - -
275B LYS* 1.3 82.4 - - - +
277B LYS* 1.3 60.9 + - + +
278B SER 3.6 0.3 + - - -
279B GLY* 3.9 6.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLU* 5.3 14.5 + - - +
273B CYS* 3.1 20.9 + - + +
274B ALA* 3.9 5.2 - - - +
275B LYS 3.3 0.4 - - - -
276B ALA* 1.3 80.3 - - + +
278B SER* 1.3 57.1 + - - +
279B GLY 3.5 0.2 - - - -
288B GLN* 3.2 24.9 + - + +
292B ARG* 4.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ALA 2.8 15.9 + - - -
275B LYS* 3.4 10.4 + - - -
276B ALA 3.3 0.4 - - - -
277B LYS* 1.3 78.3 - - - +
279B GLY* 1.3 58.9 + - - +
282B VAL* 3.2 35.4 + - - +
283B LYS 4.5 2.7 - - - -
284B PRO* 3.6 16.2 - - - +
288B GLN* 3.1 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 3.3 17.8 + - - +
276B ALA 3.9 5.7 + - - -
277B LYS 3.5 2.6 - - - -
278B SER* 1.3 82.6 - - - +
280B GLU* 1.3 65.6 + - - -
281B GLY 3.7 1.2 + - - -
282B VAL* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
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