Contacts of the helix formed by residues 251 - 273 (chain B) in PDB entry 5Y7G
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).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B ARG* 4.9 14.5 - - - +
214B LEU* 5.4 1.0 - - - +
217B ASP* 3.2 25.3 + - - +
249B TYR* 3.9 1.9 - - - +
250B ALA* 1.3 80.0 - - - +
252B PRO* 1.3 81.1 - - - +
253B TRP* 3.4 25.8 + - - +
254B LEU* 3.4 27.6 + - + +
255B GLU* 3.1 20.1 + - - +
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Residues in contact with PRO 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ALA 3.9 6.3 - - - +
251B ASN* 1.3 96.3 - - - +
253B TRP* 1.3 55.8 + - - +
255B GLU* 3.2 8.6 + - + +
256B GLY* 3.0 24.3 + - - -
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Residues in contact with TRP 253 (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 GLY* 3.8 25.4 - - - -
211B GLY 4.4 16.2 - - - -
212B PHE* 4.2 26.7 - + - -
217B ASP* 6.5 0.4 - - + -
221B TYR* 4.0 16.8 - + - -
251B ASN* 3.4 18.5 + - - +
252B PRO* 1.3 78.6 - - - +
254B LEU* 1.3 74.4 + - + +
256B GLY* 3.2 4.4 + - - -
257B ARG* 3.1 56.2 + - + +
411B PHE* 6.1 3.1 - + - -
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Residues in contact with LEU 254 (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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212B PHE* 5.0 1.8 - - + -
217B ASP* 3.6 44.0 - - + +
220B ALA* 3.6 22.7 - - + -
221B TYR* 4.4 23.3 - - + +
224B LEU* 3.9 6.4 - - + +
249B TYR* 4.4 18.6 - - + -
251B ASN* 3.4 22.6 + - + +
252B PRO 3.2 0.4 - - - -
253B TRP* 1.3 98.8 - - + +
255B GLU* 1.3 57.0 + - - +
257B ARG* 2.9 13.1 + - + +
258B ARG* 2.9 26.7 + - - +
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PRO* 3.7 14.8 - - + +
249B TYR* 3.0 35.3 + - - +
251B ASN 3.1 13.1 + - - +
252B PRO* 3.2 11.8 + - + +
254B LEU* 1.3 75.4 - - - +
256B GLY* 1.3 62.9 + - - +
258B ARG* 2.4 42.2 + - - -
259B VAL* 3.0 32.4 + - + +
286B SER* 4.7 5.9 + - - +
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Residues in contact with GLY 256 (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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252B PRO 3.0 14.4 + - - -
253B TRP* 3.2 5.1 + - - -
254B LEU 3.2 0.4 - - - -
255B GLU* 1.3 78.7 - - - +
257B ARG* 1.3 63.0 - - - +
259B VAL* 3.3 4.3 + - - +
260B LYS* 2.9 24.0 + - - +
287B HIS* 5.1 2.1 - - - -
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Residues in contact with ARG 257 (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 ASN* 5.3 3.6 - - - +
184B TRP* 6.1 0.8 - - - -
221B TYR* 2.5 46.4 + - + -
224B LEU* 4.0 16.8 - - + -
253B TRP* 3.1 46.9 + - + +
254B LEU* 2.9 14.5 + - + +
256B GLY* 1.3 74.1 - - - +
258B ARG* 1.3 57.9 + - - +
260B LYS* 3.1 14.8 + - - +
261B LEU* 2.9 27.4 + - - +
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Residues in contact with ARG 258 (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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224B LEU* 3.7 16.5 - - + +
245B PRO* 3.9 32.5 + - + -
246B GLY* 4.6 11.7 + - - -
247B GLU 4.2 3.6 + - - -
248B PRO* 4.0 21.3 - - - +
249B TYR* 4.0 23.6 - - + -
254B LEU 2.9 12.1 + - - +
255B GLU* 2.4 49.4 + - - +
256B GLY 3.2 0.2 - - - -
257B ARG* 1.3 75.4 - - - +
259B VAL* 1.3 71.8 + - - +
261B LEU* 2.9 19.9 + - - +
262B LEU* 2.9 38.2 + - + +
284B GLN* 4.5 11.7 + - - +
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Residues in contact with VAL 259 (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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255B GLU* 3.0 22.9 + - + +
256B GLY* 4.1 3.8 - - - +
258B ARG* 1.3 103.2 - - - +
260B LYS* 1.3 57.4 + - - +
262B LEU* 3.4 16.6 + - + +
263B PHE* 2.9 27.5 + - - +
284B GLN 4.1 3.1 - - - +
285B SER* 3.5 3.0 + - - +
286B SER* 3.5 23.8 - - - +
287B HIS* 3.1 41.5 - - + +
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Residues in contact with LYS 260 (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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228B ARG* 5.8 3.7 - - - +
256B GLY 2.9 13.8 + - - +
257B ARG* 3.4 17.9 - - - +
259B VAL* 1.3 79.5 - - - +
261B LEU* 1.3 57.5 + - - +
263B PHE* 3.2 3.6 - - + +
264B GLN* 2.9 52.3 + - + +
287B HIS* 3.7 31.4 - - + +
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Residues in contact with LEU 261 (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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224B LEU* 3.9 24.2 - - + +
227B CYS* 3.7 14.6 - - + -
228B ARG* 3.6 26.9 - - + -
244B LEU* 3.7 30.5 - - + -
257B ARG 2.9 11.3 + - - +
258B ARG* 2.9 10.2 + - - +
260B LYS* 1.3 73.0 - - - +
262B LEU* 1.3 67.1 + - - +
264B GLN* 2.9 23.7 + - + +
265B PHE* 2.9 51.5 + - + +
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Residues in contact with LEU 262 (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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241B LEU* 4.9 1.8 - - + -
244B LEU* 4.6 19.5 - - + +
245B PRO 5.2 6.3 - - - +
258B ARG* 2.9 42.0 + - + +
259B VAL* 3.5 17.9 - - + +
261B LEU* 1.3 74.9 - - - +
263B PHE* 1.3 63.0 + - - +
265B PHE* 3.5 6.1 + - - +
266B ALA* 3.0 24.7 + - - +
281B LEU* 4.2 28.5 - - + +
284B GLN* 3.4 40.8 - - + +
285B SER* 4.3 6.1 - - - -
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Residues in contact with PHE 263 (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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259B VAL 2.9 13.7 + - - +
260B LYS* 3.2 14.8 - - + +
262B LEU* 1.3 77.0 - - - +
264B GLN* 1.3 60.9 + - + +
266B ALA* 3.0 9.9 + - - +
267B GLN* 2.8 63.7 + - + +
282B TYR* 4.0 12.9 - + - -
285B SER* 3.6 21.7 + - - +
287B HIS* 3.9 26.9 - + + -
288B PRO 4.8 1.3 - - - -
289B GLY* 3.8 7.6 - - - -
290B ALA* 3.8 27.1 - - + -
293B ARG* 3.9 17.3 - - + -
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Residues in contact with GLN 264 (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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228B ARG* 3.7 45.2 + - + +
231B PHE* 5.3 4.2 - - + -
260B LYS* 2.9 46.5 + - + +
261B LEU* 2.9 20.7 + - + +
263B PHE* 1.3 76.6 - - + +
265B PHE* 1.3 68.5 + - + +
267B GLN* 3.0 26.8 + - - +
268B HIS* 3.0 22.2 + - - +
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Residues in contact with PHE 265 (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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227B CYS* 3.8 13.5 - - + -
228B ARG* 4.5 2.0 - - + -
231B PHE* 3.3 46.7 - + + -
237B LEU* 4.9 9.3 - - + +
240B LEU* 4.0 24.2 - - + -
241B LEU* 3.5 33.7 - - + -
244B LEU* 3.7 23.8 - - + -
261B LEU* 2.9 41.6 + - + +
262B LEU 3.8 3.4 - - - +
264B GLN* 1.3 78.8 - - + +
266B ALA* 1.3 62.9 + - - +
268B HIS* 3.2 6.9 + - - +
269B CYS* 3.0 27.3 + - - -
281B LEU* 4.8 1.3 - - + -
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Residues in contact with ALA 266 (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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262B LEU 3.0 15.3 + - - +
263B PHE* 3.4 9.0 - - - +
265B PHE* 1.3 75.6 - - - +
267B GLN* 1.3 62.1 + - - +
269B CYS* 3.3 9.7 - - - +
270B GLU* 3.3 15.4 + - - +
278B ALA* 3.7 11.6 - - - +
281B LEU* 3.8 30.2 - - + +
282B TYR* 3.5 30.0 + - + -
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Residues in contact with GLN 267 (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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263B PHE* 2.8 46.5 + - + +
264B GLN* 3.0 33.5 + - - +
266B ALA* 1.3 77.0 - - - +
268B HIS* 1.3 59.5 + - - +
270B GLU* 3.2 17.6 + - - +
271B LYS* 3.3 11.0 + - - +
282B TYR* 3.6 13.2 - - - +
293B ARG* 6.1 0.9 - - - +
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Residues in contact with HIS 268 (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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231B PHE* 3.1 46.2 - + + -
237B LEU* 4.1 11.1 - - + +
264B GLN 3.0 9.7 + - - +
265B PHE 3.9 4.5 - - - +
267B GLN* 1.3 72.8 - - - +
269B CYS* 1.3 60.8 + - - +
271B LYS* 2.7 35.7 + - + +
272B GLN* 2.9 48.7 + - + +
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Residues in contact with CYS 269 (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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237B LEU* 3.9 22.2 - - - +
241B LEU* 5.4 1.6 - - - -
265B PHE* 3.0 18.9 + - - -
266B ALA* 3.3 16.4 - - - +
267B GLN 3.2 0.2 - - - -
268B HIS* 1.3 75.4 + - - +
270B GLU* 1.3 50.8 + - - +
272B GLN* 2.9 9.2 + - - +
273B ARG 2.6 32.1 + - - -
274B ASP* 2.9 33.8 + - + +
277B LEU* 4.3 22.7 - - - -
278B ALA* 3.8 5.8 - - + -
281B LEU* 4.4 7.9 - - - -
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Residues in contact with GLU 270 (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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266B ALA 3.3 4.2 + - - +
267B GLN* 3.2 12.7 + - - +
269B CYS* 1.3 78.0 - - - +
271B LYS* 1.3 60.4 + - - +
273B ARG* 3.3 9.0 + - - +
274B ASP 4.5 0.2 + - - -
275B PHE* 3.5 29.6 - - + -
278B ALA* 4.6 1.3 - - + -
282B TYR* 2.4 34.4 + - - +
293B ARG* 2.8 34.5 + - - +
296B ARG* 4.5 2.1 - - - +
297B SER* 3.6 25.1 + - - +
300B ARG* 3.1 34.7 + - - +
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Residues in contact with LYS 271 (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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267B GLN 3.3 10.8 + - - +
268B HIS* 2.7 37.4 + - + +
270B GLU* 1.3 74.3 + - - +
272B GLN* 1.3 61.3 + - - +
273B ARG* 3.2 6.5 + - - +
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Residues in contact with GLN 272 (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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237B LEU* 4.8 8.1 - - + -
268B HIS* 2.9 47.4 + - + +
269B CYS* 2.9 10.8 + - - +
271B LYS* 1.3 79.0 - - - +
273B ARG* 1.3 71.3 + - - +
274B ASP* 3.6 7.1 + - + +
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Residues in contact with ARG 273 (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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269B CYS 2.6 10.3 + - - -
270B GLU 3.3 3.5 + - - +
271B LYS 3.2 9.4 - - - +
272B GLN* 1.3 77.6 - - - +
274B ASP* 1.3 56.0 + - - +
275B PHE* 3.0 68.1 + - - -
300B ARG* 3.4 25.7 + - - +
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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