Contacts of the helix formed by residues 246 - 268 (chain B) in PDB entry 4JYI
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 THR 246 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLY 4.1 0.2 + - - -
245B LEU* 1.3 75.2 - - - +
247B ILE* 1.3 65.2 + - - +
248B ALA* 4.1 4.0 - - - -
249B ASP* 2.9 34.2 + - - +
250B GLN* 3.0 12.0 + - - +
336B GLU* 3.1 27.1 + - + +
337B GLU* 4.3 23.0 + - + +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU 3.6 1.4 + - - +
246B THR* 1.3 71.8 - - - +
248B ALA* 1.3 63.2 + - - +
250B GLN* 3.3 25.4 + - - +
251B ILE* 3.0 32.6 + - + +
634F HIS* 3.4 44.6 - - + +
637F LEU* 4.3 26.2 - - + +
638F GLN* 5.1 8.3 - - + +
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Residues in contact with ALA 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B THR* 3.1 2.1 - - - +
247B ILE* 1.3 80.5 - - - +
249B ASP* 1.3 57.8 + - - +
251B ILE* 3.5 8.1 + - - +
252B THR* 2.9 32.5 + - - +
336B GLU* 3.9 30.5 - - + +
634F HIS* 5.7 0.6 - - - -
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Residues in contact with ASP 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 4.2 17.1 - - + +
246B THR* 2.9 20.8 + - - +
248B ALA* 1.3 75.9 - - - +
250B GLN* 1.3 61.6 + - - +
252B THR* 3.2 1.9 + - - -
253B LEU* 2.8 36.8 + - - +
334B ASP 4.4 1.7 - - - +
335B LEU* 3.7 20.5 - - + +
336B GLU* 2.8 32.9 + - - +
337B GLU* 3.0 34.4 + - - +
341B VAL* 4.6 3.1 - - - +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.3 53.3 + - + +
243B THR* 3.5 19.2 + - - +
245B LEU* 2.8 27.8 + - + +
246B THR 3.0 11.6 + - - +
247B ILE* 3.6 25.4 - - - +
249B ASP* 1.3 75.7 - - - +
251B ILE* 1.3 58.0 + - - +
253B LEU* 3.5 0.6 + - - -
254B LEU* 3.0 35.4 + - - +
637F LEU* 3.4 33.2 - - + +
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ILE* 3.0 24.0 + - + +
248B ALA* 3.7 7.0 - - - +
250B GLN* 1.3 73.7 - - - +
252B THR* 1.3 66.1 + - - +
254B LEU* 3.8 4.7 - - - +
255B LYS* 2.9 46.4 + - + +
630F HIS* 3.7 35.9 - - + -
633F LEU* 4.0 16.4 - - + -
634F HIS* 3.9 26.5 - - + +
637F LEU* 3.5 20.0 - - + -
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ALA 2.9 24.1 + - - -
249B ASP* 3.2 5.8 + - - -
251B ILE* 1.3 79.6 - - - +
253B LEU* 1.3 61.3 + - - +
255B LYS* 3.5 5.9 + - - +
256B ALA* 3.1 23.0 + - + +
332B ARG* 4.2 9.2 - - + -
333B GLN 3.5 24.9 - - - +
334B ASP* 4.2 12.1 + - + +
335B LEU* 3.7 22.2 - - + +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.1 12.8 - - + -
245B LEU* 3.7 29.8 - - + -
249B ASP 2.8 18.8 + - - +
250B GLN 3.9 3.6 - - - +
252B THR* 1.3 76.2 - - - +
254B LEU* 1.3 62.6 + - - +
256B ALA* 3.3 4.8 + - - +
257B ALA* 3.2 20.1 + - - +
327B LEU* 3.4 35.6 - - + +
328B ILE* 4.5 5.8 - - + -
329B CYS 3.3 27.8 - - - +
332B ARG* 3.6 11.8 + - + -
335B LEU* 3.9 14.6 - - + -
341B VAL* 4.2 13.7 - - + -
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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
----------------------------------------------------------
232B ILE* 4.3 20.9 - - + +
233B VAL* 4.2 20.6 - - + -
236B ALA* 3.8 17.5 - - + -
242B PHE* 4.1 9.0 - - + -
250B GLN 3.0 22.3 + - - +
251B ILE* 3.8 4.7 - - - +
253B LEU* 1.3 76.4 - - - +
255B LYS* 1.3 58.7 + - + +
258B CYS* 2.8 36.1 + - + +
327B LEU* 3.7 17.9 - - + -
406B MET* 3.8 18.8 - - + -
633F LEU* 4.6 4.3 - - + -
637F LEU* 3.9 33.2 - - + -
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Residues in contact with LYS 255 (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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251B ILE* 2.9 41.0 + - + +
252B THR* 3.9 5.2 - - - +
254B LEU* 1.3 77.3 - - - +
256B ALA* 1.3 61.6 + - - +
257B ALA 3.5 0.2 + - - -
258B CYS* 4.1 5.0 + - - +
259B LEU 5.3 1.0 + - - -
405B GLU 2.7 31.1 + - - +
406B MET* 3.2 37.3 + - - +
407B MET* 5.4 2.4 - - - +
408B GLU* 2.8 38.3 + - - +
630F HIS* 3.8 12.6 - - + +
633F LEU* 4.2 1.8 - - + -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B THR* 3.1 19.6 + - + +
253B LEU 3.7 3.1 - - - +
254B LEU 3.2 0.4 - - - -
255B LYS* 1.3 79.4 - - - +
257B ALA* 1.3 57.5 + - - +
258B CYS 3.7 0.4 - - - -
259B LEU 5.4 0.3 + - - -
260B ASP* 3.4 2.9 - - - +
332B ARG* 3.6 36.1 - - + +
378B ARG* 2.9 31.5 + - - +
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Residues in contact with ALA 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU 3.2 15.4 + - - +
254B LEU 3.7 0.2 - - - -
256B ALA* 1.3 77.2 - - - +
258B CYS* 1.3 65.9 + - - +
259B LEU 3.4 2.7 - - - -
260B ASP* 3.2 10.6 + - - +
261B ILE* 3.0 28.3 + - + +
326B CYS* 3.8 20.2 - - - +
327B LEU* 3.7 29.4 - - + -
332B ARG* 3.9 4.3 - - - +
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Residues in contact with CYS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 3.8 30.5 - - - -
232B ILE* 4.1 12.6 - - + +
254B LEU* 2.8 18.9 + - + +
255B LYS 4.1 3.5 + - - +
256B ALA 3.7 1.2 - - - -
257B ALA* 1.3 76.8 - - - +
259B LEU* 1.3 58.0 + - - +
261B ILE* 3.2 9.5 + - - +
262B LEU* 2.9 37.9 + - - +
327B LEU* 6.4 0.2 - - - -
406B MET* 3.8 33.9 - - + -
407B MET* 4.2 9.0 - - + -
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Residues in contact with LEU 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 LYS 5.3 0.6 + - - -
256B ALA 5.4 0.8 + - - +
257B ALA 3.4 0.4 - - - -
258B CYS* 1.3 76.8 - - - +
260B ASP* 1.3 67.3 + - - +
262B LEU* 3.2 9.5 + - + -
263B ILE* 2.9 35.1 + - + +
381B SER* 3.5 34.3 - - - +
384B GLY* 3.6 11.2 - - - +
385B ALA* 3.6 20.9 - - + +
388B VAL* 4.7 1.1 - - + -
407B MET* 4.1 22.1 - - + +
501B JYI 4.0 46.7 - - + -
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ALA 3.4 8.3 - - - +
257B ALA* 3.4 7.7 - - - +
259B LEU* 1.3 79.2 + - - +
261B ILE* 1.3 58.4 + - - +
263B ILE* 3.5 6.5 + - - +
264B LEU* 3.1 27.2 + - - +
326B CYS* 3.6 22.3 - - - -
374B ILE* 4.9 0.9 - - - +
377B LEU* 3.5 25.5 - - + +
378B ARG* 2.7 42.0 + - - +
381B SER* 2.9 27.3 + - - -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE* 3.7 37.2 - - + -
235B PHE* 5.5 4.9 - - + -
257B ALA* 3.0 21.3 + - + +
258B CYS 3.7 3.6 - - - +
259B LEU 3.2 0.2 - - - -
260B ASP* 1.3 73.7 - - - +
262B LEU* 1.3 61.2 + - - +
264B LEU* 3.4 6.7 + - + +
265B ARG* 2.8 47.6 + - + +
323B SER* 4.0 41.5 - - - +
326B CYS* 4.6 8.3 - - - -
327B LEU* 4.1 20.6 - - + -
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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
----------------------------------------------------------
225B ALA* 4.6 3.4 - - + +
228B CYS* 3.7 34.1 - - + -
229B ILE* 4.1 24.9 - - + -
232B ILE* 3.7 11.2 - - + -
258B CYS* 2.9 23.3 + - - +
259B LEU* 3.5 14.1 - - + +
261B ILE* 1.3 77.2 - - - +
263B ILE* 1.3 62.2 + - - +
265B ARG* 3.3 2.5 + - - +
266B ILE* 3.0 21.5 + - - +
407B MET* 5.0 2.9 - - + -
501B JYI 3.5 62.3 - - + -
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU* 2.9 28.0 + - + +
260B ASP* 3.6 5.2 - - - +
262B LEU* 1.3 73.7 - - - +
264B LEU* 1.3 67.4 + - - +
266B ILE* 3.4 1.0 - - - +
267B CYS* 3.0 39.1 + - - -
302B VAL* 4.8 5.6 - - + -
305B PHE* 4.4 4.5 - - + -
377B LEU* 3.6 18.6 - - + +
380B ILE* 3.7 33.7 - - + -
381B SER* 3.7 27.1 - - - +
501B JYI 3.8 31.0 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASP 3.1 15.1 + - - +
261B ILE* 3.7 6.7 - - - +
263B ILE* 1.3 79.2 - - - +
265B ARG* 1.3 65.6 + - + +
267B CYS* 3.3 3.2 + - - +
268B THR* 3.1 39.7 + - + +
305B PHE* 4.5 5.6 - - + -
309B LEU* 4.1 17.0 - - + -
314B MET* 5.5 3.6 - - + -
319B THR* 4.1 20.0 - - + +
322B LEU* 4.2 25.6 - - + -
323B SER* 3.5 31.6 - - - +
326B CYS* 6.5 0.2 - - + -
377B LEU* 3.9 22.6 - - + +
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Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B HIS* 4.3 13.8 + - + -
191B THR* 3.0 43.0 + - - -
192B PHE* 3.2 53.8 - - + +
228B CYS* 3.8 17.6 - - - -
231B LYS* 3.7 16.0 - - - +
232B ILE* 3.9 12.5 - - - +
235B PHE* 3.8 24.9 - - - +
261B ILE* 2.8 35.8 + - + +
262B LEU 3.7 4.3 - - - +
263B ILE 3.3 0.2 - - - -
264B LEU* 1.3 78.5 - - + +
266B ILE* 1.3 62.3 + - - +
268B THR* 2.5 26.0 + - - -
269B ARG* 3.5 3.3 + - - +
319B THR* 5.8 1.1 - - + -
323B SER* 5.4 3.4 + - - +
501B JYI 4.5 4.3 - - + -
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B LEU 3.0 12.6 + - - +
263B ILE* 3.4 10.3 - - - +
265B ARG* 1.3 76.7 - - - +
267B CYS* 1.3 70.1 + - - +
269B ARG* 3.2 20.8 + - - +
270B TYR 4.0 0.2 + - - -
277B MET* 4.0 28.7 - - + +
278B THR 3.7 25.4 - - - +
279B PHE* 3.8 28.7 - - + -
290B MET* 4.3 9.0 - - + -
295B PHE* 4.3 8.3 - - + -
302B VAL* 4.8 0.2 - - + -
501B JYI 3.7 43.9 - - + +
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Residues in contact with CYS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.0 26.7 + - - +
264B LEU 3.8 3.8 - - - +
266B ILE* 1.3 75.1 - - - +
268B THR* 1.3 60.0 + - - +
269B ARG 3.1 6.1 + - - -
270B TYR* 3.4 18.1 + - - +
277B MET* 4.3 4.0 - - - -
302B VAL* 3.6 42.6 - - - -
305B PHE* 3.7 17.0 - - + -
306B ALA* 3.9 24.9 - - + +
309B LEU* 4.0 15.4 - - + +
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Residues in contact with THR 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B HIS* 5.7 0.2 + - - -
192B PHE* 3.5 15.9 - - - -
195B LEU* 4.7 8.3 - - - +
264B LEU* 3.1 25.0 + - + +
265B ARG* 2.5 20.8 + - - -
267B CYS* 1.3 77.7 - - - +
269B ARG* 1.3 57.7 + - - +
270B TYR 3.4 4.0 + - - +
309B LEU* 4.3 7.6 - - + -
314B MET* 6.3 2.2 - - + -
319B THR* 4.1 30.7 - - + +
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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
------------------------------------------------------------
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