Contacts of the helix formed by residues 248 - 270 (chain B) in PDB entry 5TIN
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 ALA 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ALA* 3.8 29.2 - - + -
250A PRO* 5.2 2.2 - - + -
244B ILE* 4.1 6.7 - - + -
245B ASN* 3.0 21.0 + - + +
247B ASP* 1.3 74.9 - - - +
249B ALA* 1.3 65.3 + - - +
250B PRO* 3.4 5.8 - - - -
251B ALA* 3.3 9.5 + - + -
252B ARG* 3.1 23.8 + - - +
301B TYR* 4.2 1.3 - - - -
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B MET 5.2 0.2 - - - +
247B ASP 3.0 11.3 + - - +
248B ALA* 1.3 71.3 - - - +
250B PRO* 1.4 67.2 - - + +
252B ARG* 3.8 0.5 - - - -
253B VAL* 2.9 34.9 + - + +
301B TYR* 3.1 25.9 - - + +
305B ASN* 4.1 9.9 - - - +
244C ILE* 5.3 0.9 - - + -
248C ALA* 3.9 24.0 - - + -
251C ALA* 4.2 5.2 - - + -
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Residues in contact with PRO 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PRO* 4.1 28.0 - - + +
247B ASP 4.9 1.1 - - - +
248B ALA* 3.6 4.3 - - - -
249B ALA* 1.4 96.1 - - + +
251B ALA* 1.3 56.4 + - - +
253B VAL* 4.3 0.4 - - + +
254B ALA* 3.0 30.3 + - - +
248C ALA* 5.2 3.1 - - + -
250C PRO* 4.2 33.7 - - + -
251C ALA* 4.0 18.3 - - + +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 4.1 1.3 - - + -
250A PRO* 4.0 25.6 - - + +
253A VAL* 3.8 27.3 - - + +
244B ILE* 4.4 4.9 - - + -
248B ALA* 3.3 23.3 + - + +
249B ALA 3.2 0.4 - - - -
250B PRO* 1.3 80.4 - - - +
252B ARG* 1.3 58.5 + - - +
254B ALA* 3.4 4.6 + - - +
255B LEU* 3.0 32.2 + - - +
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Residues in contact with ARG 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 3.0 61.4 + - - +
242B PHE* 3.6 6.5 - - - +
244B ILE* 3.1 24.5 + - + -
245B ASN 3.5 21.9 + - - -
246B MET* 4.2 1.6 - - - +
248B ALA 3.1 8.8 + - - +
249B ALA 4.1 0.2 - - - +
251B ALA* 1.3 77.1 - - - +
253B VAL* 1.3 63.9 + - - +
255B LEU* 3.6 6.4 + - - +
256B GLY* 3.2 17.7 + - - -
298B LEU* 4.7 3.3 - - - +
300B GLU* 3.9 7.1 + - - -
301B TYR* 3.0 60.7 - - + +
323B ASP* 2.6 41.7 + - - -
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ALA* 2.9 20.8 + - + +
250B PRO 4.3 1.6 - - - +
252B ARG* 1.3 75.1 - - - +
254B ALA* 1.3 58.7 - - - +
256B GLY* 3.2 0.9 + - - -
257B ILE* 2.9 48.7 + - + +
298B LEU* 4.4 14.2 - - + +
301B TYR* 3.9 22.4 - - + -
244C ILE* 4.4 15.3 - - + -
251C ALA* 3.8 34.3 - - + +
254C ALA* 5.2 1.1 - - + -
255C LEU* 4.0 12.6 - - + -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 5.2 0.9 - - + -
254A ALA* 6.0 3.6 - - + -
257A ILE* 3.8 15.0 - - + -
250B PRO 3.0 21.8 + - - +
251B ALA* 3.6 6.5 - - - +
253B VAL* 1.3 78.3 - - - +
255B LEU* 1.3 58.9 + - - +
257B ILE* 4.6 7.9 - - - -
258B THR* 2.8 36.3 + - + +
254C ALA* 6.0 3.6 - - + -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A VAL* 4.0 17.0 - - + -
257A ILE* 3.7 15.2 - - + +
298A LEU* 4.9 1.3 - - + -
237B LEU* 3.2 44.4 - - + +
238B SER* 5.0 3.5 - - - +
240B VAL* 3.6 23.3 - - + -
241B SER* 3.7 27.1 - - - +
244B ILE* 4.4 9.0 - - + -
251B ALA 3.0 18.3 + - - +
252B ARG* 3.6 10.3 - - - +
254B ALA* 1.3 75.7 - - - +
256B GLY* 1.3 57.4 + - - +
258B THR* 3.5 1.0 + - - -
259B THR* 2.8 34.0 + - + +
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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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238B SER* 6.1 0.7 - - - -
241B SER* 6.0 0.4 - - - -
252B ARG 3.2 8.7 + - - -
253B VAL 3.2 6.5 + - - -
255B LEU* 1.3 76.1 - - - +
257B ILE* 1.3 64.6 + - - +
259B THR* 3.2 4.5 + - - -
260B VAL* 3.1 30.0 + - - +
294B VAL 5.1 1.1 - - - -
297B ALA* 6.3 0.9 - - - -
298B LEU* 4.0 30.1 - - - -
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Residues in contact with ILE 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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253B VAL* 2.9 42.7 + - + +
254B ALA* 3.9 6.3 - - - +
256B GLY* 1.3 72.2 - - - +
258B THR* 1.3 65.3 + - + +
260B VAL* 3.6 4.3 - - - +
261B LEU* 2.8 43.6 + - + +
298B LEU* 4.4 3.5 - - + +
237C LEU* 4.7 9.2 - - + -
254C ALA* 3.8 13.7 - - + +
255C LEU* 3.7 43.5 - - + +
258C THR* 3.3 33.0 - - + +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 3.3 34.3 - - + +
258A THR* 6.4 0.4 - - + -
261A LEU* 3.9 13.5 - - + -
237B LEU* 5.3 0.7 - - - +
254B ALA* 2.8 25.8 + - + +
255B LEU* 3.5 6.2 + - - -
257B ILE* 1.3 82.8 - - + +
259B THR* 1.3 62.1 + - - +
261B LEU* 4.1 5.1 - - + +
262B THR* 2.8 36.3 + - - -
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.9 0.2 - - - -
234B ILE* 3.6 33.9 - - + +
237B LEU* 3.9 22.9 - - + -
238B SER* 3.9 20.9 - - - +
255B LEU 2.8 23.2 + - - +
256B GLY* 3.2 8.8 + - - -
258B THR* 1.3 76.7 + - - +
260B VAL* 1.3 60.4 + - - +
262B THR* 4.6 0.2 - - - -
263B MET* 3.0 31.4 + - - +
294B VAL* 3.3 21.3 + - - +
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Residues in contact with VAL 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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256B GLY 3.1 20.5 + - - +
257B ILE* 3.6 4.5 - - - +
259B THR* 1.3 75.8 + - - +
261B LEU* 1.3 64.7 + - + +
263B MET* 3.3 5.2 + - - +
264B THR* 3.1 27.2 + - + +
291B LEU* 3.8 8.8 - - + +
294B VAL* 3.4 21.3 - - + +
295B PHE* 3.8 41.1 - - + -
298B LEU* 4.6 8.7 - - + -
233C LEU* 5.8 3.1 - - + +
234C ILE* 5.3 2.7 - - + -
237C LEU* 4.1 20.2 - - + -
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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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257B ILE* 2.8 41.5 + - + +
258B THR* 4.1 5.6 - - + +
260B VAL* 1.3 70.1 - - - +
262B THR* 1.3 65.0 + - - +
264B THR* 2.6 22.1 + - - +
265B THR* 3.2 13.2 + - + +
234C ILE* 3.5 28.7 - - + -
237C LEU* 4.2 12.6 - - + -
258C THR* 3.8 17.0 - - + +
259C THR 5.8 0.2 - - - +
262C THR* 3.4 31.0 - - + +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 3.4 27.0 - - + +
264A THR* 5.2 5.4 - - - +
234B ILE* 3.7 30.5 - - + -
258B THR 2.8 24.3 + - - -
259B THR* 4.0 3.8 - - - -
261B LEU* 1.3 76.4 - - - +
263B MET* 1.3 57.3 + - - +
265B THR* 3.0 11.1 + - - +
266B GLN* 2.8 38.3 + - - +
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Residues in contact with MET 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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231B SER* 3.5 21.8 - - - +
234B ILE* 4.0 26.7 - - - -
235B VAL* 5.1 2.0 - - - -
259B THR 3.0 18.7 + - - +
260B VAL* 3.4 5.6 - - - +
261B LEU 3.2 0.2 - - - -
262B THR* 1.3 78.2 - - - +
264B THR* 1.3 57.1 + - - +
266B GLN* 3.5 12.3 - - + +
267B SER* 3.0 27.5 + - - -
287B MET* 3.4 35.8 - - - +
290B CYS* 3.7 21.1 - - + +
291B LEU* 3.7 38.0 - - + +
294B VAL* 4.6 3.4 - - + -
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Residues in contact with THR 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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260B VAL* 3.1 16.4 + - + +
261B LEU* 2.6 27.0 + - - +
263B MET* 1.3 74.6 - - - +
265B THR* 1.3 62.9 + - - +
267B SER* 3.3 7.5 + - - -
268B SER* 3.0 26.9 + - - -
291B LEU* 4.1 22.4 - - + -
230C PRO* 5.0 21.1 - - + +
233C LEU* 5.4 3.6 - - + -
234C ILE* 4.8 16.6 - - + +
262C THR* 5.2 4.7 - - - +
266C GLN* 5.6 3.9 + - - -
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Residues in contact with THR 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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261B LEU 3.2 11.6 + - - +
262B THR* 3.0 23.1 + - - +
264B THR* 1.3 76.1 + - - +
266B GLN* 1.3 60.2 + - - +
268B SER* 3.1 9.4 + - - +
269B GLY* 2.8 29.6 + - - -
262C THR* 6.6 0.2 - - + -
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Residues in contact with GLN 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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264A THR* 5.6 4.2 + - - -
226B GLN 3.9 13.3 + - - -
227B MET* 4.1 10.0 + - - +
230B PRO* 3.8 28.3 - - - +
231B SER* 4.3 6.7 - - - -
234B ILE* 4.8 3.3 - - - +
262B THR* 2.8 31.0 + - - +
263B MET* 3.5 29.6 - - + +
265B THR* 1.3 77.8 + - - +
267B SER* 1.3 60.7 + - - +
269B GLY* 3.5 1.7 + - - -
270B SER* 3.1 23.2 + - - -
287B MET* 4.0 11.7 - - + +
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Residues in contact with SER 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 MET 3.0 18.4 + - - -
264B THR* 3.4 8.3 - - - -
265B THR 3.1 0.4 - - - -
266B GLN* 1.3 75.3 - - - +
268B SER* 1.3 62.8 + - - +
270B SER* 2.6 22.5 + - - -
271B ARG* 3.3 25.9 + - - -
287B MET* 4.0 28.7 - - - +
291B LEU* 5.6 6.9 - - - +
225C ILE* 5.3 1.9 + - - +
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Residues in contact with SER 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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264B THR 3.0 13.4 + - - -
265B THR* 3.1 16.3 + - - -
267B SER* 1.3 76.3 + - - +
269B GLY* 1.3 60.7 + - - +
271B ARG* 3.2 27.4 + - - +
272B ALA* 3.4 11.1 + - - +
226C GLN* 3.4 29.9 + - - +
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Residues in contact with GLY 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B MET* 4.5 7.2 - - - +
265B THR 2.8 21.3 + - - -
266B GLN* 3.8 2.5 - - - -
268B SER* 1.3 73.4 + - - +
270B SER* 1.3 59.6 + - - +
271B ARG 3.2 1.1 + - - -
272B ALA* 3.4 20.4 + - - +
273B SER 5.0 0.5 + - - -
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Residues in contact with SER 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PHE* 4.3 6.9 - - - -
227B MET* 3.9 30.6 - - - +
266B GLN 3.1 13.4 + - - -
267B SER 2.6 21.0 + - - -
269B GLY* 1.3 75.0 - - - +
271B ARG* 1.3 65.8 + - - +
273B SER 5.4 0.2 - - - -
274B LEU* 3.9 13.3 - - - +
283B ILE* 3.9 28.9 - - - +
284B ASP* 4.4 0.3 + - - -
287B MET* 4.0 11.6 - - - +
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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