Contacts of the helix formed by residues 257 - 279 (chain B) in PDB entry 1CCW
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 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255B CYS* 3.6 3.0 + - - +
256B GLY* 1.3 75.7 - - - +
258B MET* 1.3 58.9 + - - +
259B ILE* 3.2 11.3 + - - +
260B GLN* 2.9 30.2 + - + +
261B ASP* 2.8 30.5 + - - -
364B GLU* 5.0 3.2 + - - +
425B LEU* 3.0 34.3 + - - +
426B GLY 4.1 9.1 + - - +
427B CYS* 3.4 29.1 - - - -
478B LEU* 4.1 2.4 - - - +
357D GLN* 3.6 20.0 - - - +
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Residues in contact with MET 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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256B GLY 3.4 3.2 + - - +
257B ASN* 1.3 70.1 - - - +
259B ILE* 1.3 60.3 + - + +
261B ASP* 3.3 0.9 + - - +
262B ILE* 2.9 43.2 + - + +
313B THR* 4.2 5.4 - - + -
314B ILE* 3.8 35.4 - - + -
317B LEU* 3.9 21.1 - - + -
359B MET* 3.6 24.7 - - + -
313D THR* 4.1 17.5 - - + -
317D LEU* 3.6 33.2 - - + -
354D LEU* 5.2 5.2 - - + -
357D GLN* 2.9 17.8 + - - +
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 3.2 7.3 + - - +
258B MET* 1.3 73.9 - - + +
260B GLN* 1.3 66.3 + - - +
262B ILE* 4.7 2.0 - - + -
263B ALA* 2.9 22.7 + - - +
359B MET* 3.7 37.9 - - + -
364B GLU* 3.3 37.7 - - + +
365B LEU* 3.9 35.8 - - + +
368B GLU* 4.5 7.6 - - + +
357D GLN* 4.7 0.6 + - - -
358D ARG 5.2 2.2 - - - +
360D PRO* 4.0 23.6 - - + -
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Residues in contact with GLN 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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226B PRO* 3.7 28.0 - - + +
252B TYR* 4.5 2.0 - - - +
255B CYS* 3.7 15.5 - - - +
257B ASN* 2.9 23.5 + - + +
259B ILE* 1.3 76.6 - - - +
261B ASP* 1.3 59.0 + - - +
263B ALA* 3.4 2.1 + - - +
264B ALA* 2.8 27.5 + - - +
368B GLU* 4.1 19.5 + - + +
372B ILE* 4.0 1.6 - - + +
426B GLY 4.4 0.7 - - - +
427B CYS* 3.3 19.4 - - - +
428B VAL 2.8 47.8 + - - +
429B ARG* 4.2 10.7 - - - +
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 2.7 36.7 + - - -
254B GLU* 3.4 13.6 - - - +
255B CYS* 2.8 21.6 + - - +
256B GLY* 2.9 22.0 + - - -
257B ASN 2.8 17.1 + - - +
258B MET 3.8 0.2 - - - +
260B GLN* 1.3 76.0 - - - +
262B ILE* 1.3 59.4 + - - +
264B ALA* 3.3 2.4 + - - +
265B LEU* 3.0 29.6 + - - +
290B PHE* 3.8 9.2 - - + -
314B ILE* 3.6 27.1 - - + +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B MET* 2.9 41.0 + - + +
259B ILE* 4.0 3.4 - - - +
261B ASP* 1.3 73.0 - - - +
263B ALA* 1.3 66.3 + - - +
265B LEU* 3.3 1.2 + - - +
266B ARG* 2.9 57.0 + - - +
314B ILE* 4.1 7.2 - - + +
317B LEU* 4.1 13.7 - - + -
318B ALA* 3.8 23.3 - - + +
359B MET* 3.6 31.0 - - + -
365B LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE 2.9 18.9 + - - +
260B GLN 3.5 3.8 - - - +
262B ILE* 1.3 77.7 - - - +
264B ALA* 1.3 56.5 + - - +
266B ARG* 3.7 1.3 - - - +
267B CYS* 2.8 35.5 + - - -
365B LEU* 3.7 13.4 - - + +
368B GLU* 3.8 15.3 - - + -
369B MET* 3.7 21.3 - - + -
372B ILE* 3.8 15.9 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PRO* 3.7 15.3 - - + -
230B ASN* 3.1 15.5 + - - +
252B TYR* 3.4 38.6 - - + +
260B GLN 2.8 18.1 + - - +
261B ASP 3.5 1.8 - - - +
262B ILE 3.2 0.2 - - - -
263B ALA* 1.3 77.2 - - - +
265B LEU* 1.3 57.0 + - - +
267B CYS* 4.6 0.2 - - - -
268B LEU* 2.9 26.0 + - - +
372B ILE* 3.7 8.0 - - - +
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Residues in contact with LEU 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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252B TYR* 3.8 29.3 - - + -
261B ASP 3.0 16.1 + - - +
262B ILE 4.0 2.5 - - - +
264B ALA* 1.3 76.5 - - - +
266B ARG* 1.3 64.6 + - + +
268B LEU* 3.4 9.8 + - + +
269B GLU* 3.0 24.1 + - - +
288B THR* 3.9 25.9 - - + +
289B VAL 4.0 11.2 - - - +
290B PHE* 4.4 9.4 - - + -
318B ALA* 3.9 22.4 - - + +
319B GLY 4.9 0.2 - - - -
320B ALA* 3.7 37.2 - - + +
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Residues in contact with ARG 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 ILE* 2.9 33.5 + - + +
263B ALA 3.9 0.7 - - - +
265B LEU* 1.3 78.5 - - + +
267B CYS* 1.3 56.4 + - - +
269B GLU* 3.4 5.7 + - - +
270B GLU* 2.9 43.8 + - - +
317B LEU 2.9 27.3 + - - -
318B ALA* 3.8 22.1 + - - +
358B ARG* 4.2 8.7 - - - +
359B MET 3.2 27.3 + - - +
361B MET* 3.4 27.6 - - - +
365B LEU* 3.9 9.1 - - - +
369B MET* 3.8 27.1 - - + -
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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
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230B ASN* 4.1 1.8 - - - +
263B ALA 2.8 26.8 + - - +
264B ALA 3.9 1.6 - - - +
266B ARG* 1.3 71.8 - - - +
268B LEU* 1.3 55.5 + - - +
271B GLN* 2.7 42.4 + - - +
369B MET* 3.4 44.6 - - - +
372B ILE* 3.8 24.2 - - + -
373B LYS* 3.6 26.7 - - + +
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Residues in contact with LEU 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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230B ASN* 3.5 46.1 - - + +
233B GLY* 4.7 3.8 - - - -
234B ILE* 4.2 8.6 - - + +
250B VAL* 3.7 20.9 - - + +
251B GLY* 3.3 42.4 - - - +
252B TYR* 4.2 7.0 - - + -
264B ALA 2.9 18.1 + - - +
265B LEU* 3.6 11.2 - - + +
267B CYS* 1.3 77.1 - - - +
269B GLU* 1.3 57.6 + - - +
271B GLN* 4.5 0.2 - - - +
272B THR* 2.7 45.2 + - - +
288B THR* 5.3 0.7 - - + -
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Residues in contact with GLU 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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56B LYS* 2.7 37.3 + - - -
250B VAL* 4.7 2.7 - - - -
265B LEU 3.0 16.8 + - - +
266B ARG* 4.0 5.4 - - - +
268B LEU* 1.3 77.7 - - - +
270B GLU* 1.3 66.1 + - + +
272B THR* 3.3 5.1 + - - -
273B ASN* 3.0 44.6 + - - +
286B VAL* 3.8 14.4 - - + +
288B THR* 3.7 26.5 + - + +
319B GLY 5.3 2.3 - - - +
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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 ARG* 2.9 28.2 + - - +
267B CYS 4.0 0.9 - - - +
269B GLU* 1.3 79.5 - - + +
271B GLN* 1.3 59.0 + - - +
273B ASN* 3.7 6.0 - - - +
274B GLU* 2.9 28.6 + - - +
369B MET* 3.5 19.1 - - - +
373B LYS* 2.7 41.7 + - - +
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Residues in contact with GLN 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASN* 5.5 1.0 + - - -
234B ILE* 3.8 15.7 - - + +
267B CYS* 2.7 27.4 + - - +
270B GLU* 1.3 72.0 - - - +
272B THR* 1.3 63.6 + - - +
274B GLU* 3.9 19.6 + - - +
275B TYR* 2.9 43.9 + - + +
372B ILE* 5.3 0.2 - - - +
373B LYS* 3.4 56.2 + - + +
376B THR* 3.5 28.0 + - - +
377B LYS* 4.5 9.9 - - - +
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Residues in contact with THR 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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234B ILE* 3.5 23.6 - - + +
237B ALA* 4.0 20.9 - - + -
248B ILE* 5.6 0.4 - - + -
250B VAL* 3.9 14.2 - - + +
268B LEU* 2.7 33.4 + - - +
269B GLU* 3.7 4.0 - - - -
271B GLN* 1.3 77.2 - - - +
273B ASN* 1.3 62.8 + - - +
275B TYR* 4.0 0.9 - - - +
276B LEU* 3.0 46.5 + - + +
286B VAL* 4.1 17.9 - - + -
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Residues in contact with ASN 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 GLU* 3.0 41.1 + - - +
270B GLU* 3.7 5.1 - - - +
272B THR* 1.3 77.6 - - - +
274B GLU* 1.3 63.1 + - - +
276B LEU* 3.8 6.0 - - - +
277B LYS* 3.1 36.0 + - + +
284B VAL 4.6 5.0 - - - +
286B VAL* 3.5 29.0 + - - +
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Residues in contact with GLU 274 (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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270B GLU 2.9 17.6 + - - +
271B GLN* 3.7 26.7 + - - +
273B ASN* 1.3 75.7 - - - +
275B TYR* 1.3 68.2 + - + +
277B LYS* 3.5 5.2 + - - +
278B ALA* 2.8 30.8 + - + +
373B LYS* 5.3 4.2 + - - +
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Residues in contact with TYR 275 (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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234B ILE* 3.9 19.7 - - + -
238B LEU* 3.9 20.0 - - + -
271B GLN* 2.9 46.8 + - + +
272B THR 4.0 1.3 - - - +
274B GLU* 1.3 84.8 - - + +
276B LEU* 1.3 66.9 + - - +
278B ALA* 3.2 5.2 + - + -
279B TYR* 3.1 47.9 + + - +
377B LYS* 4.3 13.3 + - - +
380B LEU* 3.6 34.8 - - + +
381B ASP* 4.1 12.5 + - - -
384B PHE* 4.1 18.6 - + - -
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Residues in contact with LEU 276 (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 ALA* 4.1 11.9 - - + +
238B LEU* 4.0 12.6 - - + -
241B ALA* 3.5 32.1 - - + -
248B ILE* 5.0 3.1 - - + -
272B THR* 3.0 31.1 + - + +
273B ASN* 3.8 5.6 - - - +
275B TYR* 1.3 78.8 - - - +
277B LYS* 1.3 61.8 + - + +
279B TYR 3.2 1.9 + - - -
280B GLY 3.1 4.9 + - - -
281B TYR* 2.9 44.1 + - + +
284B VAL* 3.8 19.3 - - + +
286B VAL* 3.7 28.9 - - + -
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Residues in contact with LYS 277 (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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273B ASN* 3.1 24.0 + - + +
274B GLU* 4.0 4.3 - - - +
276B LEU* 1.3 75.9 - - + +
278B ALA* 1.3 64.2 + - - +
280B GLY* 3.0 12.8 + - - -
281B TYR 4.3 5.6 - - - +
282B ASN* 3.7 41.6 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B GLU* 2.8 26.0 + - + +
275B TYR* 3.2 7.8 + - + +
277B LYS* 1.3 72.9 - - - +
279B TYR* 1.3 71.9 + - + +
280B GLY 3.3 0.8 + - - -
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Residues in contact with TYR 279 (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 LEU* 4.3 10.1 - - + -
275B TYR* 3.1 39.2 + + - +
277B LYS 3.1 0.2 - - - -
278B ALA* 1.3 86.2 - - + +
280B GLY* 1.3 59.8 + - - +
281B TYR* 3.4 32.2 + - + -
384B PHE* 3.2 51.3 - + - +
389B GLY 5.2 3.4 - - - -
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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