Contacts of the helix formed by residues 224 - 247 (chain N) in PDB entry 1KYO
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 TYR 224 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443L ASP* 2.8 48.0 + - + +
445L MET* 3.7 14.2 + - + +
219N ILE* 4.0 23.3 - - + -
220N PRO* 3.6 18.4 - - + +
222N HIS 4.3 1.6 - - - -
223N SER* 1.3 86.2 - - - +
225N PHE* 1.3 76.7 - - + +
226N ILE 3.3 3.2 - - - +
227N PHE* 3.9 6.4 - - - +
228N LYS* 2.9 20.3 + - - +
291O LYS* 3.4 25.8 - - - -
292O TRP* 2.8 45.9 + + + +
294O GLY* 6.0 0.9 - - - -
295O ILE* 3.8 24.5 - - + +
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Residues in contact with PHE 225 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N GLN* 3.4 32.5 - - + -
23N PRO 3.8 10.8 - - - -
24N SER 4.5 1.1 - - - -
26N ILE* 3.3 41.5 - - + -
31N ASN* 5.7 1.3 - - - -
219N ILE* 3.6 24.2 - - + -
220N PRO 3.9 11.2 - - - -
221N MET* 3.3 22.9 + - - +
224N TYR* 1.3 78.9 - - + +
226N ILE* 1.3 63.2 + - - +
227N PHE 3.3 0.2 - - - -
228N LYS* 3.7 22.2 - - + -
229N ASP* 3.0 40.1 + - - +
292O TRP* 3.9 25.4 - + - -
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Residues in contact with ILE 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17N ILE* 3.4 42.2 - - + +
221N MET* 3.4 23.1 + - + +
222N HIS* 3.9 20.2 - - + -
223N SER 4.1 9.6 - - - +
224N TYR 3.3 0.4 - - - +
225N PHE* 1.3 79.0 - - - +
227N PHE* 1.3 72.9 + - + +
229N ASP* 3.6 7.1 - - + +
230N LEU* 3.3 29.1 + - + +
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Residues in contact with PHE 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N HIS* 5.0 7.2 - - - -
223N SER* 4.4 15.9 - - - -
224N TYR* 3.8 8.7 + - - +
226N ILE* 1.3 89.0 - - + +
228N LYS* 1.3 64.6 + - - +
229N ASP 3.2 1.6 - - - -
230N LEU* 3.3 30.2 + - + +
231N VAL* 3.5 10.9 + - - +
284O SER* 5.1 3.1 - - - +
287O VAL* 3.8 21.5 - - + -
288O LYS* 4.3 14.6 - - - +
291O LYS* 3.6 36.3 - - + -
292O TRP* 5.8 0.7 - - + +
60P VAL* 6.1 3.6 - - + -
63P MET* 3.6 28.3 - - + -
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Residues in contact with LYS 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N ILE 3.0 26.7 + - - -
27N ASN* 3.9 11.7 + - - +
28N TYR* 3.6 46.6 - - + +
31N ASN* 3.2 19.7 + - - +
224N TYR 2.9 20.3 + - - +
225N PHE* 3.9 24.6 - - + -
226N ILE 3.4 0.2 - - - -
227N PHE* 1.3 75.6 - - - +
229N ASP* 1.3 63.8 + - - +
231N VAL* 3.2 19.4 + - - +
288O LYS* 4.0 22.4 - - + +
292O TRP* 4.2 16.9 - - + +
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Residues in contact with ASP 229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30N TRP 4.9 2.1 - - - +
31N ASN* 3.2 27.1 + - - +
34N SER* 2.8 34.3 + - - +
221N MET* 5.4 5.2 - - - +
225N PHE* 3.0 29.7 + - - +
226N ILE* 3.6 8.7 - - + +
228N LYS* 1.3 78.7 - - - +
230N LEU* 1.3 60.8 + - + +
232N THR* 2.8 20.3 + - - -
233N VAL* 2.9 16.4 + - + +
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Residues in contact with LEU 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226N ILE* 3.3 19.4 + - + +
227N PHE* 3.3 26.2 + - + +
228N LYS 3.2 0.4 - - - -
229N ASP* 1.3 79.6 - - + +
231N VAL* 1.3 62.7 + - - +
233N VAL* 3.1 14.1 + - + +
234N PHE* 2.9 58.4 + - + -
284O SER* 4.7 3.6 - - - -
63P MET* 4.2 24.2 - - + -
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Residues in contact with VAL 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N TYR* 4.2 22.9 - - + +
227N PHE 3.9 10.5 - - - +
228N LYS 3.2 10.4 + - - +
230N LEU* 1.3 77.7 - - - +
232N THR* 1.3 60.1 + - + +
234N PHE* 3.4 0.7 + - - +
235N LEU* 2.9 27.3 + - + +
281O TYR* 3.7 23.1 - - + +
284O SER* 3.7 37.7 - - - +
285O ILE* 4.0 12.8 - - + +
288O LYS* 4.0 12.6 - - + -
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Residues in contact with THR 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N TYR* 3.7 19.7 - - + +
31N ASN* 2.9 39.9 + - + +
32N MET* 5.0 4.0 - - + -
34N SER* 5.3 0.5 + - - -
35N LEU* 3.8 23.6 - - + +
228N LYS 3.8 0.2 + - - -
229N ASP* 2.8 19.8 + - - +
231N VAL* 1.3 75.7 - - + +
233N VAL* 1.3 56.2 + - - +
235N LEU* 3.7 11.1 - - + +
236N PHE* 2.7 36.7 + - - +
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Residues in contact with VAL 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N SER* 5.6 6.3 - - - -
35N LEU* 3.9 17.7 - - + -
38N LEU* 3.4 27.8 - - + -
229N ASP* 2.9 29.6 + - + +
230N LEU* 3.4 17.7 - - + +
232N THR* 1.3 78.0 + - - +
234N PHE* 1.3 69.8 + - + +
236N PHE* 3.2 2.8 - - - +
237N MET* 2.9 38.7 + - + +
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Residues in contact with PHE 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230N LEU* 2.9 53.9 + - + +
231N VAL 3.8 3.6 - - - +
233N VAL* 1.3 79.3 - - + +
235N LEU* 1.3 65.3 - - - +
237N MET* 2.8 17.8 + - - +
238N LEU* 2.8 24.7 + - - +
277O LEU* 4.4 14.7 - - + +
280O LEU* 3.7 44.2 - - + -
281O TYR* 4.0 18.2 - - + +
284O SER* 3.7 22.0 - - - -
63P MET* 4.6 5.4 - - + -
67P SER* 4.1 9.9 - - - -
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Residues in contact with LEU 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231N VAL* 2.9 19.3 + - + +
232N THR* 3.7 11.7 - - + +
234N PHE* 1.3 74.7 - - - +
236N PHE* 1.3 65.7 + - - +
238N LEU* 3.2 12.6 + - + +
239N ILE* 3.2 40.5 + - + +
281O TYR* 3.6 44.5 - - + +
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Residues in contact with PHE 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N LEU* 4.0 23.3 - - + -
38N LEU* 4.4 12.6 - - + -
39N CYS* 3.6 29.6 - - - -
42N ILE* 4.2 15.5 - - + -
85N GLY* 5.8 1.1 - - - -
88N PHE* 3.7 38.4 - + + -
92N VAL* 4.1 14.6 - - + -
232N THR 2.7 21.5 + - - +
233N VAL 3.2 5.8 - - - +
235N LEU* 1.3 76.5 - - - +
237N MET* 1.3 72.5 + - + +
239N ILE* 3.2 6.1 + - - +
240N LEU* 3.1 41.2 + - + +
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Residues in contact with MET 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N LEU* 4.5 22.0 - - + -
42N ILE* 5.0 8.1 - - + -
233N VAL* 2.9 32.1 + - + +
234N PHE* 2.8 21.6 + - - +
236N PHE* 1.3 82.6 - - + +
238N LEU* 1.3 55.7 + - - +
240N LEU* 3.2 6.4 + - + +
241N ALA* 2.8 32.9 + - - +
277O LEU* 3.7 26.4 - - + +
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Residues in contact with LEU 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N PHE 2.8 14.6 + - - +
235N LEU* 3.5 20.6 - - + +
237N MET* 1.3 73.6 - - - +
239N ILE* 1.3 70.5 + - + +
241N ALA* 3.4 3.5 + - + +
242N LEU* 3.1 35.1 + - + +
274O VAL* 3.8 20.6 - - + +
277O LEU* 3.7 29.9 - - + +
278O SER* 3.4 31.9 - - - +
281O TYR* 5.4 7.0 - - + -
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Residues in contact with ILE 239 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N PHE* 3.8 21.3 - - + -
235N LEU* 3.2 36.0 + - + +
236N PHE* 4.0 6.7 - - - +
238N LEU* 1.3 84.4 - - + +
240N LEU* 1.3 65.2 + - - +
242N LEU* 3.2 21.0 + - + +
243N PHE* 3.2 27.4 + - + -
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Residues in contact with LEU 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42N ILE* 4.4 9.9 - - + -
81N LEU* 3.7 28.5 - - + -
84N ASN* 3.8 26.7 - - + -
85N GLY* 4.1 6.7 - - - +
88N PHE* 3.7 38.3 - - + -
236N PHE* 3.1 38.3 + - + +
237N MET* 3.7 7.2 - - - +
239N ILE* 1.3 76.7 - - - +
241N ALA* 1.3 56.5 + - - +
243N PHE* 3.3 1.6 + - + +
244N VAL* 2.9 31.5 + - + +
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Residues in contact with ALA 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237N MET 2.8 16.7 + - - +
238N LEU* 3.5 5.8 - - + +
240N LEU* 1.3 75.7 - - - +
242N LEU* 1.3 66.2 + - - +
244N VAL* 4.4 2.5 - - - +
245N PHE* 2.9 39.4 + - + +
246N TYR* 4.8 0.7 - - - -
273O THR* 3.7 30.5 - - + -
274O VAL* 5.0 8.2 - - + +
277O LEU* 3.8 6.5 - - + -
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Residues in contact with LEU 242 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238N LEU* 3.1 31.3 + - + +
239N ILE* 3.2 17.5 + - + +
241N ALA* 1.3 76.1 - - - +
243N PHE* 1.3 60.2 + - + +
246N TYR* 3.1 45.8 + - + +
247N SER* 3.5 4.6 + - - -
274O VAL* 3.6 31.0 - - + -
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Residues in contact with PHE 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N ASN* 4.3 14.1 - - - +
88N PHE* 3.5 26.0 - + + -
91N MET* 5.2 7.9 - - + -
239N ILE* 3.2 34.1 + - + -
240N LEU 3.7 5.4 - - - +
241N ALA 3.2 0.4 - - - -
242N LEU* 1.3 79.6 - - + +
244N VAL* 1.3 59.5 + - - +
245N PHE 3.3 0.2 - - - -
247N SER* 2.8 25.1 + - - +
248N PRO* 2.6 33.2 - - - -
250N THR* 4.8 11.9 - - + -
251N LEU* 4.0 35.2 - - + -
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Residues in contact with VAL 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N TYR* 6.4 0.7 - - + -
77N ILE* 4.7 11.4 - - + +
80N TYR* 3.5 46.3 - - + +
81N LEU* 3.7 21.5 - - + +
84N ASN* 3.6 13.9 - - + +
240N LEU* 2.9 30.0 + - + +
241N ALA* 4.2 2.7 - - - +
243N PHE* 1.3 73.2 - - - +
245N PHE* 1.3 86.2 + - + +
248N PRO* 3.6 15.9 - - - +
266O ARG* 4.1 2.9 - - - -
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Residues in contact with PHE 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N TYR* 4.8 2.2 - + - -
77N ILE* 3.9 36.3 - - + -
241N ALA* 2.9 28.4 + - + +
244N VAL* 1.3 93.5 - - + +
246N TYR* 1.3 62.0 + - + +
247N SER 3.7 0.2 - - - -
266O ARG* 2.7 62.1 + - + +
267O LYS* 4.8 0.9 - - - +
269O LEU* 3.9 20.0 - - + -
270O GLY* 3.6 22.0 - - - -
273O THR* 3.7 28.5 - - + -
274O VAL* 6.2 0.4 - - + -
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Residues in contact with TYR 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242N LEU* 3.1 32.8 + - + +
245N PHE* 1.3 81.3 - - + +
247N SER* 1.3 62.9 + - - +
248N PRO* 3.6 3.9 - - - +
81O PRO* 3.1 50.1 + - + +
82O PHE* 6.2 0.2 - + - -
266O ARG* 4.4 4.0 + - - +
267O LYS* 3.4 27.0 + - + +
270O GLY* 3.1 13.4 - - - -
271O LEU* 2.9 37.3 + - + +
274O VAL* 3.8 24.0 - - + -
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Residues in contact with SER 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N ASN* 5.0 0.2 - - - +
242N LEU 3.5 7.0 + - - -
243N PHE* 2.8 27.4 + - - +
246N TYR* 1.3 79.6 - - - +
248N PRO* 1.3 69.9 - - - +
249N ASN 3.1 3.8 + - - -
250N THR* 2.5 42.2 + - - -
251N LEU 4.7 0.2 + - - -
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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) + - + + + + + -
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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