Contacts of the helix formed by residues 224 - 247 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ASP* 2.7 49.3 + - + +
444A TYR* 5.9 0.2 - - - +
445A MET* 3.6 13.9 + - + +
219C ILE* 4.0 19.1 - - + -
220C PRO* 3.4 19.3 - - + +
222C HIS 3.9 2.7 - - - -
223C SER* 1.3 92.4 - - - +
225C PHE* 1.3 78.7 - - + +
226C ILE 3.3 2.0 - - - +
227C PHE* 3.4 8.6 + - - +
228C LYS* 2.9 20.8 + - - +
291D LYS* 3.6 21.7 + - - -
292D TRP* 3.0 42.6 + + + +
294D GLY* 5.9 1.0 - - - -
295D ILE* 3.8 26.1 - - + +
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 3.7 21.3 - - + -
23C PRO 4.1 7.2 - - - -
24C SER 4.7 0.7 - - - -
26C ILE* 3.3 46.0 - - + -
31C ASN* 5.4 2.5 - - - -
219C ILE* 3.5 32.1 - - + -
221C MET* 3.0 30.3 + - - +
224C TYR* 1.3 79.7 - - + +
226C ILE* 1.3 60.6 + - - +
227C PHE 3.1 1.3 - - - -
228C LYS* 3.6 19.1 - - + -
229C ASP* 2.7 47.9 + - - +
292D TRP* 3.6 26.5 - + - -
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Residues in contact with ILE 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ILE* 3.6 40.8 - - + +
221C MET* 3.4 16.1 + - + +
222C HIS* 3.7 31.2 - - + +
223C SER 4.5 2.5 - - - +
224C TYR 3.3 0.4 - - - -
225C PHE* 1.3 80.0 - - - +
227C PHE* 1.3 73.3 + - + +
229C ASP* 4.0 5.7 - - + +
230C LEU* 3.3 22.5 + - + +
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Residues in contact with PHE 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C HIS* 4.8 10.5 - - - -
223C SER* 4.6 10.3 - - - -
224C TYR* 3.4 10.5 + - - +
225C PHE 3.1 0.4 - - - -
226C ILE* 1.3 94.8 - - + +
228C LYS* 1.3 62.0 + - - +
230C LEU* 3.3 28.7 - - + +
231C VAL* 3.5 11.4 + - - +
284D SER* 4.8 2.2 - - - +
287D VAL* 3.9 22.7 - - + -
288D LYS* 4.3 12.7 - - + +
291D LYS* 3.9 38.4 - - + -
292D TRP* 5.7 0.4 - - - +
60E VAL* 5.9 4.9 - - + -
63E MET* 3.7 27.4 - - + -
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ILE 3.0 27.5 + - - -
27C ASN* 3.6 12.9 + - - +
28C TYR* 3.5 46.7 - - + +
31C ASN* 3.0 23.4 + - - +
224C TYR 2.9 18.6 + - - +
225C PHE* 4.0 25.5 - - + -
227C PHE* 1.3 73.1 - - - +
229C ASP* 1.3 66.4 + - - +
230C LEU 3.1 1.8 - - - -
231C VAL* 3.3 16.8 + - - +
232C THR 3.8 0.2 + - - -
288D LYS* 4.0 20.7 - - + +
292D TRP* 4.2 14.6 - - + +
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Residues in contact with ASP 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TRP 5.3 0.9 - - - +
31C ASN* 3.5 25.6 - - - +
34C SER* 3.3 32.8 - - - +
221C MET* 5.4 5.1 - - - +
225C PHE* 2.7 40.9 + - - +
226C ILE* 4.0 6.9 - - + +
228C LYS* 1.3 72.9 - - - +
230C LEU* 1.3 57.0 + - - +
232C THR* 2.8 18.5 + - - -
233C VAL* 2.9 24.4 + - + +
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Residues in contact with LEU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ILE* 3.3 14.1 + - + +
227C PHE* 3.3 28.5 - - + +
228C LYS 3.1 0.2 - - - -
229C ASP* 1.3 77.3 - - - +
231C VAL* 1.3 62.8 + - - +
233C VAL* 3.5 16.3 - - + +
234C PHE* 3.0 65.4 + - + -
284D SER* 4.6 3.1 - - - -
63E MET* 4.3 21.8 - - + -
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Residues in contact with VAL 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 4.1 23.3 - - + +
227C PHE 3.5 4.4 + - - +
228C LYS 3.3 10.3 + - - +
230C LEU* 1.3 80.1 - - - +
232C THR* 1.3 60.9 + - + +
234C PHE* 3.4 0.7 + - - +
235C LEU* 3.1 23.0 + - + +
281D TYR* 3.7 28.6 - - + +
284D SER* 3.4 40.6 - - - +
285D ILE* 3.8 12.8 - - + +
288D LYS* 3.9 14.6 - - + -
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Residues in contact with THR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C TYR* 3.5 22.0 - - + +
31C ASN* 2.8 39.6 + - + +
32C MET* 5.1 5.6 - - + -
34C SER* 4.9 0.2 + - - -
35C LEU* 3.9 18.0 - - - +
228C LYS 3.8 0.4 + - - -
229C ASP* 2.8 19.3 + - - -
231C VAL* 1.3 79.1 - - + +
233C VAL* 1.3 60.3 + - - +
235C LEU* 3.8 10.4 - - + +
236C PHE* 2.9 30.1 + - - +
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Residues in contact with VAL 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C SER* 4.7 7.2 - - - +
35C LEU* 3.9 20.0 - - + -
38C LEU* 3.7 13.5 - - + -
229C ASP* 2.9 30.6 + - + +
230C LEU* 3.5 22.9 - - + +
231C VAL 3.2 0.2 - - - -
232C THR* 1.3 76.7 - - - +
234C PHE* 1.3 62.7 + - + +
236C PHE* 3.1 4.7 + - - +
237C MET* 2.9 59.4 + - + +
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Residues in contact with PHE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C LEU* 3.0 55.8 + - + +
231C VAL 3.8 3.6 - - - +
233C VAL* 1.3 83.5 - - + +
235C LEU* 1.3 62.9 + - - +
237C MET* 3.2 12.0 + - + +
238C LEU* 2.9 23.4 + - - +
277D LEU* 4.3 17.2 - - + +
280D LEU* 3.7 54.3 - - + -
281D TYR* 3.9 20.0 - - - +
284D SER* 3.7 9.9 - - - -
63E MET* 4.6 7.6 - - + -
67E SER* 4.0 13.5 - - - -
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C VAL* 3.1 17.1 + - + +
232C THR* 3.9 11.4 - - + +
233C VAL 3.3 0.2 - - - -
234C PHE* 1.3 73.7 - - - +
236C PHE* 1.3 65.8 + - - +
238C LEU* 3.0 19.9 + - + +
239C ILE* 2.9 42.9 + - + +
281D TYR* 3.6 47.0 - - + +
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Residues in contact with PHE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.1 24.9 - - + -
38C LEU* 4.4 15.3 - - + -
39C CYS* 3.6 25.1 - - - -
42C ILE* 4.3 23.8 - - + -
85C GLY* 5.8 1.1 - - - -
88C PHE* 3.8 33.7 - + + -
92C VAL* 3.8 23.8 - - + -
232C THR 2.9 20.0 + - - +
233C VAL* 3.3 6.1 - - - +
235C LEU* 1.3 77.2 - - - +
237C MET* 1.3 70.8 + - + +
239C ILE* 3.6 4.5 + - - +
240C LEU* 3.1 33.0 + - + +
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Residues in contact with MET 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.6 22.9 - - + -
42C ILE* 5.9 0.7 - - + -
233C VAL* 2.9 42.9 + - + +
234C PHE* 3.6 13.7 - - + +
235C LEU 3.2 0.2 - - - -
236C PHE* 1.3 87.2 - - + +
238C LEU* 1.3 52.2 + - - +
240C LEU* 3.1 6.5 + - - +
241C ALA* 2.7 36.2 + - - +
277D LEU* 3.9 28.4 - - + +
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C PHE 2.9 12.9 + - - +
235C LEU* 3.3 26.9 - - + +
237C MET* 1.3 73.9 - - - +
239C ILE* 1.3 69.2 + - + +
241C ALA* 3.0 14.6 + - + +
242C LEU* 3.0 23.6 + - + +
274D VAL* 3.9 29.8 - - + +
277D LEU* 4.0 17.9 - - + +
278D SER* 3.7 32.8 - - - +
281D TYR* 5.2 6.1 - - + -
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PHE* 3.9 18.4 - - + -
235C LEU* 2.9 37.8 + - + +
236C PHE* 4.2 3.6 - - - +
238C LEU* 1.3 80.7 - - + +
240C LEU* 1.3 61.2 + - - +
242C LEU* 3.4 18.1 + - + +
243C PHE* 3.2 28.7 + - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 4.5 15.0 - - + -
81C LEU* 3.5 27.4 - - + -
84C ASN* 3.8 25.8 - - + +
85C GLY* 4.3 6.1 - - - +
88C PHE* 3.6 41.0 - - + -
236C PHE* 3.1 24.3 + - + +
237C MET* 3.1 11.5 + - - +
239C ILE* 1.3 73.4 - - - +
241C ALA* 1.3 66.3 + - - +
243C PHE* 3.0 3.3 + - - -
244C VAL* 2.8 33.6 + - + +
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Residues in contact with ALA 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C MET 2.7 17.0 + - - +
238C LEU* 3.0 10.7 + - - +
240C LEU* 1.3 72.2 - - - +
242C LEU* 1.3 62.2 + - - +
244C VAL* 4.5 3.4 - - - -
245C PHE* 2.9 39.3 + - + +
273D THR* 3.5 32.5 - - + -
274D VAL* 4.8 8.7 - - + -
277D LEU* 3.8 7.4 - - + -
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C LEU* 3.0 29.7 + - + +
239C ILE* 3.5 19.1 - - + +
240C LEU 3.1 0.2 - - - -
241C ALA* 1.3 75.6 - - - +
243C PHE* 1.3 61.2 + - + +
246C TYR* 2.8 53.2 + - + +
247C SER* 3.4 2.9 + - - -
274D VAL* 3.6 31.6 - - + -
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Residues in contact with PHE 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 3.8 15.5 - - + +
88C PHE* 3.5 24.9 - + + -
91C MET* 5.7 4.3 - - + -
239C ILE* 3.2 32.3 - - + -
240C LEU 3.0 6.7 + - - +
242C LEU* 1.3 77.6 - - + +
244C VAL* 1.3 64.3 + - - +
247C SER* 2.8 27.3 + - - +
248C PRO* 2.7 32.5 - - - +
250C THR* 4.8 12.3 - - + -
251C LEU* 3.8 33.4 - - + -
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Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 5.9 0.3 - - - -
77C ILE* 4.3 13.9 - - + +
80C TYR* 3.8 34.4 - - + +
81C LEU* 4.1 22.2 - - + +
84C ASN* 4.1 8.3 - - + +
240C LEU* 2.8 46.8 + - + +
241C ALA* 3.9 4.3 - - - +
243C PHE* 1.3 72.0 - - - +
245C PHE* 1.3 77.1 + - + +
248C PRO* 3.7 13.7 - - - +
266D ARG* 4.0 8.1 - - - -
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Residues in contact with PHE 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 5.0 0.9 - + - -
77C ILE* 4.1 38.4 - - + -
241C ALA* 2.9 33.3 + - + +
244C VAL* 1.3 94.3 - - + +
246C TYR* 1.3 63.6 + - + +
247C SER 3.7 0.9 - - - -
248C PRO* 4.3 0.2 - - - -
266D ARG* 2.7 61.7 + - + +
267D LYS* 4.8 0.7 + - - -
269D LEU* 3.7 21.1 - - + -
270D GLY* 3.6 24.7 - - - -
273D THR* 3.8 26.2 - - + -
274D VAL* 6.1 0.2 - - + -
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Residues in contact with TYR 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 2.8 36.6 + - + +
245C PHE* 1.3 80.5 - - + +
247C SER* 1.3 63.8 + - - +
248C PRO* 3.5 4.2 - - - +
81D PRO* 3.2 49.6 + - + +
82D PHE* 4.9 1.8 - + - -
266D ARG* 4.5 3.1 - - - +
267D LYS* 3.2 23.9 + - + -
270D GLY* 3.7 12.3 - - - -
271D LEU* 2.8 36.8 + - - +
274D VAL* 3.7 24.9 - - + -
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 4.6 0.9 - - - +
242C LEU 3.4 2.3 + - - -
243C PHE* 2.8 36.0 + - - +
246C TYR* 1.3 81.5 + - - +
248C PRO* 1.4 66.4 - - - +
249C ASN 3.2 3.9 + - - -
250C THR* 2.5 36.9 + - - +
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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