Contacts of the helix formed by residues 216 - 253 (chain C) in PDB entry 4KNF
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 216 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C ALA 3.5 24.2 - - - +
207C GLY* 3.1 13.8 + - - -
210C MET* 4.4 21.1 - - + -
211C GLY* 4.6 17.2 + - - -
214C GLY 4.6 6.1 - - - -
215C VAL* 1.3 72.7 - - - +
217C ALA* 1.3 63.6 + - - +
218C SER 3.2 4.4 + - - -
219C ASN* 3.3 22.0 + - - +
220C LEU* 3.3 19.1 + - - +
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 4.5 19.5 - - + -
87C GLY 5.3 2.7 - - - +
89C THR* 4.8 13.0 - - + +
215C VAL* 3.0 17.0 + - + +
216C TYR* 1.3 74.3 - - - +
218C SER* 1.3 61.9 + - - +
220C LEU* 3.6 7.4 - - - +
221C ASN* 2.8 33.8 + - - +
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Residues in contact with SER 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 5.9 1.3 - - - -
29C VAL* 3.5 23.9 - - - +
83C TRP* 4.5 10.1 - - - -
216C TYR 3.3 1.0 - - - -
217C ALA* 1.3 77.3 - - - +
219C ASN* 1.3 67.6 + - - +
221C ASN 3.2 2.3 + - - -
222C LEU* 2.9 39.4 + - - +
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Residues in contact with ASN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C ALA* 4.5 16.6 - - + +
216C TYR* 3.3 31.3 + - + +
218C SER* 1.3 79.6 - - - +
220C LEU* 1.3 66.9 + - - +
222C LEU* 4.3 12.6 - - - +
223C ILE* 3.1 36.6 + - + +
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Residues in contact with LEU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C THR* 3.8 27.6 - - + +
142C GLU* 3.7 8.5 - - - +
203C GLY* 3.5 26.6 - - - +
204C TYR* 4.0 0.9 - - - -
207C GLY* 4.3 5.8 - - - -
208C TYR* 3.6 40.2 - - + +
215C VAL* 4.6 6.1 - - + -
216C TYR 3.3 10.8 + - - +
217C ALA* 3.6 9.6 - - - +
219C ASN* 1.3 80.1 - - - +
221C ASN* 1.3 58.3 + - - +
223C ILE* 3.9 1.6 - - - +
224C TYR* 3.0 67.2 + - + +
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Residues in contact with ASN 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.0 17.7 - - + -
33C PHE* 4.0 6.0 - - + -
83C TRP* 4.0 9.3 - - - -
89C THR* 3.4 37.3 + - - +
90C PRO* 3.6 12.6 - - - +
94C ARG* 3.1 24.8 + - - +
217C ALA 2.8 24.5 + - - +
218C SER 3.2 3.8 + - - +
220C LEU* 1.3 80.0 - - - +
222C LEU* 1.3 60.0 + - - +
224C TYR* 4.3 3.3 - - - -
225C ASN* 2.9 39.0 + - - +
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Residues in contact with LEU 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C THR* 3.8 25.1 - - - +
29C VAL* 3.8 13.5 - - + +
32C SER* 3.6 31.8 + - - +
218C SER* 2.9 27.0 + - - +
219C ASN* 4.0 13.0 - - - +
220C LEU 3.4 0.2 - - - -
221C ASN* 1.3 77.9 - - - +
223C ILE* 1.3 58.7 + - + +
225C ASN* 3.5 3.3 + - - +
226C LEU* 3.1 26.9 + - - +
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Residues in contact with ILE 223 (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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199C ILE* 3.3 36.7 - - + +
202C ALA* 4.4 6.5 - - + +
203C GLY* 3.5 24.0 - - - +
206C ALA* 3.9 17.7 - - + -
219C ASN* 3.1 23.6 + - + +
220C LEU 3.9 0.2 - - - +
222C LEU* 1.3 75.7 - - + +
224C TYR* 1.3 66.1 + - - +
226C LEU* 3.1 10.7 + - + +
227C ALA* 2.8 21.0 + - - +
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Residues in contact with TYR 224 (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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94C ARG* 3.4 45.3 - - + +
98C TRP* 3.7 28.0 - + + -
142C GLU* 2.4 33.8 + - - -
200C TYR* 3.5 33.4 - + - -
203C GLY* 4.3 1.8 - - - -
204C TYR* 3.8 10.0 - - - +
220C LEU* 3.0 47.9 + - + +
221C ASN* 3.8 2.7 - - - +
223C ILE* 1.3 74.4 - - - +
225C ASN* 1.3 58.0 + - - +
227C ALA* 3.0 7.1 + - - +
228C ASP* 2.9 32.1 + - - +
301C RET 3.7 13.8 - - + +
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Residues in contact with ASN 225 (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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29C VAL* 4.4 1.0 + - - +
32C SER* 3.2 30.4 + - - +
33C PHE* 3.3 39.6 - - - +
36C VAL* 3.5 22.0 - - + +
76C TYR* 3.0 14.7 + - - +
94C ARG* 2.8 30.3 + - - -
221C ASN* 2.9 24.1 + - - +
222C LEU 3.5 2.0 - - - +
223C ILE 3.2 0.2 - - - -
224C TYR* 1.3 72.6 - - - +
226C LEU* 1.3 62.3 + - - +
228C ASP* 3.7 1.9 + - - +
229C PHE* 3.3 16.3 + - - +
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Residues in contact with LEU 226 (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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36C VAL* 5.5 0.4 - - - -
199C ILE* 4.5 18.6 - - + -
222C LEU 3.1 14.6 + - - +
223C ILE* 3.1 11.6 + - + +
225C ASN* 1.3 75.3 - - - +
227C ALA* 1.3 59.9 + - - +
229C PHE* 3.5 12.1 - - + +
230C VAL* 3.1 44.1 + - + +
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Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ILE* 3.7 26.9 - - + -
200C TYR* 3.1 39.6 + - + +
223C ILE 2.8 13.4 + - - +
224C TYR* 3.0 9.4 + - - +
226C LEU* 1.3 77.6 - - - +
228C ASP* 1.3 52.5 + - - +
230C VAL* 3.4 0.5 + - - -
231C ASN* 2.7 37.5 + - - +
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Residues in contact with ASP 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 5.0 2.0 - - + -
40C MET* 5.1 4.5 - - - -
76C TYR* 2.7 39.9 + - + +
94C ARG* 3.2 12.7 + - - -
97C ASN* 4.5 1.6 + - - -
98C TRP* 3.1 15.4 + - - -
200C TYR* 2.8 37.7 + - - -
224C TYR 2.9 12.0 + - - +
225C ASN 4.2 1.1 - - - +
226C LEU 3.4 0.2 - - - -
227C ALA* 1.3 73.1 - - - +
229C PHE* 1.3 58.0 + - - +
232C LYS* 2.7 59.9 + - + +
233C ILE* 3.6 0.9 + - - +
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Residues in contact with PHE 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU 5.8 1.1 - - - -
36C VAL* 4.4 22.7 - - + +
39C GLY* 5.1 6.7 - - - -
225C ASN 3.3 13.5 + - - +
226C LEU* 3.5 17.5 - - + +
228C ASP* 1.3 75.0 - - - +
230C VAL* 1.3 72.8 + - + +
233C ILE* 3.0 42.4 + - + +
234C LEU* 3.0 47.6 + - + -
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Residues in contact with VAL 230 (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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192C ILE* 4.1 9.9 - - + +
196C GLY* 4.9 4.0 - - - -
199C ILE* 4.1 22.9 - - + -
226C LEU* 3.1 39.0 + - + +
227C ALA 3.8 2.2 - - - +
229C PHE* 1.3 78.5 - - + +
231C ASN* 1.3 69.4 + - - +
234C LEU* 3.2 29.8 - - + +
235C PHE 3.2 24.3 + - - -
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Residues in contact with ASN 231 (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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105C LEU* 4.2 9.6 - - - +
192C ILE* 3.0 29.2 - - - +
196C GLY* 3.0 36.4 - - - +
197C TRP* 3.6 19.9 - - + +
200C TYR* 3.2 24.6 - - + +
227C ALA* 2.7 28.1 + - - +
230C VAL* 1.3 78.7 - - - +
232C LYS* 1.3 57.4 + - + +
235C PHE* 3.2 25.5 - - - +
301C RET 4.5 5.2 - - + -
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Residues in contact with LYS 232 (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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40C MET* 4.0 12.8 - - + -
47C PHE* 4.4 0.3 - - - -
65C SER* 5.4 1.0 - - - +
68C ILE* 3.7 30.0 - - + +
69C THR* 4.1 10.6 - - + +
72C ALA* 4.0 18.2 - - + -
97C ASN* 4.1 13.7 - - - +
98C TRP* 4.0 2.0 - - - -
101C THR* 2.9 17.4 + - - -
105C LEU* 5.4 2.5 - - + +
228C ASP* 2.7 46.8 + - + +
231C ASN* 1.3 73.8 - - - +
233C ILE* 1.3 63.6 + - - +
235C PHE* 4.6 0.2 - - - +
236C GLY* 3.4 16.0 + - - -
301C RET 1.3 71.6 - - + +
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Residues in contact with ILE 233 (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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36C VAL* 4.7 1.3 - - + +
39C GLY* 3.4 32.5 - - - +
40C MET* 3.9 23.6 - - - +
43C ALA* 3.7 24.5 - - + -
47C PHE* 3.7 2.2 - - - -
69C THR* 4.6 4.5 - - + -
229C PHE* 3.0 44.5 + - + +
232C LYS* 1.3 74.7 - - - +
234C LEU* 1.3 66.9 + - + +
236C GLY* 3.2 4.2 + - - -
237C LEU* 2.8 39.4 + - + +
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Residues in contact with LEU 234 (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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192C ILE* 5.7 0.9 - - + -
229C PHE* 3.0 41.6 + - + +
230C VAL* 3.2 34.8 - - + +
233C ILE* 1.3 74.1 - - + +
235C PHE* 1.3 63.5 + - - +
237C LEU* 3.1 21.8 + - + +
238C ILE* 2.9 34.8 + - + +
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Residues in contact with PHE 235 (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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105C LEU* 3.7 26.2 - - + -
108C GLU* 3.8 24.2 - - + -
109C PHE* 4.0 27.8 - + - -
112C ILE* 4.5 12.3 - - + -
188C ALA* 4.3 9.4 - - + -
189C MET* 4.2 18.8 - - - -
192C ILE* 3.9 28.4 - - + +
230C VAL 3.2 8.5 + - - -
231C ASN 3.2 19.0 + - - +
232C LYS 5.8 0.2 - - - -
233C ILE 3.4 0.4 - - - -
234C LEU* 1.3 70.0 - - - +
236C GLY* 1.3 68.2 + - - +
238C ILE* 3.0 16.8 + - + +
239C ILE* 3.0 42.1 + - + +
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Residues in contact with GLY 236 (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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47C PHE* 3.3 30.9 - - - -
62C LEU* 4.9 0.7 - - - +
65C SER* 3.9 18.1 + - - -
108C GLU* 5.4 0.4 - - - -
232C LYS 3.4 9.2 + - - -
233C ILE 3.2 3.6 + - - -
235C PHE* 1.3 79.1 - - - +
237C LEU* 1.3 56.2 + - - +
239C ILE* 3.4 5.7 + - - +
240C TRP* 3.0 23.4 + - - +
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Residues in contact with LEU 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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43C ALA* 5.9 1.6 - - + -
46C PHE* 3.6 35.7 - - + -
47C PHE* 3.5 12.7 - - + -
233C ILE* 2.8 29.4 + - + +
234C LEU* 3.4 25.8 - - + +
235C PHE 3.1 0.4 - - - -
236C GLY* 1.3 73.1 - - - +
238C ILE* 1.3 63.1 + - + +
240C TRP* 3.4 13.2 + - + +
241C ASN* 3.0 20.3 + - - +
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Residues in contact with ILE 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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188C ALA* 3.7 31.6 - - + +
191C MET* 6.5 0.4 - - + -
192C ILE* 4.9 10.5 - - + -
234C LEU* 2.9 28.2 + - + +
235C PHE* 3.0 10.5 + - + +
237C LEU* 1.3 72.6 - - + +
239C ILE* 1.3 68.8 + - - +
241C ASN* 3.0 9.5 + - + +
242C VAL* 2.9 29.3 + - + +
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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
----------------------------------------------------------
58C TRP* 4.6 13.2 - - + -
61C SER* 4.2 20.9 - - - +
62C LEU* 4.9 6.7 - - + -
65C SER* 5.1 0.9 - - - +
108C GLU* 4.1 20.4 - - - +
112C ILE* 4.3 17.0 - - + -
185C ALA* 4.4 19.1 - - + -
188C ALA* 4.6 4.7 - - + -
235C PHE* 3.0 45.8 + - + +
236C GLY* 3.7 7.4 - - - +
238C ILE* 1.3 76.8 - - + +
240C TRP* 1.3 52.7 + - - +
242C VAL* 3.3 7.2 + - + +
243C ALA* 2.7 36.6 + - + +
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Residues in contact with TRP 240 (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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46C PHE* 3.4 32.3 - + - -
47C PHE* 4.5 5.2 - + + -
50C GLU* 3.3 45.0 + - + +
62C LEU* 3.9 29.3 - - + +
236C GLY 3.0 14.8 + - - +
237C LEU* 3.6 19.1 - - + +
238C ILE 3.2 0.2 - - - -
239C ILE* 1.3 75.6 - - - +
241C ASN* 1.3 95.7 + - + +
243C ALA* 3.3 3.7 + - - +
244C VAL* 2.8 55.0 + - + +
60D THR* 3.8 19.1 - - + -
111D LEU* 5.5 7.6 - - + -
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Residues in contact with ASN 241 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU 3.0 12.6 + - - +
238C ILE* 3.0 11.7 + - - +
240C TRP* 1.3 95.2 - - + +
242C VAL* 1.3 67.0 + - - +
244C VAL* 4.0 3.0 - - - +
245C LYS* 3.0 61.4 + - - +
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Residues in contact with VAL 242 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TRP* 3.4 30.5 - - + -
181C ALA* 3.6 22.0 - - + +
184C SER* 3.4 27.6 - - - +
185C ALA* 4.4 8.1 - - + +
238C ILE* 2.9 24.0 + - + +
239C ILE* 3.7 9.6 - - + +
241C ASN* 1.3 77.0 - - - +
243C ALA* 1.3 60.2 + - - +
245C LYS* 3.7 5.1 - - - +
246C GLU* 2.9 29.6 + - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C VAL* 3.6 18.6 - - + +
58C TRP* 3.6 39.8 - - + +
62C LEU* 5.1 4.0 - - + -
239C ILE* 2.7 24.4 + - + +
240C TRP* 3.4 9.0 - - - +
242C VAL* 1.3 73.0 - - - +
244C VAL* 1.3 56.5 + - - +
247C SER* 3.0 31.7 + - - -
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Residues in contact with VAL 244 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN* 3.6 35.9 - - + +
54C VAL* 3.8 6.5 - - + -
240C TRP* 2.8 58.9 + - + +
241C ASN* 4.1 4.0 - - - +
243C ALA* 1.3 69.6 - - - +
245C LYS* 1.3 68.9 + - + +
247C SER* 3.2 2.3 + - - -
248C SER* 2.9 28.4 + - - -
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Residues in contact with LYS 245 (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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241C ASN* 3.0 49.2 + - - +
242C VAL* 3.7 5.2 - - - +
244C VAL* 1.3 79.7 - - + +
246C GLU* 1.3 61.4 + - - +
248C SER* 3.7 4.0 - - - -
249C ASN* 3.1 33.4 + - - +
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Residues in contact with GLU 246 (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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55C SER* 4.5 3.5 + - - -
57C LYS* 3.4 26.9 + - - +
58C TRP* 3.1 29.0 + - + +
179C SER* 5.2 4.8 + - - +
181C ALA* 3.4 31.0 - - + -
242C VAL 2.9 20.0 + - - +
245C LYS* 1.3 73.1 - - - +
247C SER* 1.3 70.1 + - - +
249C ASN* 3.4 6.8 + - + +
250C ALA* 3.2 25.4 + - - +
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Residues in contact with SER 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN 4.1 4.9 - - - -
54C VAL* 3.3 12.8 - - - -
55C SER* 2.7 43.0 + - - -
58C TRP* 3.9 2.4 - - - -
243C ALA 3.0 18.3 + - - -
244C VAL 3.2 4.9 + - - -
246C GLU* 1.3 84.6 + - - +
248C SER* 1.3 58.8 + - - +
250C ALA* 3.7 5.2 + - - +
251C LYS* 3.3 33.4 + - - +
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Residues in contact with SER 248 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 2.9 20.4 + - - -
245C LYS* 3.7 6.1 - - - -
247C SER* 1.3 76.0 - - - +
249C ASN* 1.3 67.4 + - - +
251C LYS* 3.2 24.4 + - - +
252C LEU* 3.2 22.7 + - - +
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Residues in contact with ASN 249 (chain C).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C LYS* 3.1 20.0 + - - +
246C GLU* 3.4 6.2 + - - +
248C SER* 1.3 77.4 + - - +
250C ALA* 1.3 64.2 + - - +
252C LEU* 3.4 28.1 + - + +
253C LEU* 3.3 23.1 + - + +
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Residues in contact with ALA 250 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C LYS* 5.1 8.7 - - - +
246C GLU* 3.2 24.2 + - - +
247C SER* 3.8 6.3 - - - +
248C SER 3.4 0.2 - - - -
249C ASN* 1.3 76.5 - - - +
251C LYS* 1.3 64.9 + - - +
253C LEU* 3.6 27.4 + - - +
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Residues in contact with LYS 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASP 5.1 4.9 + - - -
53C GLN* 4.9 16.0 + - - +
54C VAL 6.1 2.0 - - - -
55C SER* 6.2 3.1 - - - -
247C SER* 3.3 22.9 + - - +
248C SER* 3.2 17.3 + - - +
250C ALA* 1.3 77.1 - - - +
252C LEU* 1.3 69.5 + - + +
253C LEU 3.3 5.9 + - - +
56D ALA* 4.2 20.0 - - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C SER* 3.2 16.8 + - - +
249C ASN* 3.4 28.0 + - - +
251C LYS* 1.3 78.4 - - + +
253C LEU* 1.3 68.2 + - + +
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ASN* 3.3 18.2 - - + +
250C ALA* 3.8 19.0 - - - +
251C LYS 3.3 8.2 + - - -
252C LEU* 1.3 86.5 - - + +
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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