Contacts of the helix formed by residues 216 - 253 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B ALA 3.3 25.6 - - - +
207B GLY* 3.1 12.9 + - - -
210B MET* 3.9 31.0 - - + -
211B GLY* 3.4 27.9 + - - -
215B VAL* 1.3 74.2 - - - +
217B ALA* 1.3 64.8 + - - +
218B SER* 3.2 3.1 - - - -
219B ASN* 3.2 26.0 + - + +
220B LEU* 2.9 24.7 + - - +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 4.4 11.9 - - + -
87B GLY 5.5 1.8 - - - +
89B THR* 3.5 22.7 - - - +
215B VAL* 3.2 15.8 + - + +
216B TYR* 1.3 72.4 - - - +
218B SER* 1.3 58.1 + - - +
220B LEU* 3.3 8.6 + - - +
221B ASN* 2.9 38.9 + - - +
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Residues in contact with SER 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 5.9 1.0 - - - -
29B VAL* 3.6 19.9 - - - +
83B TRP* 4.6 6.1 - - - -
216B TYR* 3.2 0.9 - - - -
217B ALA* 1.3 79.9 - - - +
219B ASN* 1.3 69.2 + - - +
222B LEU* 3.1 39.0 + - - +
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ALA* 4.6 14.8 - - + +
210B MET* 5.4 6.3 - - + +
216B TYR* 3.2 32.1 + - + +
218B SER* 1.3 79.6 + - - +
220B LEU* 1.3 62.8 + - - +
222B LEU* 3.3 14.2 + - - +
223B ILE* 3.1 35.7 + - + +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 4.1 27.8 - - + +
142B GLU* 3.8 14.6 - - - +
203B GLY* 3.4 27.5 - - - +
204B TYR* 4.1 0.2 - - - -
207B GLY* 4.0 8.1 - - - +
208B TYR* 3.8 28.7 - - + +
215B VAL* 4.8 5.4 - - + -
216B TYR 2.9 17.6 + - - +
217B ALA* 3.5 7.0 - - - +
219B ASN* 1.3 77.8 - - - +
221B ASN* 1.3 58.4 + - - +
223B ILE* 3.4 2.1 + - - +
224B TYR* 3.0 63.7 + - + +
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Residues in contact with ASN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.8 22.7 - - + -
33B PHE* 4.1 6.5 - - + -
83B TRP* 3.8 10.9 - - - -
89B THR* 2.6 44.7 + - - +
90B PRO* 3.8 6.7 - - - +
94B ARG* 2.5 29.6 + - - +
217B ALA 2.9 28.6 + - - +
218B SER 4.2 0.9 - - - +
220B LEU* 1.3 75.2 - - - +
222B LEU* 1.3 57.0 + - - +
224B TYR* 4.8 1.4 - - - -
225B ASN* 2.9 38.4 + - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.0 30.5 - - + +
29B VAL* 4.1 10.3 - - + -
32B SER* 3.8 29.5 + - - +
218B SER* 3.1 33.8 + - - +
219B ASN* 3.7 14.8 - - - +
220B LEU 3.3 0.4 - - - -
221B ASN* 1.3 76.3 - - - +
223B ILE* 1.3 59.8 + - + +
225B ASN* 3.8 1.9 - - - +
226B LEU* 3.2 28.3 + - - +
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Residues in contact with ILE 223 (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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199B ILE* 3.3 38.6 - - + +
202B ALA* 4.1 7.6 - - + +
203B GLY* 3.7 17.0 - - - +
206B ALA* 3.5 32.3 - - + -
219B ASN* 3.1 17.8 + - + +
220B LEU 4.0 0.2 - - - +
222B LEU* 1.3 76.5 - - + +
224B TYR* 1.3 55.9 + - - +
226B LEU* 3.2 8.1 + - + +
227B ALA* 2.7 36.8 + - - +
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Residues in contact with TYR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B THR* 6.1 1.6 - - + -
94B ARG* 3.4 42.2 - - + +
95B TYR* 5.2 0.2 - + - -
98B TRP* 3.7 27.4 - + + -
142B GLU* 2.6 31.6 + - - -
200B TYR* 3.5 34.7 - + - -
203B GLY* 4.1 2.7 - - - -
204B TYR* 3.8 14.0 + - - +
220B LEU* 3.0 47.5 + - + +
221B ASN* 4.8 1.1 - - - -
223B ILE* 1.3 76.5 - - - +
225B ASN* 1.3 63.7 + - - +
227B ALA* 3.2 4.1 + - - +
228B ASP* 2.9 27.7 + - - +
301B RET 3.8 11.3 - - + +
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Residues in contact with ASN 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.2 1.4 + - - +
32B SER* 2.7 37.1 + - - +
33B PHE* 3.4 34.4 - - - +
36B VAL* 4.2 9.8 - - + +
76B TYR* 3.5 14.0 + - - -
94B ARG* 2.9 26.7 + - - -
221B ASN 2.9 25.2 + - - +
222B LEU 3.8 2.5 - - - +
224B TYR* 1.3 75.2 - - - +
226B LEU* 1.3 58.5 + - - +
228B ASP* 3.3 2.6 + - - +
229B PHE* 2.9 30.2 + - - +
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 4.8 13.2 - - + -
222B LEU 3.2 16.2 + - - +
223B ILE* 3.2 8.5 + - + +
225B ASN* 1.3 78.5 - - - +
227B ALA* 1.3 58.3 + - - +
229B PHE* 3.3 10.1 + - + +
230B VAL* 2.9 47.7 + - + +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 3.6 31.0 - - + -
200B TYR* 3.5 34.5 - - + -
223B ILE 2.7 21.6 + - - +
224B TYR* 3.2 1.8 + - - +
226B LEU* 1.3 72.7 - - - +
228B ASP* 1.3 53.3 + - - +
230B VAL* 3.2 0.9 + - - -
231B ASN* 2.8 43.1 + - - +
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Residues in contact with ASP 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.8 2.0 - - + -
40B MET* 4.6 2.8 - - - +
76B TYR* 2.6 43.5 + - + +
94B ARG* 3.9 9.4 + - - -
97B ASN* 4.4 3.1 + - - -
98B TRP* 2.9 27.1 + - - -
200B TYR* 2.7 28.1 + - - -
224B TYR 2.9 15.0 + - - +
225B ASN 3.6 0.2 - - - +
227B ALA* 1.3 67.7 - - - +
229B PHE* 1.3 67.3 + - - +
232B LYS* 2.9 49.2 + - + +
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Residues in contact with PHE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 4.8 7.4 - - + -
36B VAL* 4.2 26.8 - - + +
39B GLY* 4.5 11.4 - - - -
40B MET* 5.3 0.2 - - - -
225B ASN 2.9 20.5 + - - +
226B LEU* 3.4 12.8 - - + +
228B ASP* 1.3 76.5 - - - +
230B VAL* 1.3 73.1 + - + +
233B ILE* 3.1 56.3 + - + +
234B LEU* 5.1 11.7 - - + -
100C LEU* 5.8 4.7 - - + -
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Residues in contact with VAL 230 (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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192B ILE* 4.8 5.7 - - + +
196B GLY* 4.9 6.7 - - - -
199B ILE* 4.2 21.1 - - + -
226B LEU* 2.9 41.8 + - + +
227B ALA 3.9 1.8 - - - +
229B PHE* 1.3 76.2 - - + +
231B ASN* 1.3 67.7 + - - +
234B LEU* 2.9 61.7 + - + +
235B PHE 3.7 0.7 + - - -
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Residues in contact with ASN 231 (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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105B LEU* 4.9 5.5 - - + +
192B ILE* 3.5 11.8 - - + +
196B GLY* 3.1 42.8 + - - -
197B TRP* 3.3 23.2 - - + +
199B ILE* 4.5 2.8 - - - +
200B TYR* 3.4 27.1 - - + +
227B ALA* 2.8 32.9 + - - +
230B VAL* 1.3 74.7 - - - +
232B LYS* 1.3 60.6 + - + +
235B PHE* 2.9 29.3 - - - +
301B RET 5.0 2.7 - - + -
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Residues in contact with LYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 4.1 15.5 - - + -
47B PHE* 4.4 1.6 - - - -
65B SER* 5.4 0.9 - - - +
68B ILE* 3.8 25.2 - - + +
69B THR* 4.2 11.5 - - + +
72B ALA* 4.0 23.3 - - + -
97B ASN* 4.6 2.9 - - - +
98B TRP* 4.2 3.1 - - - -
101B THR* 2.9 18.8 + - - -
105B LEU* 5.6 4.3 - - + -
228B ASP* 2.9 38.9 + - - +
231B ASN* 1.3 76.9 - - + +
233B ILE* 1.3 66.5 + - - +
235B PHE* 4.7 1.0 - - - +
236B GLY* 3.6 14.0 + - - -
301B RET 1.3 76.2 - - + +
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL 5.4 0.2 - - - +
39B GLY* 3.8 27.1 - - - +
40B MET* 3.7 23.8 - - + +
43B ALA* 3.9 16.8 - - + -
47B PHE* 3.8 5.5 - - + -
229B PHE* 3.1 52.8 + - + +
232B LYS* 1.3 76.3 - - - +
234B LEU* 1.3 67.1 + - + +
236B GLY* 3.2 4.0 + - - -
237B LEU* 2.8 45.5 + - + +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE* 5.3 4.0 - - + -
229B PHE* 4.7 10.5 - - + +
230B VAL* 2.9 52.3 + - + +
233B ILE* 1.3 76.2 - - + +
235B PHE* 1.3 56.9 + - - +
237B LEU* 3.1 23.8 + - + +
238B ILE* 2.8 36.5 + - + +
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Residues in contact with PHE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 5.4 0.4 - - - -
105B LEU* 3.2 39.5 - - + -
108B GLU* 3.2 17.9 - - + -
109B PHE* 5.1 3.1 - + - -
188B ALA 4.5 3.1 - - - -
189B MET* 3.6 59.9 - - + -
192B ILE* 3.5 31.9 - - + +
193B ILE* 6.1 0.7 - - + -
230B VAL 3.7 1.2 + - - -
231B ASN 2.9 22.6 + - - +
232B LYS* 5.6 0.7 - - - -
233B ILE 3.3 0.6 - - - -
234B LEU* 1.3 79.4 - - - +
236B GLY* 1.3 63.3 + - - +
238B ILE* 3.2 24.6 + - + +
239B ILE* 3.2 21.7 + - + +
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Residues in contact with GLY 236 (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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47B PHE* 3.4 22.4 - - - -
62B LEU* 4.7 1.0 - - - +
65B SER* 3.5 25.0 + - - -
232B LYS 3.6 8.2 + - - -
233B ILE 3.2 3.8 + - - -
235B PHE* 1.3 79.1 - - - +
237B LEU* 1.3 57.0 + - - +
239B ILE* 3.5 4.4 + - - +
240B TRP* 2.9 29.5 + - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.6 37.2 - - + -
47B PHE* 3.6 5.3 - - + -
233B ILE* 2.8 34.2 + - + +
234B LEU* 3.3 25.4 - - + +
236B GLY* 1.3 73.2 - - - +
238B ILE* 1.3 58.6 + - + +
240B TRP* 3.4 12.4 + - + +
241B ASN* 2.9 30.9 + - - +
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Residues in contact with ILE 238 (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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185B ALA* 5.2 2.7 - - - +
188B ALA* 3.3 41.7 - - + +
192B ILE* 4.8 9.0 - - + -
234B LEU* 2.8 25.9 + - + +
235B PHE* 3.2 20.2 + - + +
237B LEU* 1.3 72.0 - - + +
239B ILE* 1.3 63.2 + - + +
241B ASN* 2.9 22.9 + - - +
242B VAL* 3.0 23.9 + - + +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 4.6 12.8 - - + +
61B SER* 3.9 34.5 - - - +
62B LEU* 4.9 6.5 - - + +
65B SER* 4.9 2.2 - - - +
108B GLU* 4.4 15.3 - - + +
112B ILE* 4.9 3.8 - - + -
185B ALA* 4.6 13.7 - - + -
189B MET* 3.6 29.6 - - + -
235B PHE* 3.2 28.5 + - + +
236B GLY* 3.9 9.0 - - - +
238B ILE* 1.3 76.5 - - + +
240B TRP* 1.3 65.0 + - - +
242B VAL* 3.4 5.7 + - - +
243B ALA* 2.9 27.4 + - + +
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Residues in contact with TRP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.7 24.0 - + - -
47B PHE* 4.6 2.9 - - + -
50B GLU* 2.9 48.8 + - + +
62B LEU* 4.1 26.0 - - + +
236B GLY 2.9 18.3 + - - +
237B LEU* 3.5 18.8 - - + +
239B ILE* 1.3 75.3 - - - +
241B ASN* 1.3 93.3 + - + +
243B ALA* 3.6 4.3 - - - +
244B VAL* 2.9 61.9 + - + +
60C THR* 3.7 25.8 - - + -
111C LEU* 6.1 3.4 - - + -
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Residues in contact with ASN 241 (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 LEU 2.9 17.2 + - - +
238B ILE* 2.9 11.3 + - - +
240B TRP* 1.3 92.8 - - + +
242B VAL* 1.3 66.7 + - + +
244B VAL* 4.1 2.9 - - - +
245B LYS* 3.1 56.6 + - - +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TRP* 3.6 19.7 - - + -
181B ALA* 3.5 29.2 - - + +
184B SER* 4.0 15.9 - - - +
185B ALA* 4.1 22.7 - - + +
188B ALA* 5.8 0.2 - - + -
238B ILE* 3.0 23.5 + - + +
239B ILE* 3.9 8.1 - - - +
241B ASN* 1.3 76.2 - - - +
243B ALA* 1.3 55.1 + - - +
245B LYS* 3.1 8.7 + - - +
246B GLU* 2.8 32.9 + - - +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.7 13.7 - - + -
58B TRP* 3.4 46.4 - - + -
62B LEU* 4.9 2.5 - - + -
239B ILE* 2.9 21.7 + - + +
240B TRP* 3.6 4.5 - - - +
242B VAL* 1.3 73.3 - - - +
244B VAL* 1.3 58.7 + - - +
247B SER* 2.9 35.9 + - - -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN* 3.8 36.7 - - + +
54B VAL* 3.9 4.9 - - + -
240B TRP* 2.9 62.9 + - + +
241B ASN* 4.1 4.7 - - - +
243B ALA* 1.3 71.4 - - - +
245B LYS* 1.3 59.0 + - + +
247B SER* 3.4 1.7 + - - -
248B SER* 3.0 32.3 + - - -
60C THR* 5.8 0.9 - - - +
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Residues in contact with LYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ASN* 3.1 47.6 + - - +
242B VAL* 3.1 7.8 + - - +
244B VAL* 1.3 75.8 - - + +
246B GLU* 1.3 64.6 + - - +
248B SER* 3.1 21.3 + - - +
249B ASN* 3.1 20.8 + - - +
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 3.7 8.1 + - - -
57B LYS* 3.6 20.4 + - - +
58B TRP* 3.0 35.3 + - + +
181B ALA* 3.4 32.8 - - + -
242B VAL 2.8 19.0 + - - +
243B ALA 4.0 0.2 - - - +
245B LYS* 1.3 73.2 - - - +
247B SER* 1.3 66.4 + - - +
249B ASN* 3.5 8.1 + - - +
250B ALA* 3.0 30.4 + - - +
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Residues in contact with SER 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLN 4.1 4.9 - - - -
54B VAL* 3.3 8.1 - - - -
55B SER* 2.7 44.0 + - - -
58B TRP* 3.8 2.3 - - - -
243B ALA 2.9 22.2 + - - -
244B VAL 3.9 2.7 - - - -
246B GLU* 1.3 80.1 - - - +
248B SER* 1.3 56.5 + - - +
250B ALA* 3.3 4.7 + - - +
251B LYS* 3.0 41.4 + - - +
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B VAL* 3.0 18.7 + - - -
245B LYS* 3.1 13.9 + - - +
247B SER* 1.3 74.7 - - - +
249B ASN* 1.3 61.9 + - - +
251B LYS* 3.4 7.4 + - - +
252B LEU* 2.8 45.2 + - - +
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LYS* 3.1 23.1 + - - +
246B GLU* 3.6 7.4 - - - +
248B SER* 1.3 86.4 + - - +
250B ALA* 1.3 55.3 + - - +
252B LEU* 3.3 15.9 + - - +
253B LEU* 3.0 37.6 + - + +
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Residues in contact with ALA 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 6.2 2.2 - - - -
57B LYS* 4.8 9.2 - - - +
246B GLU* 3.0 33.6 + - - +
247B SER* 3.8 5.6 - - - +
248B SER 3.3 0.2 - - - -
249B ASN* 1.3 73.6 - - - +
251B LYS* 1.3 65.3 + - + +
253B LEU* 3.6 11.0 + - - +
254B GLU* 3.6 16.7 + - - +
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP 5.1 5.3 + - - -
53B GLN* 5.1 3.6 - - - +
54B VAL 5.0 14.1 + - - +
55B SER* 5.0 8.3 - - - +
247B SER* 3.0 32.0 + - - +
248B SER* 3.9 5.4 - - - +
250B ALA* 1.3 76.0 - - + +
252B LEU* 1.3 62.2 + - - +
254B GLU* 3.2 35.6 + - - +
255B HIS* 4.8 4.2 - - - -
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER* 2.8 31.1 + - - +
249B ASN* 3.3 19.0 + - - +
251B LYS* 1.3 74.6 - - - +
253B LEU* 1.3 63.2 + - + +
254B GLU 3.1 6.0 + - - -
255B HIS* 3.8 20.7 - - + +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ASN* 3.0 26.1 + - + +
250B ALA* 4.0 8.1 - - - +
251B LYS 3.4 0.4 - - - -
252B LEU* 1.3 75.0 - - + +
254B GLU* 1.3 54.5 + - - +
255B HIS 3.0 18.5 + - - +
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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