Contacts of the helix formed by residues 225 - 247 (chain N) in PDB entry 3FKS
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 PRO 225 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302J TYR* 3.2 33.8 - - + +
19N ALA* 4.6 11.2 - - + -
63N ALA 4.3 8.3 - - - +
64N MET* 3.5 8.7 - - - +
65N ASP* 3.5 47.8 - - - +
223N ASN 4.3 0.4 - - - +
224N GLU* 1.3 92.0 - - + +
226N PRO* 1.3 78.6 - - + +
227N GLY 3.0 2.4 + - - +
228N ALA* 3.2 13.9 + - - +
229N ARG* 3.9 2.6 - - - -
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Residues in contact with PRO 226 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298J GLY 4.1 3.1 - - - +
299J ASP* 4.4 5.8 - - + -
302J TYR* 4.0 15.3 - - + -
19N ALA* 4.7 4.7 - - + -
224N GLU 3.7 0.2 - - - -
225N PRO* 1.3 87.2 - - + +
227N GLY* 1.3 63.0 + - - +
228N ALA 3.4 0.3 + - - -
229N ARG* 3.6 16.6 + - - +
230N ALA* 3.4 17.3 + - - +
264N ALA* 4.2 3.5 - - + +
267N GLU* 3.7 33.7 - - + +
268N VAL* 3.5 25.6 - - + +
271N LEU* 3.8 24.9 - - + -
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Residues in contact with GLY 227 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N ALA* 6.1 1.0 - - - +
62N ILE* 4.1 15.2 - - - +
63N ALA 3.6 17.2 + - - -
64N MET* 3.7 6.7 - - - -
225N PRO* 3.0 2.8 + - - +
226N PRO* 1.3 81.5 - - - +
228N ALA* 1.3 61.7 + - - +
230N ALA* 3.6 2.3 + - - +
231N ARG* 3.2 27.9 + - - +
268N VAL* 3.8 12.5 - - - +
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Residues in contact with ALA 228 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ALA 4.3 1.6 + - - -
64N MET* 3.7 29.6 - - - +
98N VAL* 4.0 18.4 - - + -
224N GLU* 3.4 26.5 - - + +
225N PRO 3.2 10.6 + - - +
227N GLY* 1.3 75.4 - - - +
229N ARG* 1.3 59.0 + - - +
231N ARG* 2.8 21.3 + - - +
232N VAL* 2.9 18.0 + - - +
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Residues in contact with ARG 229 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301J PHE* 3.2 30.1 - - - -
302J TYR* 3.9 9.7 - - - +
187N VAL* 3.4 13.5 - - - +
188N GLY* 4.4 11.8 - - - +
220N GLY 3.9 9.0 - - - +
221N GLN 3.6 16.8 - - - +
222N MET* 3.7 13.5 + - - +
224N GLU* 3.1 31.3 + - - +
225N PRO 3.9 4.0 - - - +
226N PRO* 3.6 18.7 + - - +
227N GLY 3.6 0.4 - - - -
228N ALA* 1.3 78.9 - - - +
230N ALA* 1.3 58.7 + - - +
232N VAL* 3.1 25.5 - - - +
233N ALA 4.4 0.9 + - - -
260N ARG* 4.7 6.8 + - - +
261N PHE* 4.4 3.3 - - - -
263N GLN* 5.4 2.0 - - - +
264N ALA* 4.0 20.5 - - + +
267N GLU* 2.7 39.7 + - - -
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Residues in contact with ALA 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226N PRO 3.4 15.2 + - - +
227N GLY 3.9 4.7 - - - +
228N ALA 3.1 1.2 - - - -
229N ARG* 1.3 79.6 - - - +
231N ARG* 1.3 75.0 + - + +
233N ALA 4.6 0.6 + - - -
234N LEU* 4.3 4.0 - - - +
261N PHE* 3.2 32.0 - - + +
264N ALA* 4.0 22.6 - - + +
265N GLY* 4.3 7.0 - - - +
268N VAL* 4.3 9.2 - - + -
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Residues in contact with ARG 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34N LEU* 4.9 6.4 - - - +
49N GLU* 3.3 29.2 + - - +
51N ALA* 6.3 0.8 - - - +
62N ILE* 5.1 7.2 - - + +
64N MET* 4.0 9.6 - - + -
83N ILE* 5.4 3.1 - - + -
98N VAL* 4.2 11.4 - - + -
117N ILE* 5.2 5.8 - - + +
118N HIS* 3.2 27.6 - - - -
227N GLY* 3.2 16.9 + - - +
228N ALA 2.8 5.8 + - - +
230N ALA* 1.3 88.4 + - - +
232N VAL* 1.3 58.6 + - - +
233N ALA 3.1 2.7 - - - -
234N LEU* 2.9 38.1 + - + +
235N THR* 3.0 14.8 + - - +
268N VAL* 5.4 11.3 - - - +
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Residues in contact with VAL 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N VAL* 3.5 26.5 - - + +
185N THR* 3.3 17.7 - - + +
186N GLY 4.7 0.2 - - - +
187N VAL* 3.9 17.9 - - + -
218N VAL* 4.2 5.6 - - + +
220N GLY* 3.5 35.2 - - - +
224N GLU* 4.7 0.9 - - - +
228N ALA* 2.9 21.6 + - + +
229N ARG* 3.1 26.7 - - - +
231N ARG* 1.3 78.4 - - - +
233N ALA* 1.3 61.6 + - - +
235N THR* 3.3 18.6 + - - -
236N GLY 3.5 3.8 + - - -
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Residues in contact with ALA 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185N THR* 4.2 4.2 - - - +
187N VAL* 3.9 22.7 - - + -
229N ARG 4.4 0.2 + - - -
231N ARG 3.1 0.6 - - - -
232N VAL* 1.3 82.6 - - - +
234N LEU* 1.3 58.6 + - - +
236N GLY* 4.2 1.0 + - - -
237N LEU* 3.5 19.9 + - - +
253N LEU* 5.0 0.2 - - - +
255N ILE* 4.7 14.4 - - + +
261N PHE* 3.7 35.4 - - + -
292N LEU* 3.7 18.7 - - + +
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Residues in contact with LEU 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N ILE* 4.1 15.9 - - + +
118N HIS* 3.7 31.4 - - + +
230N ALA 4.3 5.8 - - - +
231N ARG* 2.9 33.9 + - + +
233N ALA* 1.3 77.5 - - + +
235N THR* 1.3 66.1 + - - +
236N GLY 3.2 2.2 - - - -
237N LEU* 3.1 11.7 + - - +
238N THR* 3.1 21.0 + - - -
261N PHE* 5.4 4.0 - - + -
291N LEU* 4.1 12.1 - - + +
292N LEU* 3.6 23.8 - - + -
295N ARG* 3.5 23.7 + - - +
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Residues in contact with THR 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N VAL* 3.7 23.0 - - + +
96N ILE* 4.8 4.9 - - + -
97N ASN 3.7 13.9 - - - +
98N VAL* 3.0 32.4 + - - +
117N ILE* 4.1 14.3 - - - +
218N VAL* 4.0 12.3 - - + -
231N ARG* 3.0 13.8 + - - +
232N VAL* 3.5 15.7 - - - -
234N LEU* 1.3 79.5 - - - +
236N GLY* 1.3 58.5 + - - +
238N THR* 3.9 0.7 + - - -
239N ILE* 3.2 25.8 + - + +
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Residues in contact with GLY 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N VAL* 3.7 7.9 - - - +
185N THR* 3.8 17.7 - - - -
218N VAL* 4.1 12.0 - - - +
232N VAL 3.5 6.5 + - - -
234N LEU 3.2 0.2 - - - -
235N THR* 1.3 76.2 - - - +
237N LEU* 1.3 65.3 + - - +
238N THR 3.1 2.0 - - - -
239N ILE* 3.0 26.0 + - - +
240N ALA 3.2 5.4 + - - -
253N LEU* 4.0 8.0 - - - +
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Residues in contact with LEU 237 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233N ALA 3.5 17.6 + - - +
234N LEU* 3.1 6.8 + - - +
236N GLY* 1.3 77.8 - - - +
238N THR* 1.3 58.9 + - - +
240N ALA* 3.4 2.4 + - - +
241N GLU* 3.1 22.4 + - + +
253N LEU* 3.4 28.6 - - + +
292N LEU* 3.5 32.5 - - + +
295N ARG* 3.2 53.2 - - + +
296N ILE* 3.8 17.5 - - + -
304N VAL* 4.9 6.5 - - + -
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Residues in contact with THR 238 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N VAL* 4.6 4.3 - - + -
87N VAL* 4.2 5.2 - - + +
115N LYS* 3.9 27.4 - - + +
116N PRO 3.2 20.6 - - - +
117N ILE* 3.1 16.4 + - - -
234N LEU 3.1 13.3 + - - -
235N THR 4.1 5.6 - - - -
236N GLY 3.1 0.2 - - - -
237N LEU* 1.3 74.1 - - - +
239N ILE* 1.3 65.2 + - - +
241N GLU* 3.2 22.5 + - - +
242N TYR* 3.3 13.0 + - - +
295N ARG* 2.9 19.5 + - - +
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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
----------------------------------------------------------
85N VAL* 3.8 17.0 - - + -
86N PRO* 3.2 26.5 - - + +
87N VAL* 4.0 10.0 - - + +
88N GLY 5.3 0.4 - - - +
91N THR* 4.2 16.6 - - + +
96N ILE* 6.3 5.2 - - + -
183N VAL* 3.9 17.3 - - + -
216N ALA* 4.6 7.2 - - + -
218N VAL* 4.9 7.2 - - + -
235N THR* 3.2 22.9 - - + +
236N GLY* 3.0 13.2 + - - +
238N THR* 1.3 78.0 - - - +
240N ALA* 1.3 59.0 + - - +
241N GLU 3.5 0.2 + - - -
242N TYR* 3.6 8.3 + - - +
243N PHE* 3.0 39.8 - - + -
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Residues in contact with ALA 240 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183N VAL* 4.1 8.7 - - + +
236N GLY 3.2 6.7 + - - +
237N LEU* 3.9 7.4 - - - +
238N THR 3.3 0.2 - - - -
239N ILE* 1.3 77.7 - - - +
241N GLU* 1.3 65.3 + - - +
242N TYR 3.4 0.2 + - - -
243N PHE* 3.5 2.8 + - - -
244N ARG 3.2 15.4 + - - -
251N VAL* 3.4 35.3 - - + +
253N LEU* 4.5 11.9 - - + -
304N VAL* 3.5 24.3 - - + +
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Residues in contact with GLU 241 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N LYS* 5.8 5.5 - - + +
119N ALA* 4.4 13.0 - - - +
120N ASP 5.3 2.1 - - - +
122N PRO* 5.3 2.6 - - - +
237N LEU* 3.1 17.9 + - + +
238N THR* 3.2 19.7 + - + +
240N ALA* 1.3 74.2 - - - +
242N TYR* 1.3 60.4 + - - +
244N ARG* 3.0 36.0 + - - +
245N ASP* 2.8 38.6 + - - +
295N ARG* 3.3 50.8 + - - +
304N VAL* 4.5 1.3 - - + +
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Residues in contact with TYR 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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87N VAL* 3.4 39.3 - - + -
88N GLY* 4.0 25.4 - - - +
112N LYS* 3.4 28.2 + - - -
113N LEU* 4.1 14.8 - - + +
115N LYS* 4.1 25.5 - - + +
238N THR 3.3 4.6 + - - +
239N ILE 3.8 9.9 - - - +
240N ALA 3.3 0.6 - - - -
241N GLU* 1.3 78.2 - - - +
243N PHE* 1.3 61.7 + + + +
245N ASP* 5.1 0.7 - - - -
246N GLU* 2.6 80.9 + - + +
247N GLU* 4.2 12.8 - - - -
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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
----------------------------------------------------------
88N GLY* 2.9 41.5 - - - -
89N ARG* 4.2 11.7 - - + -
91N THR* 4.6 2.2 - - - -
92N LEU* 4.6 12.6 - - + -
181N PHE* 4.3 12.6 - + + -
183N VAL* 4.5 7.2 - - + -
239N ILE* 3.0 44.2 - - + -
240N ALA* 3.9 6.3 - - - +
241N GLU 3.4 0.6 - - - -
242N TYR* 1.3 77.5 - + - +
244N ARG* 1.3 56.8 + - - +
247N GLU* 3.0 42.3 + - - +
249N GLN* 3.0 46.5 + - - +
251N VAL* 3.6 17.5 - - + -
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Residues in contact with ARG 244 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N PRO* 4.2 13.3 - - - +
240N ALA 3.2 2.0 + - - +
241N GLU* 3.0 38.4 + - - +
243N PHE* 1.3 80.1 - - - +
245N ASP* 1.3 75.5 + - - +
248N GLY* 3.3 10.7 - - - -
249N GLN 3.8 8.3 - - - -
251N VAL* 3.8 0.8 - - + +
295N ARG 3.2 22.6 + - - -
297N THR* 2.9 26.9 + - - +
299N THR* 3.6 22.8 - - - +
301N LYS* 3.3 4.2 - - - +
302N GLY 3.2 23.8 + - - -
303N SER* 3.2 33.0 - - - +
304N VAL* 3.4 31.9 - - + +
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Residues in contact with ASP 245 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115N LYS* 5.4 10.5 + - - +
122N PRO* 6.0 0.2 - - - +
241N GLU* 2.8 26.3 + - - +
242N TYR* 4.3 1.3 - - - +
244N ARG* 1.3 103.2 + - - +
246N GLU* 1.3 64.1 + - - +
299N THR* 3.5 20.3 + - - +
301N LYS* 3.5 34.8 + - + +
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Residues in contact with GLU 246 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112N LYS* 4.5 5.7 + - - -
113N LEU* 4.6 6.3 - - - +
115N LYS* 5.7 3.3 + - - +
242N TYR* 2.6 73.0 + - + +
245N ASP* 1.3 79.0 - - + +
247N GLU* 1.3 61.6 + - + +
248N GLY 3.4 2.2 + - - -
301N LYS* 5.8 1.8 + - - +
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Residues in contact with GLU 247 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY* 5.0 2.1 - - - +
300E LYS* 3.9 10.4 + - - +
89N ARG* 3.5 40.5 + - - +
242N TYR* 4.2 11.1 - - + -
243N PHE* 3.0 30.1 + - - +
246N GLU* 1.3 88.6 - - + +
248N GLY* 1.3 65.8 + - - +
249N GLN* 3.0 27.7 + - + +
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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