Contacts of the helix formed by residues 249 - 276 (chain F) in PDB entry 2NQB
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 LEU 249 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721E PRO* 3.6 26.9 - - + +
247F SER* 3.0 4.1 + - - +
248F GLY* 1.3 78.4 - - - +
250F ILE* 1.3 62.3 + - - +
251F TYR 3.3 1.0 + - - -
252F GLU* 3.7 9.9 + - + +
253F GLU* 3.4 20.3 + - - +
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Residues in contact with ILE 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704E PHE* 4.1 16.6 - - + -
719E ILE* 3.3 33.0 - - + +
720E MET 3.6 29.2 - - - +
721E PRO* 3.8 1.6 - - + -
724E ILE* 3.6 20.6 - - + -
234F ILE* 4.6 4.9 - - + -
246F ILE* 3.4 23.1 - - + -
247F SER* 2.9 18.6 + - - +
249F LEU* 1.3 79.3 - - - +
251F TYR* 1.3 55.3 + - - +
253F GLU* 3.4 4.1 + - - +
254F THR* 2.7 48.3 + - - +
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Residues in contact with TYR 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F LYS* 3.5 53.5 - - + -
234F ILE* 3.6 33.8 - - + +
235F ARG* 3.0 34.8 + - + -
246F ILE* 3.7 23.9 + - + +
247F SER 4.1 8.7 - - - -
248F GLY* 3.3 26.0 - - - +
249F LEU 3.3 0.8 - - - -
250F ILE* 1.3 77.0 - - + +
252F GLU* 1.3 62.6 + - - +
254F THR 3.4 0.9 + - - -
255F ARG* 3.1 45.7 + - - +
81I G 4.4 1.0 + - - -
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Residues in contact with GLU 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ILE* 5.9 0.2 - - - +
227F GLN* 3.7 14.1 + - - +
248F GLY 5.1 0.6 + - - -
249F LEU* 3.7 12.9 + - + +
250F ILE 3.4 0.2 - - - -
251F TYR* 1.3 76.4 - - - +
253F GLU* 1.3 65.4 + - - +
255F ARG* 3.0 42.8 + - - +
256F GLY* 3.2 17.7 + - - -
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Residues in contact with GLU 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721E PRO* 4.1 15.3 - - + +
724E ILE* 4.2 27.9 - - + +
725E GLN* 2.6 41.3 + - - +
249F LEU 3.4 14.9 + - - +
250F ILE* 3.4 5.3 + - - +
251F TYR 3.3 0.4 - - - -
252F GLU* 1.3 77.8 - - - +
254F THR* 1.3 62.0 + - - +
256F GLY* 3.3 3.4 + - - +
257F VAL* 3.1 31.0 + - + +
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Residues in contact with THR 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700E LEU* 4.2 26.0 - - + +
704E PHE* 3.5 33.6 - - + -
724E ILE* 4.2 6.4 - - - +
229F ILE* 5.8 1.8 - - + -
234F ILE* 4.0 22.0 - - + -
237F LEU* 5.7 0.4 - - + -
250F ILE* 2.7 27.1 + - - +
251F TYR 3.6 5.4 - - - -
252F GLU 3.2 0.2 - - - -
253F GLU* 1.3 75.0 - - - +
255F ARG* 1.3 59.0 + - - +
257F VAL* 3.2 6.8 + - - +
258F LEU* 2.8 28.3 + - + +
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Residues in contact with ARG 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226F ILE* 3.5 42.0 + - + +
227F GLN* 3.7 27.3 + - - +
229F ILE* 3.0 28.7 + - + +
230F THR* 3.9 2.4 - - - +
231F LYS* 3.7 20.4 - - - +
234F ILE* 4.2 10.6 - - + +
251F TYR* 3.1 35.5 + - - +
252F GLU* 3.0 41.4 + - - +
253F GLU 3.3 0.2 - - - -
254F THR* 1.3 75.5 - - - +
256F GLY* 1.3 57.7 + - - +
258F LEU* 3.2 4.5 + - - -
259F LYS* 2.9 30.9 + - - +
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Residues in contact with GLY 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F GLU 3.2 11.0 + - - -
253F GLU* 3.3 4.5 + - - -
254F THR 3.2 0.2 - - - -
255F ARG* 1.3 80.6 - - - +
257F VAL* 1.3 59.6 + - - +
259F LYS* 3.4 6.9 + - - +
260F VAL* 3.2 29.3 + - - +
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Residues in contact with VAL 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699E TYR* 3.6 21.7 - - + +
700E LEU* 4.4 4.7 - - + -
703E LEU* 3.6 27.4 - - + -
724E ILE* 4.2 18.8 - - + -
728E ARG* 4.0 27.7 + - - +
253F GLU* 3.1 22.5 + - + +
254F THR* 3.6 10.1 - - - +
256F GLY* 1.3 72.9 - - - +
258F LEU* 1.3 66.6 + - - +
260F VAL* 3.4 7.0 + - - +
261F PHE* 3.1 21.3 + - - +
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Residues in contact with LEU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662E ILE* 4.4 6.1 - - + -
667E PHE* 4.8 2.0 - - + -
670E LEU* 4.3 7.9 - - + -
696E SER* 3.8 28.3 - - - -
699E TYR* 5.7 0.7 - - + -
700E LEU* 4.1 30.9 - - + +
226F ILE* 4.7 1.8 - - + -
229F ILE* 3.8 40.8 - - + -
254F THR* 2.8 17.8 + - + +
255F ARG* 3.7 5.2 - - - +
257F VAL* 1.3 79.1 - - - +
259F LYS* 1.3 58.1 + - - +
261F PHE* 3.2 9.4 + - + +
262F LEU* 2.8 44.6 + - + +
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Residues in contact with LYS 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670E LEU* 5.7 1.1 - - + -
673E GLU* 4.9 11.4 + - - -
674E ILE* 4.2 21.1 - - + -
226F ILE* 4.4 26.2 - - + +
255F ARG 2.9 16.7 + - - +
256F GLY* 3.7 8.1 - - - +
257F VAL 3.3 0.2 - - - -
258F LEU* 1.3 78.4 - - - +
260F VAL* 1.3 58.2 + - + +
262F LEU* 3.7 5.4 - - - +
263F GLU* 2.8 59.7 + - + +
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Residues in contact with VAL 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728E ARG* 4.5 22.4 - - - +
256F GLY 3.2 16.9 + - - +
257F VAL* 3.8 6.7 - - - +
258F LEU 3.3 0.2 - - - -
259F LYS* 1.3 77.4 - - + +
261F PHE* 1.3 64.9 + - - +
263F GLU* 3.7 14.8 - - - +
264F ASN* 3.1 41.5 + - - +
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Residues in contact with PHE 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692E LEU* 5.2 1.6 - - + -
695E ALA* 4.0 9.0 - - + -
696E SER* 3.7 37.9 - - - -
699E TYR* 3.5 55.6 - + + -
257F VAL 3.1 14.3 + - - +
258F LEU* 3.5 9.0 - - + +
260F VAL* 1.3 79.4 - - - +
262F LEU* 1.3 67.2 + - + +
264F ASN* 3.4 5.5 + - - +
265F VAL* 3.1 45.4 + - + +
290F LEU* 4.3 12.8 - - + -
293F GLN* 4.1 16.8 - - - -
295F ARG* 4.4 13.7 - - - -
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667E PHE* 3.9 23.6 - - + -
670E LEU* 3.6 35.7 - - + -
671E VAL* 4.5 7.0 - - + -
674E ILE* 3.9 12.6 - - + -
692E LEU* 4.3 17.0 - - + -
696E SER* 3.4 23.3 - - - +
258F LEU* 2.8 24.6 + - + +
259F LYS* 3.8 2.7 - - - +
261F PHE* 1.3 78.6 - - + +
263F GLU* 1.3 60.1 + - - +
265F VAL* 3.4 1.7 + - + +
266F ILE* 2.8 51.3 + - + +
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Residues in contact with GLU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674E ILE* 4.0 24.5 - - + +
259F LYS* 2.8 61.9 + - + +
260F VAL* 3.7 18.8 + - - +
262F LEU* 1.3 72.5 - - - +
264F ASN* 1.3 59.9 + - - +
266F ILE* 4.1 0.6 - - - +
267F ARG* 2.9 47.7 + - - +
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Residues in contact with ASN 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F VAL* 3.1 39.6 + - - +
261F PHE* 3.8 4.7 - - - +
263F GLU* 1.3 79.5 - - - +
265F VAL* 1.3 61.3 + - - +
267F ARG* 3.0 28.5 + - - +
268F ASP* 3.4 26.9 + - - +
293F GLN* 3.4 18.8 + - - +
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Residues in contact with VAL 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692E LEU* 3.8 24.0 - - + -
261F PHE* 3.1 29.3 + - + +
262F LEU* 4.1 3.4 - - - +
264F ASN* 1.3 73.5 - - - +
266F ILE* 1.3 62.1 + - - +
268F ASP* 3.3 1.8 + - - -
269F ALA* 2.8 26.6 + - + +
286F VAL* 4.6 3.1 - - + +
289F ALA* 3.5 19.5 - - + +
290F LEU* 3.9 31.4 - - + +
293F GLN* 3.2 29.2 - - - +
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Residues in contact with ILE 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671E VAL* 3.9 29.6 - - + +
674E ILE* 3.7 24.2 - - + +
675E ALA* 3.8 31.2 - - + +
678E PHE* 5.3 3.8 - - + -
684E PHE* 5.4 2.2 - - + -
692E LEU* 4.2 21.1 - - + -
262F LEU* 2.8 40.1 + - + +
263F GLU 4.1 1.6 - - - +
265F VAL* 1.3 69.4 - - - +
267F ARG* 1.3 59.3 + - - +
269F ALA* 3.0 7.2 + - + -
270F VAL* 2.7 42.5 + - + +
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Residues in contact with ARG 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678E PHE* 3.5 44.5 - - + -
263F GLU* 2.9 35.9 + - - +
264F ASN* 3.0 38.2 + - - +
266F ILE* 1.3 78.9 - - - +
268F ASP* 1.3 62.0 + - - +
270F VAL 3.5 0.9 + - - -
271F THR* 2.8 36.7 + - - +
1496H ARG 6.1 1.3 - - - -
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Residues in contact with ASP 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ASN 3.4 13.0 + - - +
265F VAL* 3.3 7.3 + - - +
266F ILE 3.2 0.4 - - - -
267F ARG* 1.3 85.5 - - - +
269F ALA* 1.3 67.9 + - - +
271F THR* 3.0 11.6 + - - -
272F TYR* 3.1 19.7 + - + -
289F ALA* 3.7 19.3 - - + +
292F ARG* 3.0 34.7 + - - +
293F GLN* 4.7 8.5 + - - +
1496H ARG 5.6 0.2 - - - +
1497H LEU* 3.6 23.7 - - + +
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Residues in contact with ALA 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692E LEU* 5.7 0.9 - - + -
265F VAL* 2.8 23.1 + - + +
266F ILE* 3.5 9.0 - - + +
268F ASP* 1.3 73.0 - - - +
270F VAL* 1.3 63.5 + - + +
272F TYR* 3.2 6.6 + - - +
273F THR* 3.1 23.5 + - - -
281F VAL* 4.3 9.0 - - + -
285F ASP* 3.7 25.5 - - - +
286F VAL* 4.2 15.5 - - + +
289F ALA* 3.4 9.8 - - + +
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Residues in contact with VAL 270 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675E ALA* 4.7 2.0 - - + -
678E PHE* 3.5 32.1 - - + -
679E LYS* 3.9 9.2 - - + -
682E LEU* 3.5 36.6 - - + -
684E PHE* 5.4 0.4 - - + -
266F ILE* 2.7 37.8 + - + +
267F ARG 3.9 0.2 - - - +
269F ALA* 1.3 73.4 - - + +
271F THR* 1.3 62.3 + - - +
273F THR* 3.2 7.5 + - - -
274F GLU* 3.0 31.1 + - + +
281F VAL* 4.2 12.1 - - + -
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Residues in contact with THR 271 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678E PHE* 4.0 12.5 - - - -
267F ARG* 2.8 22.6 + - - +
268F ASP* 3.0 9.6 + - - -
270F VAL* 1.3 78.1 - - - +
272F TYR* 1.3 56.1 + - - +
274F GLU* 3.5 10.5 + - + +
275F HIS* 3.0 27.2 + - - +
1493H THR* 3.7 27.3 - - + +
1496H ARG* 4.9 14.8 - - + +
1497H LEU* 3.9 21.7 - - + +
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Residues in contact with TYR 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F ASP* 3.1 25.9 + - + -
269F ALA 3.2 4.0 + - - +
271F THR* 1.3 73.7 - - - +
273F THR* 1.3 66.1 + - - +
275F HIS* 3.4 6.5 + - - +
276F ALA* 3.2 22.5 + - - +
278F ARG* 4.4 0.2 + - - -
285F ASP* 3.6 26.5 - - + +
288F TYR* 3.8 30.8 + + + -
289F ALA* 3.9 10.8 - - - -
292F ARG* 3.0 28.8 - - - +
1473H GLU* 2.9 22.9 + - - -
1476H ARG* 5.6 0.7 - - - -
1477H LEU* 3.5 30.3 - - + -
1480H TYR* 3.7 26.2 + + + -
1481H ASN* 5.1 4.0 + - - +
1497H LEU* 3.8 11.4 - - + -
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Residues in contact with THR 273 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682E LEU* 4.8 6.1 - - + -
269F ALA 3.1 11.9 + - - -
270F VAL* 3.2 12.1 + - - -
272F TYR* 1.3 77.5 - - - +
274F GLU* 1.3 65.0 + - + +
276F ALA* 3.0 14.0 + - - +
277F LYS 3.1 8.3 + - - -
278F ARG* 3.2 36.4 + - - +
279F LYS* 4.3 2.2 - - - -
280F THR 3.6 27.1 - - - +
281F VAL* 3.6 15.5 - - + +
285F ASP* 2.8 23.1 + - - +
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Residues in contact with GLU 274 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678E PHE* 4.2 10.6 - - - -
679E LYS* 3.1 42.7 - - + +
682E LEU* 5.7 2.9 - - + -
270F VAL* 3.0 29.9 + - + +
271F THR* 3.8 8.4 + - - +
273F THR* 1.3 78.3 - - + +
275F HIS* 1.3 57.6 + - - +
277F LYS* 2.7 21.4 + - - +
278F ARG 4.6 7.9 - - - +
1489H ARG* 3.2 11.3 + - - -
----------------------------------------------------------
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Residues in contact with HIS 275 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271F THR 3.0 17.9 + - - +
272F TYR 3.7 6.3 - - - +
273F THR 3.3 0.2 - - - -
274F GLU* 1.3 75.8 - - - +
276F ALA* 1.3 58.7 + - - +
277F LYS* 3.1 0.7 - - - +
1477H LEU* 4.0 19.3 + - + +
1478H ALA* 5.7 0.2 - - - -
1481H ASN* 3.5 26.1 + - - +
1483H ARG* 6.3 0.6 - - - +
1489H ARG* 2.7 62.9 + - + +
1490H GLU* 3.1 39.4 + - + +
1493H THR* 2.8 34.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 276 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F TYR 3.2 11.1 + - - +
273F THR 3.0 10.5 + - - +
275F HIS* 1.3 74.6 - - - +
277F LYS* 1.3 72.0 + - - +
278F ARG* 3.5 32.3 + - - +
1481H ASN* 2.9 27.8 - - - +
----------------------------------------------------------
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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