Contacts of the helix formed by residues 259 - 291 (chain B) in PDB entry 3NA0
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 ARG 259 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B TRP* 3.7 33.1 - - - -
246B PRO* 3.1 49.7 + - - +
247B MET* 3.9 14.6 - - + -
250B LEU* 4.1 11.4 - - + +
255B PHE* 3.0 26.3 + - + +
258B PHE* 1.3 97.4 + - + +
260B THR* 1.3 65.3 + - - +
261B LYS 3.2 2.7 - - - -
262B THR* 3.0 10.7 + - - +
263B TRP* 2.8 20.4 + - - +
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Residues in contact with THR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE 3.3 2.3 + - - -
256B ARG* 2.7 29.7 + - - +
257B LEU* 3.7 12.0 + - - -
258B PHE 3.6 1.4 - - - -
259B ARG* 1.3 76.1 - - - +
261B LYS* 1.3 56.7 + - - +
263B TRP* 3.5 9.2 + - + +
264B LYS* 3.0 30.4 + - + +
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Residues in contact with LYS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG 3.2 0.8 - - - -
260B THR* 1.3 75.7 - - - +
262B THR* 1.3 67.1 + - - +
264B LYS* 3.3 10.2 + - + +
265B ASP* 3.0 56.5 + - - +
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Residues in contact with THR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 3.0 36.3 - - - +
246B PRO* 3.8 24.4 - - + +
247B MET* 3.7 17.9 - - + -
259B ARG* 3.0 17.7 + - - -
261B LYS* 1.3 78.5 - - - +
263B TRP* 1.3 52.1 + - - +
265B ASP* 3.2 9.8 + - - +
266B HIS* 2.8 32.4 + - - +
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Residues in contact with TRP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.7 20.2 - - + -
128B ALA* 3.9 10.1 - - + -
129B TYR* 3.7 26.9 - - + -
132B TYR* 5.3 2.5 - + + -
133B TYR* 4.4 15.5 + + - -
247B MET* 3.6 24.5 - - + -
255B PHE* 3.6 32.5 - + + +
256B ARG* 4.1 36.7 - - + +
259B ARG 2.8 16.6 + - - +
260B THR* 3.6 11.2 - - + +
262B THR* 1.3 74.0 - - - +
264B LYS* 1.3 71.5 + - + +
266B HIS* 3.2 10.1 + + - +
267B VAL* 2.9 46.3 + - + +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B THR* 3.0 17.2 + - + +
261B LYS* 3.4 14.1 - - + +
263B TRP* 1.3 83.2 - - + +
265B ASP* 1.3 62.5 + - - +
267B VAL* 3.3 7.0 + - - +
268B ALA* 3.0 26.2 + - - +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B GLN* 5.5 2.2 - - - +
243B THR* 4.0 17.3 - - + +
261B LYS* 3.0 43.0 + - - +
262B THR* 3.5 9.6 - - - +
264B LYS* 1.3 84.4 - - - +
266B HIS* 1.3 60.2 + - - +
268B ALA* 3.3 8.6 + - - +
269B ALA* 3.0 27.7 + - - +
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Residues in contact with HIS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PRO* 3.7 16.9 + - + +
126B TRP* 3.5 15.2 - + - -
129B TYR* 5.0 1.6 - - + -
240B MET* 3.2 22.4 + - + -
243B THR* 2.9 28.6 + - - +
244B SER* 3.3 19.3 + - - -
247B MET* 3.6 20.6 - - + -
262B THR 2.8 18.9 + - - +
263B TRP* 3.5 11.9 - + - +
265B ASP* 1.3 73.6 - - - +
267B VAL* 1.3 56.4 + - - +
269B ALA* 3.2 4.8 + - - +
270B TRP* 3.1 62.2 + + - -
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.9 18.8 - - + -
133B TYR* 3.9 33.2 - - + +
263B TRP* 2.9 52.4 + - + +
264B LYS* 3.4 10.3 - - - +
266B HIS* 1.3 72.4 - - + +
268B ALA* 1.3 66.3 + - - +
270B TRP 3.4 1.0 + - - -
271B ASP* 3.0 38.7 + - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LYS 3.0 14.5 + - - +
265B ASP* 3.3 12.5 + - - +
267B VAL* 1.3 75.8 - - - +
269B ALA* 1.3 62.4 + - - +
271B ASP* 3.3 9.8 + - - +
272B VAL* 3.1 28.1 + - + +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ALA* 3.6 18.4 - - - +
239B GLN* 3.8 12.3 - - + -
240B MET* 3.6 31.0 - - - +
265B ASP 3.0 16.6 + - - +
266B HIS* 3.5 5.6 - - - +
267B VAL 3.2 0.4 - - - -
268B ALA* 1.3 73.2 - - - +
270B TRP* 1.3 64.5 + - - +
272B VAL* 3.4 2.5 + - - -
273B ILE* 3.2 26.9 + - - +
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Residues in contact with TRP 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TRP* 3.8 26.0 - + - +
129B TYR* 3.2 38.6 - + + -
130B HIS* 4.0 22.9 - + - -
140B LEU* 6.0 0.4 - - + -
240B MET* 3.3 39.9 - - + +
266B HIS* 3.1 53.2 + + - +
269B ALA* 1.3 72.8 - - - +
271B ASP* 1.3 61.4 + - - +
273B ILE* 3.1 26.4 + - + +
274B PHE* 2.8 56.8 + + - -
321B THR* 5.5 2.5 - - + -
322B GLU* 6.0 3.4 - - + -
325B ALA* 5.2 1.8 - - + -
602B 2DC 4.4 20.9 - - + -
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 2.6 28.7 + - - -
133B TYR* 5.4 4.8 - - - -
135B ARG* 3.5 20.7 + - - +
267B VAL* 3.0 35.4 + - - +
268B ALA* 3.5 8.9 - - - +
269B ALA 3.3 0.2 - - - -
270B TRP* 1.3 75.3 - - - +
272B VAL* 1.3 56.6 + - + +
274B PHE* 3.4 2.3 + - - +
275B SER* 2.7 40.0 + - - +
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Residues in contact with VAL 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ARG* 3.8 47.1 - - - +
233B PHE* 4.1 5.6 - - - -
236B ALA* 3.6 27.6 - - + -
268B ALA* 3.1 17.8 + - + +
269B ALA* 3.7 1.1 - - - +
270B TRP 3.3 0.2 - - - -
271B ASP* 1.3 74.6 - - + +
273B ILE* 1.3 63.8 + - - +
275B SER* 4.0 3.3 - - - -
276B LYS* 3.2 40.8 + - + +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 3.3 21.0 - - + -
236B ALA* 4.1 8.3 - - + +
237B ILE* 3.9 30.3 - - + -
240B MET* 4.0 31.4 - - + -
269B ALA 3.2 14.4 + - - +
270B TRP* 3.1 28.1 + - + +
272B VAL* 1.3 76.2 - - - +
274B PHE* 1.3 56.8 + - - +
277B ALA* 3.2 25.6 + - - +
321B THR* 3.8 20.2 - - + -
325B ALA* 4.3 17.7 - - + -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B TYR* 3.6 25.4 - + - +
130B HIS* 3.4 36.6 - + - -
135B ARG* 3.7 36.6 - - + +
136B PRO* 3.9 24.9 - - + -
270B TRP* 2.8 42.4 + + - +
271B ASP 4.1 1.3 - - - +
273B ILE* 1.3 73.8 - - - +
275B SER* 1.3 66.1 + - - +
278B ASP* 2.9 44.8 + - - +
317B LYS* 6.2 0.4 - - + -
318B ALA* 5.7 1.8 - - - -
321B THR* 4.0 26.9 - - + -
322B GLU* 6.3 2.0 - - + -
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 5.2 3.5 + - - +
232B ARG* 6.3 0.7 - - - -
271B ASP* 2.7 26.0 + - - +
272B VAL* 4.0 4.2 - - - -
274B PHE* 1.3 76.6 - - - +
276B LYS* 1.3 66.7 + - - +
278B ASP* 3.4 4.4 + - - +
279B ILE* 3.0 42.4 + - - +
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Residues in contact with LYS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLU* 2.6 56.4 + - + +
232B ARG* 3.8 16.7 - - - +
233B PHE* 3.4 36.1 - - + -
272B VAL* 3.2 23.0 + - + +
275B SER* 1.3 84.1 - - - +
277B ALA* 1.3 65.7 + - - +
279B ILE* 3.5 14.2 + - - +
280B TYR* 3.1 43.8 + - + +
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Residues in contact with ALA 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 4.4 3.7 - - + -
273B ILE 3.2 19.7 + - - +
274B PHE 4.2 1.3 - - - +
276B LYS* 1.3 76.2 - - - +
278B ASP* 1.3 58.5 + - - +
280B TYR* 3.3 11.0 + - - +
281B THR* 2.9 36.0 + - - +
317B LYS* 5.3 0.2 - - - -
320B VAL* 5.1 0.3 - - - +
321B THR* 3.2 39.3 - - + +
324B LEU* 4.0 13.7 - - + -
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Residues in contact with ASP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 5.5 2.9 + - - -
136B PRO* 6.0 0.2 - - - +
274B PHE* 2.9 37.1 + - - +
275B SER* 3.4 6.4 - - - +
277B ALA* 1.3 75.4 - - - +
279B ILE* 1.3 58.0 + - + +
281B THR* 3.2 1.9 + - - -
282B GLN* 2.8 45.8 + - - +
317B LYS* 3.1 40.8 - - - +
321B THR* 4.3 2.3 + - - -
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B SER* 3.0 31.5 + - - +
276B LYS* 3.9 15.7 - - + +
278B ASP* 1.3 74.8 - - + +
280B TYR* 1.3 64.1 + - + +
282B GLN* 4.0 4.4 - - - +
283B ASN* 2.9 55.5 + - - +
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Residues in contact with TYR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.9 29.6 - + - -
211B THR* 5.3 1.3 - - + -
215B PHE* 3.6 33.4 - + + -
219B GLN* 4.0 22.4 + - - -
227B ASN* 5.5 4.0 + - - -
229B GLU 5.0 0.5 + - - -
230B ALA* 3.9 19.8 + - - +
233B PHE* 5.1 5.2 - + - +
276B LYS* 3.1 42.5 + - + +
277B ALA* 3.6 9.4 - - - +
279B ILE* 1.3 82.0 - - + +
281B THR* 1.3 61.2 + - - +
283B ASN* 4.0 5.3 - - - +
284B PHE* 3.1 25.3 + - - +
324B LEU* 4.5 7.0 - - + -
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PHE* 4.4 0.2 - - - -
277B ALA 2.9 20.4 + - - -
278B ASP 3.7 2.9 - - - -
280B TYR* 1.3 71.3 - - - +
282B GLN* 1.3 58.0 + - - +
284B PHE* 3.4 4.0 + - - +
285B TYR* 3.0 27.3 + - - +
302B LEU* 4.2 29.0 - - + +
306B LEU* 5.4 0.4 - - + +
313B PHE* 3.9 20.6 - - + -
316B ILE* 5.1 0.2 - - + -
317B LYS* 3.7 33.9 - - + +
320B VAL* 3.5 23.1 - - + +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ASP* 2.8 32.1 + - - +
279B ILE* 4.0 4.4 - - - +
281B THR* 1.3 75.7 - - - +
283B ASN* 1.3 67.1 + - - +
285B TYR* 3.2 9.3 + - - +
286B TRP* 3.0 35.1 + - + +
313B PHE* 4.3 18.5 - - + -
317B LYS* 4.1 20.6 - - - +
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Residues in contact with ASN 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 2.9 39.8 + - - +
280B TYR* 4.0 6.6 - - - +
282B GLN* 1.3 74.7 - - - +
284B PHE* 1.3 64.1 + - - +
286B TRP* 3.1 5.9 + - - +
287B GLU* 2.9 43.3 + - - +
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE 5.1 0.4 - - - -
215B PHE* 3.5 43.3 - + + -
217B GLU* 4.5 14.8 - - - -
280B TYR 3.1 16.9 + - - +
281B THR 3.5 4.5 - - - +
283B ASN* 1.3 78.8 - - - +
285B TYR* 1.3 57.2 + - - +
287B GLU* 3.5 7.8 + - - +
288B LEU* 2.9 47.2 + - + +
299B ARG* 5.2 2.9 - - + -
302B LEU* 3.5 24.9 - - + -
303B TYR* 3.8 30.7 - + + -
306B LEU* 3.7 23.1 - - + -
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Residues in contact with TYR 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B THR 3.0 15.2 + - - +
282B GLN* 3.3 12.1 - - - +
284B PHE* 1.3 77.6 - - - +
286B TRP* 1.3 97.6 + + - +
288B LEU* 3.4 17.3 - - + +
289B ARG* 3.5 52.0 + - - -
306B LEU* 4.2 24.2 - - + -
313B PHE* 3.6 38.4 - + + -
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Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN* 3.0 32.0 + - + +
283B ASN* 3.9 4.0 - - - +
285B TYR* 1.3 103.3 - + - +
287B GLU* 1.3 57.2 + - - +
289B ARG* 3.0 35.4 + - + +
290B GLN* 3.0 39.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 4.2 15.1 - - - +
283B ASN* 2.9 35.9 + - - +
284B PHE* 4.0 5.7 - - - +
286B TRP* 1.3 71.0 - - - +
288B LEU* 1.3 65.7 + - - +
289B ARG 3.1 1.6 - - - -
290B GLN* 3.7 25.4 - - - +
291B LYS* 3.0 58.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B PHE* 2.9 26.4 + - + +
285B TYR* 3.4 12.8 - - + +
286B TRP 3.2 0.2 - - - -
287B GLU* 1.3 76.3 - - - +
289B ARG* 1.3 65.7 + - + +
291B LYS* 4.0 1.8 - - - -
292B GLY* 3.1 24.8 + - - -
293B SER 4.7 0.2 + - - -
303B TYR* 3.5 39.9 - - + +
306B LEU* 4.2 33.4 - - + -
307B GLY* 5.5 2.0 - - - +
----------------------------------------------------------
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Residues in contact with ARG 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B TYR* 3.5 54.6 + - - -
286B TRP* 3.0 38.9 + - + +
288B LEU* 1.3 88.1 - - + +
290B GLN* 1.3 61.6 + - + +
292B GLY* 3.7 8.7 + - - -
----------------------------------------------------------
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B TRP* 3.0 34.7 + - + +
287B GLU* 3.3 25.0 + - - +
289B ARG* 1.3 75.9 - - + +
291B LYS* 1.3 64.3 + - + +
292B GLY* 3.1 7.5 + - - -
----------------------------------------------------------
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Residues in contact with LYS 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLU* 5.0 5.9 + - - -
287B GLU* 3.0 55.6 + - + +
288B LEU* 4.0 1.8 - - - +
290B GLN* 1.3 78.1 - - + +
292B GLY* 1.3 64.4 + - - +
293B SER* 2.8 14.1 + - - -
295B HIS* 4.8 8.3 + - - +
299B ARG* 6.1 3.1 - - - +
----------------------------------------------------------
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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).
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