Contacts of the helix formed by residues 250 - 275 (chain B) in PDB entry 3QNQ
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 HIS 250 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 4.2 14.1 - - + +
245B TRP* 3.2 29.7 - + + -
249B ILE* 1.3 78.9 - - + +
251B GLY* 1.3 64.0 + - - +
252B ALA* 3.0 12.4 + - + +
253B THR* 3.0 45.3 + - + +
254B ILE* 3.1 14.8 + - + +
334B GLU* 3.7 3.6 - - - -
1G NAG 2.9 26.7 - - - -
2G NAG 2.9 32.3 + - - -
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Residues in contact with GLY 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.4 23.8 - - - -
244B LEU* 3.7 26.7 - - - +
245B TRP* 3.8 5.3 - - - +
249B ILE 3.3 7.7 + - - -
250B HIS* 1.3 73.5 - - - +
252B ALA* 1.3 59.1 + - - +
254B ILE* 4.0 0.9 - - - -
255B VAL* 2.7 35.0 + - - +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 3.7 15.4 - - - +
245B TRP* 3.8 1.4 - - - +
250B HIS* 3.0 4.4 + - + -
251B GLY* 1.3 75.9 - - - +
253B THR* 1.3 58.6 + - - +
256B GLY* 2.9 26.2 + - - -
294B TYR* 5.3 2.2 - - + -
1G NAG 3.3 30.5 + - - +
2G NAG 2.9 41.1 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 5.9 2.5 - - + -
180A VAL* 5.5 2.9 - - + -
26B ARG* 3.3 24.0 - - - +
250B HIS* 3.0 39.9 + - + +
252B ALA* 1.3 74.7 - - - +
254B ILE* 1.3 67.6 + - - +
256B GLY* 4.7 0.2 - - - -
257B GLY* 2.8 21.3 + - - +
1G NAG 3.6 35.7 - - - +
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Residues in contact with ILE 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 5.9 0.4 - - - +
16B VAL* 4.1 23.3 - - + -
17B ALA* 3.7 19.3 - - + +
26B ARG* 3.3 42.4 + - - +
244B LEU* 3.6 23.6 - - + -
249B ILE* 4.2 19.3 - - + -
250B HIS* 3.1 12.4 + - + +
251B GLY 3.0 5.7 + - - +
253B THR* 1.3 83.4 + - - +
255B VAL* 1.3 70.0 + - + +
257B GLY* 3.4 4.5 + - - -
258B VAL* 3.4 16.6 + - + +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA* 4.2 8.5 - - + -
240B LEU* 3.7 38.6 - - + +
241B VAL* 3.5 21.1 - - + +
244B LEU* 4.8 7.9 - - + -
251B GLY 2.7 16.7 + - - +
254B ILE* 1.3 70.1 - - + +
256B GLY* 1.3 59.2 + - - +
257B GLY 2.9 1.3 - - - -
258B VAL* 2.6 30.6 + - - +
259B MET* 2.8 22.4 + - + -
263B TRP* 3.5 25.4 - - + -
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Residues in contact with GLY 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B VAL* 5.0 0.4 - - - +
252B ALA 2.9 23.9 + - - -
253B THR* 3.8 1.1 - - - -
255B VAL* 1.3 78.6 - - - +
257B GLY* 1.3 55.7 + - - +
260B SER* 2.8 37.3 + - - -
263B TRP* 3.8 19.9 - - - -
1G NAG 5.6 1.1 - - - -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.9 1.5 - - - +
25B ILE* 4.1 12.0 - - - +
26B ARG* 3.6 35.1 - - - -
29B LEU* 4.4 0.8 - - - +
253B THR 2.8 20.6 + - - -
254B ILE 3.8 1.3 - - - -
255B VAL 2.7 2.6 + - - -
256B GLY* 1.3 74.9 - - - +
258B VAL* 1.3 61.3 + - - +
260B SER* 4.0 4.8 + - - -
261B PRO* 4.0 9.5 - - - +
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 5.7 3.4 - - + -
22B LEU* 4.0 35.7 - - + -
254B ILE* 3.4 12.9 + - + +
255B VAL* 2.6 15.3 + - - +
257B GLY* 1.3 73.5 - - - +
259B MET* 1.3 70.9 + - + +
261B PRO* 3.3 18.0 - - - +
262B ILE* 5.3 3.1 - - - +
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Residues in contact with MET 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B GLY* 4.4 15.9 - - - -
233B GLY* 4.9 9.9 - - - +
237B ALA* 5.0 3.4 - - + -
255B VAL* 2.8 17.6 + - + +
258B VAL* 1.3 90.0 - - + +
260B SER* 1.3 59.7 + - - +
261B PRO* 3.3 1.8 - - - -
262B ILE* 3.1 30.7 + - + +
263B TRP* 2.9 79.0 + - + +
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Residues in contact with SER 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.4 18.9 - - - +
256B GLY* 2.8 24.4 + - - -
257B GLY* 4.0 3.1 + - - -
259B MET* 1.3 73.6 - - - +
261B PRO* 1.3 71.0 - - - +
262B ILE 2.8 6.7 + - - -
263B TRP* 4.0 11.9 - - - +
264B LEU* 2.8 42.9 + - - +
286B ALA* 6.4 1.1 - - - -
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Residues in contact with PRO 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 4.7 1.1 - - + -
29B LEU* 3.9 15.7 - - + -
146B LEU* 3.4 35.6 - - + +
147B PHE* 4.0 23.2 - - + -
150B MET* 3.7 27.1 - - + -
221B GLN* 4.5 0.3 - - - +
257B GLY 4.0 2.9 - - - +
258B VAL 3.3 20.2 - - - +
259B MET 3.4 0.2 - - - -
260B SER* 1.3 98.2 - - - +
262B ILE* 1.3 58.4 + - + +
264B LEU* 3.9 2.2 - - + -
265B SER* 3.6 13.0 + - - -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 3.9 19.5 - - + -
221B GLN* 5.4 0.2 - - - -
224B LEU* 3.7 34.5 - - + +
225B SER* 3.6 31.0 - - - +
228B GLY* 4.4 11.0 - - - -
258B VAL 5.3 1.8 - - - +
259B MET* 3.1 31.4 + - + +
260B SER 2.9 0.6 - - - -
261B PRO* 1.3 83.0 - - + +
263B TRP* 1.3 65.0 + - + +
264B LEU 3.2 2.0 - - - -
265B SER* 3.1 3.6 + - - -
266B LEU* 3.0 42.7 + - + +
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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
----------------------------------------------------------
228B GLY 4.4 4.9 + - - -
233B GLY 5.0 1.0 + - - -
237B ALA* 3.5 24.9 - - + -
241B VAL* 5.7 0.7 - - + -
255B VAL* 3.5 17.9 - - + -
256B GLY* 3.8 21.3 - - - -
259B MET* 2.9 60.0 + - + +
260B SER* 3.1 9.1 + - - -
262B ILE* 1.3 83.9 - - + +
264B LEU* 1.3 57.0 + - - +
266B LEU* 4.8 2.7 - - + -
267B MET* 3.2 16.3 + - - +
284B ILE* 3.9 23.6 - - + +
285B THR* 3.7 2.1 - - - -
286B ALA* 3.2 40.7 + - + +
289B PHE* 3.6 35.3 - + - -
294B TYR* 5.2 9.6 - + - -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 5.8 5.4 - - + -
32B THR* 4.8 9.2 - - - +
36B LEU* 3.6 26.5 - - + -
80B MET* 3.5 12.1 - - + -
143B SER* 3.7 2.5 - - - -
146B LEU* 3.3 31.2 - - + -
260B SER* 2.8 43.7 + - - +
261B PRO* 3.9 4.0 - - + +
263B TRP* 1.3 75.7 - - - +
265B SER* 1.3 64.3 + - - +
267B MET* 3.3 24.6 - - + +
268B ASP* 2.8 29.6 + - - +
286B ALA* 5.0 5.2 - - + -
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B SER* 3.9 19.7 - - - -
144B GLN* 2.8 21.8 + - - +
221B GLN* 3.0 22.6 + - - -
225B SER* 4.2 3.2 + - - -
261B PRO 3.6 11.0 - - - -
262B ILE* 3.1 10.0 + - - -
264B LEU* 1.3 81.0 - - - +
266B LEU* 1.3 65.4 + - - +
268B ASP* 3.2 4.3 + - - +
269B GLN* 3.1 30.9 + - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B SER* 3.8 32.3 - - - +
228B GLY 4.5 1.3 - - - -
229B ALA* 3.4 34.8 - - + +
262B ILE* 3.0 25.6 + - + +
263B TRP* 4.3 2.0 - - + +
265B SER* 1.3 73.1 - - - +
267B MET* 1.3 67.6 + - - +
268B ASP 3.2 0.3 + - - -
269B GLN* 3.3 20.1 + - - +
270B ASN* 3.1 27.2 + - - +
282B ASN* 3.7 17.0 - - - +
284B ILE* 3.2 34.5 - - + +
285B THR* 4.2 1.1 - - - -
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Residues in contact with MET 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.1 10.1 - - + -
77B PHE* 3.5 24.9 - - + -
80B MET* 4.4 2.9 - - - -
263B TRP 3.2 20.5 + - - +
264B LEU* 3.3 39.3 - - + +
266B LEU* 1.3 79.3 - - - +
268B ASP* 1.3 67.0 + - + +
270B ASN* 3.4 5.4 + - - +
271B ARG* 3.1 16.6 + - - +
285B THR* 3.7 21.0 - - - +
286B ALA 4.4 0.4 - - - +
287B GLN* 3.5 21.1 - - - +
377B GLY* 3.3 20.7 - - - +
379B ALA* 3.6 28.7 - - - -
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.8 13.0 - - - +
78B ASN* 4.9 1.2 - - - +
142B GLY* 5.1 0.3 - - - -
143B SER* 2.5 42.3 + - - +
264B LEU 2.8 15.2 + - - +
265B SER 3.5 1.1 - - - +
266B LEU 3.1 0.4 - - - -
267B MET* 1.3 79.2 - - + +
269B GLN* 1.3 67.7 + - - +
271B ARG* 2.5 59.0 + - - +
272B ILE* 2.9 17.1 + - - +
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B GLN* 3.5 24.2 + - + +
225B SER* 5.3 3.6 + - - -
265B SER* 3.3 19.1 + - - +
266B LEU* 3.5 16.8 - - - +
268B ASP* 1.3 75.7 - - + +
270B ASN* 1.3 64.0 + - - +
272B ILE* 3.0 20.7 + - - +
273B ALA* 3.1 13.0 + - - +
281B PRO* 4.6 10.0 - - + +
282B ASN* 2.9 23.9 + - - +
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Residues in contact with ASN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU 3.1 13.6 + - - +
267B MET 3.5 8.7 - - - +
269B GLN* 1.3 75.5 - - - +
271B ARG* 1.3 57.3 + - - +
273B ALA* 3.4 0.7 + - - +
274B PHE* 2.9 26.3 + - - +
280B VAL* 3.5 12.1 - - + +
281B PRO* 3.6 12.3 - - - +
282B ASN* 2.7 56.9 + - - +
285B THR* 4.0 9.4 - - + +
375B PRO 3.3 19.1 + - - +
376B SER 3.0 16.8 - - - +
377B GLY* 4.3 0.9 - - - -
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Residues in contact with ARG 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.2 19.4 - - + +
73B VAL* 4.0 11.9 - - - +
77B PHE* 3.6 32.0 - - + +
78B ASN* 3.4 34.2 + - - +
267B MET 3.1 13.2 + - - +
268B ASP* 2.5 49.3 + - - +
270B ASN* 1.3 77.9 - - - +
272B ILE* 1.3 78.1 + - - +
274B PHE* 3.5 3.3 + - - +
275B GLN* 3.1 50.8 + - - +
376B SER 3.3 9.6 + - - -
377B GLY 3.7 17.0 - - - +
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 5.5 2.5 - - - +
268B ASP* 2.9 13.8 + - - +
269B GLN* 3.0 11.9 + - - +
271B ARG* 1.3 104.5 - - - +
273B ALA* 1.3 71.8 + - + +
275B GLN* 3.5 17.6 + - - +
276B ALA* 4.0 9.0 + - - +
278B GLN* 5.5 2.0 - - - +
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLN 3.1 10.8 + - - +
270B ASN 3.7 7.4 - - - +
272B ILE* 1.3 82.3 - - + +
274B PHE* 1.3 65.8 + - - +
276B ALA* 3.0 10.8 + - - +
278B GLN* 3.3 42.0 + - + +
279B ASP 3.5 26.0 - - - +
281B PRO* 4.0 11.0 - - + -
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.9 8.3 - - + -
47B THR* 3.3 40.6 - - + -
49B PRO* 5.3 1.6 - - + -
270B ASN 2.9 18.9 + - - +
271B ARG* 3.7 3.8 - - - +
273B ALA* 1.3 75.4 - - - +
275B GLN* 1.3 60.1 + - + +
276B ALA 2.7 11.8 + - - -
277B GLY* 3.1 13.7 + - - -
278B GLN 4.3 9.8 - - - +
280B VAL* 4.0 10.5 - - + +
376B SER* 3.6 34.5 - - - +
395B GLY* 3.5 31.0 - - - -
397B LYS* 4.3 22.7 - - - -
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Residues in contact with GLN 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.4 23.7 - - + +
47B THR* 4.4 19.4 - - + +
70B GLY* 5.6 4.0 - - - -
73B VAL* 4.6 8.8 - - - +
271B ARG* 3.1 50.4 + - - +
272B ILE* 3.7 10.9 - - - +
273B ALA 3.2 0.6 + - - -
274B PHE* 1.3 79.3 - - + +
276B ALA* 1.3 58.1 + - + +
277B GLY 3.8 0.4 - - - -
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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