Contacts of the helix formed by residues 237 - 267 (chain B) in PDB entry 3MDR
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 237 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LYS* 1.3 68.2 - - - +
238B LYS* 1.3 71.4 + - + +
239B GLN 3.7 0.4 - - - -
240B LEU* 3.6 15.4 - - - +
241B ARG* 3.4 22.5 + - - +
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Residues in contact with LYS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LYS* 2.3 62.7 + - + +
237B ARG* 1.3 76.9 - - + +
239B GLN* 1.3 70.1 + - - +
240B LEU 3.0 1.8 - - - -
241B ARG* 3.0 20.2 + - - +
242B GLU* 2.8 48.9 + - + +
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 5.4 3.3 - - + -
217B LEU* 4.7 8.9 - - + +
220B GLU* 2.9 40.0 - - - +
224B ALA* 5.4 9.9 - - - +
236B LYS* 3.2 12.6 + - + +
238B LYS* 1.3 94.0 - - - +
240B LEU* 1.3 56.3 + - - +
242B GLU* 4.2 8.1 - - - -
243B VAL* 2.9 48.2 + - + +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 3.6 45.7 - - + -
236B LYS 4.3 8.6 + - - +
237B ARG* 3.6 21.4 + - - +
238B LYS 3.0 0.4 - - - -
239B GLN* 1.3 79.7 - - - +
241B ARG* 1.3 60.0 + - - +
243B VAL* 4.0 2.4 - - - +
244B ARG* 3.3 61.2 + - - +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ARG* 3.4 8.8 + - - +
238B LYS* 3.0 23.3 + - - +
240B LEU* 1.3 76.5 - - - +
242B GLU* 1.3 70.0 + - - +
244B ARG* 3.3 13.4 + - + +
245B GLU* 2.8 61.5 + - + +
248B ARG* 5.3 4.7 - - - +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN* 5.6 0.2 + - - -
217B LEU* 3.7 33.5 - - + +
238B LYS* 2.8 38.8 + - - +
239B GLN* 3.9 8.1 - - - +
241B ARG* 1.3 86.0 + - - +
243B VAL* 1.3 51.1 + - - +
245B GLU* 3.3 14.1 + - - +
246B SER* 2.8 39.9 + - - -
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 4.0 1.6 - - + -
116B PHE* 3.6 29.8 - - + -
217B LEU* 3.4 25.4 - - + +
218B MET* 4.6 2.2 - - - -
221B GLY* 3.7 23.1 - - - +
239B GLN* 2.9 41.5 + - + +
240B LEU 4.0 0.2 - - - +
242B GLU* 1.3 75.0 - - - +
244B ARG* 1.3 56.9 + - - +
246B SER* 3.3 6.3 + - - -
247B ILE* 3.0 47.1 + - + +
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 2.7 40.1 + - + +
117B GLY* 5.3 1.0 - - - -
118B GLU* 3.8 24.5 - - + +
240B LEU* 3.3 52.8 + - - +
241B ARG* 3.3 15.7 + - + +
243B VAL* 1.3 77.6 - - - +
245B GLU* 1.3 56.3 + - - +
247B ILE* 3.5 4.3 + - - +
248B ARG* 3.1 44.6 + - - +
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B ARG* 2.8 58.3 + - - +
242B GLU* 3.6 13.3 - - - +
244B ARG* 1.3 74.0 - - - +
246B SER* 1.3 58.2 + - - +
248B ARG* 3.6 26.6 + - - +
249B PHE* 3.0 29.3 + - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA* 3.4 31.7 - - - +
217B LEU* 3.3 27.4 - - - +
218B MET* 4.3 4.3 - - - -
242B GLU 2.8 21.8 + - - -
243B VAL* 3.6 5.6 - - - -
245B GLU* 1.3 76.2 - - - +
247B ILE* 1.3 59.2 + - - +
249B PHE* 3.4 7.8 + - - +
250B LEU* 3.0 32.5 + - - +
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Residues in contact with ILE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.8 33.9 - - + +
118B GLU* 3.9 15.7 - - + +
119B ARG 3.2 27.8 - - - +
120B LEU* 3.9 17.5 - - + -
218B MET* 3.9 23.1 - - + -
243B VAL* 3.0 38.2 + - + +
244B ARG 3.9 3.8 - - - +
246B SER* 1.3 74.5 - - - +
248B ARG* 1.3 63.9 + - - +
250B LEU* 3.3 7.5 + - - +
251B ARG* 3.1 25.7 + - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 2.9 36.0 + - - +
241B ARG* 4.8 4.2 + - - +
244B ARG* 3.1 22.0 + - - +
245B GLU* 3.6 38.7 + - - +
246B SER 3.3 0.2 - - - -
247B ILE* 1.3 73.6 - - - +
249B PHE* 1.3 67.9 + - - +
251B ARG* 3.5 6.0 + - - +
252B GLN* 3.0 24.2 + - - +
255B ARG* 5.1 1.6 + - - -
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLN* 5.8 2.2 - - - -
210B PRO* 4.0 21.1 - - + -
211B LEU* 3.6 36.3 - - + -
214B ALA* 3.8 18.6 - - + -
245B GLU 3.0 19.0 + - - +
246B SER* 3.4 7.9 - - - +
248B ARG* 1.3 75.7 - - - +
250B LEU* 1.3 56.8 + - - +
252B GLN* 3.1 10.0 + - + +
253B VAL* 2.9 46.4 + - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 5.5 2.9 - - + -
211B LEU* 4.1 9.9 - - + -
214B ALA* 4.0 26.9 - - + +
215B VAL* 4.0 23.3 - - + +
218B MET* 5.3 7.2 - - + -
246B SER 3.0 12.2 + - - +
247B ILE* 3.5 12.1 - - - +
248B ARG 3.2 0.2 - - - -
249B PHE* 1.3 76.4 - - - +
251B ARG* 1.3 61.8 + - - +
253B VAL* 3.4 8.4 + - + +
254B GLY 3.2 14.7 + - - -
296B PHE* 3.8 10.3 - - + -
297B VAL* 4.3 24.7 - - + -
300B PHE* 3.7 32.8 - - + -
301B ILE* 4.6 4.3 - - + -
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 6.1 0.7 - - - -
119B ARG* 3.2 33.7 + - - +
120B LEU* 3.0 22.4 + - + +
247B ILE* 3.1 16.1 + - + +
248B ARG* 4.1 5.4 - - - +
250B LEU* 1.3 78.8 - - + +
252B GLN* 1.3 56.7 + - - +
254B GLY* 3.2 4.4 + - - +
255B ARG* 3.1 36.1 + - - +
290B GLU* 2.8 45.7 + - - +
293B LEU* 3.4 25.4 + - + +
294B ASP* 2.9 36.7 + - - +
296B PHE* 5.3 0.2 - - - -
297B VAL* 3.6 19.3 - - + -
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Residues in contact with GLN 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG 3.0 19.3 + - - +
249B PHE* 3.1 11.6 + - + +
251B ARG* 1.3 73.8 - - - +
253B VAL* 1.3 65.3 + - - +
254B GLY 3.1 1.1 - - - -
255B ARG* 2.6 42.9 + - - +
256B ASP* 3.1 60.5 + - - +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLN* 5.9 1.3 - - - +
211B LEU* 4.1 21.3 - - + -
249B PHE* 2.9 43.2 + - + +
250B LEU* 3.5 8.5 - - + +
252B GLN* 1.3 75.8 - - - +
254B GLY* 1.3 57.3 + - - +
256B ASP* 3.4 7.4 + - - +
257B TRP* 2.9 67.9 + - + +
296B PHE* 4.2 8.5 - - + -
300B PHE* 5.1 1.3 - - + -
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Residues in contact with GLY 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU 3.2 4.6 + - - -
251B ARG 3.2 8.9 + - - -
252B GLN 3.1 1.4 - - - -
253B VAL* 1.3 78.8 - - - +
255B ARG* 1.3 51.3 + - - +
257B TRP* 3.2 3.1 + - - +
258B VAL* 2.8 40.0 + - - +
293B LEU* 4.0 7.0 - - - -
296B PHE* 3.5 33.2 - - - -
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Residues in contact with ARG 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG 5.1 1.6 + - - -
251B ARG* 3.1 19.1 + - - +
252B GLN* 2.6 68.6 + - - +
254B GLY* 1.3 75.1 - - - +
256B ASP* 1.3 51.7 + - - +
258B VAL* 3.6 7.0 - - + +
259B GLN* 2.6 34.9 + - - +
289B ASP* 5.9 3.4 - - + +
290B GLU* 4.4 8.3 + - - -
293B LEU* 3.5 35.5 - - + +
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Residues in contact with ASP 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B GLN* 3.1 41.8 + - - +
253B VAL* 3.6 8.1 - - - +
255B ARG* 1.3 76.6 - - - +
257B TRP* 1.3 61.4 + - + +
259B GLN* 3.2 19.6 - - - +
260B ARG* 2.8 41.2 + - - +
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Residues in contact with TRP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 3.8 9.6 - - + -
197B PHE* 3.7 28.8 - + + +
199B MET* 3.5 52.2 - - + +
200B GLU 5.7 1.1 - - - -
201B THR* 3.6 31.9 - - + -
208B GLN* 5.7 3.4 - - - -
211B LEU* 4.8 3.8 - - + -
253B VAL* 2.9 40.9 + - + +
254B GLY 3.8 2.9 - - - +
256B ASP* 1.3 76.5 - - + +
258B VAL* 1.3 64.6 + - - +
260B ARG* 3.5 12.5 + - - +
261B ARG* 3.2 21.8 + - - +
276B LEU* 4.4 7.5 - - + +
296B PHE* 3.5 23.1 - + + -
300B PHE* 3.9 19.7 - + - -
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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
----------------------------------------------------------
254B GLY 2.8 22.2 + - - +
255B ARG* 3.6 9.2 - - + +
257B TRP* 1.3 75.6 - - - +
259B GLN* 1.3 65.8 + - - +
261B ARG* 3.2 6.8 + - - +
262B ARG* 3.1 54.9 + - - +
276B LEU* 4.1 20.6 - - + -
280B LEU* 4.4 3.8 - - + +
289B ASP* 4.8 3.1 - - + +
292B LEU* 3.8 34.3 - - + -
293B LEU* 5.1 3.8 - - + -
296B PHE* 5.1 7.9 - - + -
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Residues in contact with GLN 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG 2.6 21.7 + - - +
256B ASP* 3.2 22.2 - - - +
258B VAL* 1.3 76.3 - - - +
260B ARG* 1.3 62.1 + - - +
262B ARG* 3.4 6.1 + - - +
263B GLU* 3.1 54.5 + - + +
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B MET* 3.8 37.1 - - - +
256B ASP* 2.8 24.5 + - - +
257B TRP* 3.7 13.9 - - - +
258B VAL 3.3 0.2 - - - -
259B GLN* 1.3 76.1 - - + +
261B ARG* 1.3 61.0 + - - +
263B GLU* 3.7 11.9 + - - +
264B ALA* 3.1 24.3 + - - +
267B ARG* 5.2 0.7 + - - -
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE 3.4 19.4 + - - -
198B GLY* 4.3 4.6 - - - +
257B TRP 3.2 14.3 + - - +
258B VAL* 3.2 8.7 + - - +
260B ARG* 1.3 75.0 - - - +
262B ARG* 1.3 59.5 + - - +
264B ALA* 3.4 5.0 + - - +
265B LEU* 3.0 47.7 + - + +
271B VAL* 3.4 35.0 - - - +
274B ASP* 2.8 42.2 + - - -
276B LEU* 3.6 22.5 - - + +
277B THR* 3.2 16.8 + - - +
280B LEU* 3.8 23.5 - - + +
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Residues in contact with ARG 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B VAL* 3.1 38.4 + - + +
259B GLN* 4.0 5.8 - - - +
261B ARG* 1.3 75.8 - - + +
263B GLU* 1.3 60.7 - - + +
265B LEU* 3.3 12.3 + - + +
266B LYS* 2.9 43.9 + - - +
280B LEU* 4.0 18.0 - - + +
283B GLU 6.0 0.4 + - - -
289B ASP* 2.8 43.4 + - - -
292B LEU* 3.8 11.9 - - - +
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B GLN* 3.1 53.0 + - + +
260B ARG* 4.0 12.2 + - - +
262B ARG* 1.3 75.4 - - + +
264B ALA* 1.3 63.2 + - - +
266B LYS* 3.2 33.0 + - - +
267B ARG* 3.2 34.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG 3.1 19.2 + - - +
261B ARG* 3.6 7.0 - - - +
263B GLU* 1.3 76.5 - - - +
265B LEU* 1.3 60.6 + - - +
267B ARG* 3.4 27.6 + - - +
269B GLU* 3.1 42.1 + - - +
271B VAL* 4.5 12.3 - - + -
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ARG* 3.0 39.3 + - + +
262B ARG* 3.7 10.1 - - + +
263B GLU 3.2 0.2 - - - -
264B ALA* 1.3 76.7 - - - +
266B LYS* 1.3 57.6 + - - +
267B ARG 3.3 0.2 - - - -
268B GLY* 3.4 14.7 + - - +
269B GLU 4.1 11.9 - - - +
271B VAL* 3.8 28.7 - - + +
280B LEU* 5.2 7.6 - - + -
----------------------------------------------------------
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ARG* 2.9 32.3 + - - +
263B GLU* 3.2 24.8 + - - +
265B LEU* 1.3 74.3 - - - +
267B ARG* 1.3 57.6 + - + +
268B GLY 3.3 4.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG 5.2 0.8 + - - -
263B GLU* 3.2 41.4 + - - +
264B ALA* 3.4 22.8 + - - +
265B LEU 3.3 0.4 - - - -
266B LYS* 1.3 77.6 - - + +
268B GLY* 1.3 62.8 + - - +
269B GLU* 2.6 33.7 + - + +
----------------------------------------------------------
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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