Contacts of the helix formed by residues 253 - 280 (chain B) in PDB entry 1MV4
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 ILE 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A GLY 4.4 0.9 - - - +
249A CYS 4.3 4.0 - - - +
253A ILE* 3.1 46.4 - - + -
257A GLU* 4.2 12.6 - - - +
249B CYS* 3.2 48.1 - - + +
250B GLY* 4.2 7.4 - - - +
251B LYS* 3.9 4.3 - - + +
252B SER* 1.3 81.5 - - - +
254B ASP* 1.3 68.1 + - - +
256B LEU* 2.6 33.7 + - + +
257B GLU* 2.9 17.4 + - + +
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B SER* 5.2 2.4 - - - -
253B ILE* 1.3 85.6 + - - +
255B ASP* 1.3 58.4 + - - +
256B LEU 2.7 9.7 + - - -
257B GLU* 2.9 16.6 + - - +
258B ASP* 3.1 10.5 + - - +
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Residues in contact with ASP 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B SER* 4.1 19.1 + - - +
253B ILE 3.4 0.2 - - - -
254B ASP* 1.3 79.0 - - - +
256B LEU* 1.3 56.1 + - - +
258B ASP* 3.4 14.4 - - - +
259B GLU* 2.8 60.1 + - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ILE* 4.6 1.8 - - + -
256A LEU* 3.6 26.0 - - + +
257A GLU* 3.4 63.3 - - + +
260A LEU* 4.4 18.8 - - + +
252B SER 3.6 14.9 + - - +
253B ILE* 2.6 29.1 + - + +
255B ASP* 1.3 77.6 - - - +
257B GLU* 1.3 52.1 + - - +
258B ASP 3.1 0.2 + - - -
259B GLU* 3.6 3.2 - - - +
260B LEU* 2.6 38.2 + - + +
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ILE* 4.3 10.7 - - - +
256A LEU* 3.3 36.5 - - + +
253B ILE* 2.9 24.4 + - + +
254B ASP* 3.7 6.7 - - - +
256B LEU* 1.3 73.5 - - - +
258B ASP* 1.3 53.6 + - - +
260B LEU* 3.4 2.9 - - - +
261B TYR* 2.8 52.3 + - + +
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Residues in contact with ASP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ASP 3.1 10.2 + - - +
255B ASP* 3.4 19.9 - - - +
256B LEU 3.0 0.4 - - - -
257B GLU* 1.3 75.2 - - - +
259B GLU* 1.3 68.8 + - - +
260B LEU 3.0 2.2 + - - -
261B TYR* 3.2 5.1 + - - +
262B ALA* 3.0 22.8 + - - +
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.4 6.7 - - + -
264A LYS* 3.3 29.4 + - - +
255B ASP* 2.8 39.7 + - - +
256B LEU* 3.9 2.7 - - - +
258B ASP* 1.3 77.9 - - - +
260B LEU* 1.3 57.6 + - - +
262B ALA* 3.7 7.3 - - + +
263B GLN* 2.9 39.4 + - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 3.9 38.6 - - + +
259A GLU* 4.6 1.6 - - + -
260A LEU* 4.1 27.1 - - + +
263A GLN* 3.5 10.5 - - - +
256B LEU 2.6 24.0 + - - +
257B GLU* 3.4 7.2 - - - +
259B GLU* 1.3 70.0 - - - +
261B TYR* 1.3 70.0 + - + +
263B GLN* 2.6 27.7 + - + +
264B LYS* 2.7 55.0 + - + +
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Residues in contact with TYR 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B GLU* 2.8 37.1 + - + +
258B ASP* 3.5 6.3 - - - +
260B LEU* 1.3 82.4 - - + +
262B ALA* 1.3 58.4 + - - +
264B LYS* 2.9 30.9 + - + +
265B LEU* 3.0 24.2 + - + +
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Residues in contact with ALA 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ASP* 3.0 13.4 + - - +
259B GLU* 3.7 9.2 - - + +
261B TYR* 1.3 79.7 - - - +
263B GLN* 1.3 62.9 + - - +
265B LEU* 3.2 8.7 + - - +
266B LYS* 2.9 29.2 + - - +
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Residues in contact with GLN 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LEU* 4.4 5.2 - - + -
263A GLN* 3.7 40.4 - - + +
264A LYS* 3.1 31.6 + - - -
267A TYR* 4.6 13.9 - - + -
259B GLU* 2.9 23.3 + - - +
260B LEU* 2.6 19.6 + - + +
262B ALA* 1.3 77.9 - - - +
264B LYS* 1.3 50.6 + - - -
266B LYS* 3.5 18.7 - - + +
267B TYR* 2.7 34.5 + - - +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU* 3.3 21.6 - - - +
263A GLN* 2.6 34.7 + - - +
260B LEU* 2.7 47.3 + - + +
261B TYR* 2.9 17.2 + - + +
263B GLN* 1.3 74.1 - - - +
265B LEU* 1.3 59.7 + - + +
266B LYS 3.0 1.3 - - - -
267B TYR* 2.8 30.9 + - + +
268B LYS* 2.9 16.4 + - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B TYR* 3.0 38.5 + - + +
262B ALA* 3.9 7.4 - - - +
264B LYS* 1.3 80.2 - - + +
266B LYS* 1.3 57.7 + - - +
268B LYS* 3.6 9.0 + - + +
269B ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 4.0 35.4 - - + -
262B ALA 2.9 17.3 + - - +
263B GLN* 3.7 15.7 - - + +
265B LEU* 1.3 78.8 - - - +
267B TYR* 1.3 52.1 + - - +
268B LYS 3.3 0.2 - - - -
269B ALA* 4.3 13.3 - - - +
270B ILE* 2.7 51.4 + - + +
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Residues in contact with TYR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLN* 4.4 29.6 - - + -
266A LYS* 4.4 34.4 + - + -
270A ILE* 5.0 8.3 - - + -
263B GLN 2.7 18.3 + - - +
264B LYS* 3.1 14.6 - - + +
266B LYS* 1.3 79.3 - - - +
268B LYS* 1.3 60.3 + - + +
270B ILE* 3.1 10.8 - - + +
271B SER* 3.0 37.1 + - - -
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B LYS 2.9 12.5 + - - +
265B LEU* 4.1 8.1 - - + +
267B TYR* 1.3 80.5 - - + +
269B ALA* 1.3 66.7 - - - +
270B ILE 3.2 0.4 - - - -
271B SER* 4.0 4.2 - - - -
272B GLU* 2.9 52.5 + - - +
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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
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265B LEU 2.9 21.4 + - - +
266B LYS* 4.1 17.3 - - - +
268B LYS* 1.3 82.4 - - - +
270B ILE* 1.3 58.0 + - - +
272B GLU* 4.0 3.6 - - - +
273B GLU* 3.0 37.5 + - - +
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 4.8 7.9 - - + +
270A ILE* 3.6 46.0 - - + -
271A SER* 4.5 17.5 - - - +
274A LEU* 4.2 12.2 - - + +
266B LYS* 2.7 40.5 + - + +
267B TYR* 3.1 19.7 - - + +
269B ALA* 1.3 75.5 - - - +
271B SER* 1.3 66.8 + - - +
272B GLU 3.1 1.3 - - - -
273B GLU* 3.6 4.2 - - + +
274B LEU* 2.7 37.8 + - - +
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Residues in contact with SER 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 4.4 10.5 - - - -
267B TYR* 3.0 27.3 + - - -
268B LYS* 4.0 4.9 - - - -
270B ILE* 1.3 82.9 - - - +
272B GLU* 1.3 59.2 - - - +
274B LEU* 3.5 6.2 - - - +
275B ASP* 3.0 32.4 + - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LYS* 2.9 40.3 + - + +
269B ALA* 4.0 5.2 - - - +
271B SER* 1.3 74.3 - - - +
273B GLU* 1.3 54.7 + - - +
274B LEU 2.9 4.4 + - - -
275B ASP* 3.1 5.0 + - + +
276B HIS* 2.7 64.9 + - + +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.4 6.9 - - + +
269B ALA* 3.0 25.6 + - - +
270B ILE* 3.9 4.5 - - + +
272B GLU* 1.3 76.6 - - - +
274B LEU* 1.3 50.7 + - - +
276B HIS* 4.3 6.1 - - + -
277B ALA* 2.7 37.9 + - + +
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Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A ILE* 3.3 36.3 - - + +
273A GLU* 5.0 5.6 - - + +
274A LEU* 3.3 41.9 - - + +
277A ALA* 5.4 7.9 - - + -
270B ILE 2.7 16.5 + - - +
271B SER* 3.5 6.7 - - - +
272B GLU 2.9 0.8 - - - -
273B GLU* 1.3 74.6 - - - +
275B ASP* 1.3 71.8 + - - +
276B HIS 3.1 1.1 - - - -
277B ALA* 2.8 20.3 + - - +
278B LEU* 2.9 20.3 + - + +
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Residues in contact with ASP 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B SER* 3.0 18.0 + - - +
272B GLU* 3.8 3.6 - - - +
274B LEU* 1.3 86.9 - - - +
276B HIS* 1.3 54.0 + - + +
278B LEU* 3.3 6.6 + - - +
279B LYS* 2.7 53.6 + - + +
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Residues in contact with HIS 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B GLU* 2.7 52.2 + - + +
273B GLU* 4.2 4.7 - - + +
275B ASP* 1.3 73.4 - - + +
277B ALA* 1.3 56.6 + - - +
278B LEU 3.1 0.2 - - - -
279B LYS* 3.7 16.0 - - + +
280B ASP* 2.6 36.6 + - - +
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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
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274A LEU* 4.5 12.6 - - + -
278A LEU* 3.5 34.4 - - + +
273B GLU* 2.7 24.0 + - + +
274B LEU* 2.8 11.6 + - - +
276B HIS* 1.3 78.4 - - - +
278B LEU* 1.3 57.6 + - - +
280B ASP* 3.7 13.8 - - - +
281B MET* 3.9 5.5 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA* 4.7 26.0 - - + +
278A LEU* 5.4 2.9 - - + -
281A MET* 2.9 44.4 - - + -
274B LEU* 2.9 16.0 + - + +
275B ASP* 3.8 8.1 - - - +
277B ALA* 1.3 75.7 - - - +
279B LYS* 1.3 60.2 + - - +
280B ASP 3.1 1.8 - - - -
281B MET* 2.9 18.8 + - - +
282B THR* 2.9 12.5 + - - +
283B SER* 5.8 0.9 - - - -
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ASP* 2.7 36.4 + - + +
276B HIS* 3.7 21.8 - - + +
278B LEU* 1.3 73.9 - - - +
280B ASP* 1.3 58.4 + - - +
282B THR* 2.8 23.9 + - - +
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B HIS 2.6 22.0 + - - +
277B ALA* 3.7 10.4 - - - +
278B LEU 3.1 0.2 - - - -
279B LYS* 1.3 74.2 - - - +
281B MET* 1.3 62.4 + - - +
282B THR* 3.2 2.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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