Contacts of the helix formed by residues 253 - 282 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLY* 3.2 23.6 + - - +
249A CYS* 3.0 37.0 - - + -
251A LYS* 4.2 7.2 - - + -
252A SER* 1.3 89.8 - - - +
254A ASP* 1.3 57.8 + - - +
255A ASP 3.3 0.4 - - - -
256A LEU* 2.5 39.3 + - + +
257A GLU* 2.7 16.4 + - + -
253B ILE* 3.1 42.8 - - + -
256B LEU* 4.6 2.0 - - + -
257B GLU* 4.3 13.7 - - - +
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLY* 3.1 33.3 + - - +
249A CYS 4.4 2.8 - - - +
250A GLY* 5.7 0.2 - - - -
251A LYS 4.3 11.8 + - - +
252A SER* 4.3 2.1 - - - -
253A ILE* 1.3 80.3 + - - +
255A ASP* 1.3 65.4 + - - +
256A LEU 2.9 0.5 + - - -
257A GLU* 3.0 5.0 + - - +
258A ASP* 2.9 23.0 + - - +
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Residues in contact with ASP 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 4.2 11.5 + - - +
253A ILE 3.3 0.2 - - - -
254A ASP* 1.3 79.3 - - - +
256A LEU* 1.3 57.4 + - + +
258A ASP* 3.5 10.3 - - - +
259A GLU* 2.8 58.4 + - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 3.6 18.2 - - - +
253A ILE* 2.5 30.2 + - + +
255A ASP* 1.3 72.2 - - + +
257A GLU* 1.3 53.0 + - - +
258A ASP 3.1 0.2 + - - -
259A GLU* 3.2 4.5 + - - +
260A LEU* 2.6 37.2 + - - +
253B ILE 4.7 0.2 - - - +
256B LEU* 3.6 23.6 - - + -
257B GLU* 3.3 55.0 - - + +
260B LEU* 3.9 23.5 - - + +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY* 2.6 27.2 + - - +
253A ILE* 2.7 21.3 + - + +
254A ASP* 3.7 5.6 - - - +
256A LEU* 1.3 72.9 - - - +
258A ASP* 1.3 57.6 + - - +
260A LEU* 3.4 3.9 - - - +
261A TYR* 2.9 43.5 + - + +
253B ILE* 4.2 4.9 - - - +
256B LEU* 3.5 37.9 - - + +
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Residues in contact with ASP 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASP 2.9 16.2 + - - +
255A ASP* 3.5 12.0 - - - +
257A GLU* 1.3 75.5 - - - +
259A GLU* 1.3 81.5 + - - +
260A LEU 3.0 1.2 + - - -
261A TYR* 3.8 3.5 - - - +
262A ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP* 2.8 47.3 + - - +
256A LEU* 3.8 3.6 - - - +
258A ASP* 1.3 85.9 - - - +
260A LEU* 1.3 51.8 + - - +
262A ALA* 4.1 8.7 - - - +
263A GLN* 2.6 56.6 + - - +
260B LEU* 4.4 2.2 - - + -
264B LYS* 3.3 27.1 - - - +
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Residues in contact with LEU 260 (chain A).
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 2.6 22.4 + - - +
257A GLU* 3.4 10.1 - - - +
258A ASP 3.0 0.8 - - - -
259A GLU* 1.3 68.8 - - - +
261A TYR* 1.3 65.2 + - + +
262A ALA 2.9 1.1 - - - -
263A GLN* 2.6 25.5 + - - +
264A LYS* 2.9 54.9 + - + +
256B LEU* 4.4 22.4 - - + +
259B GLU* 4.4 4.9 - - + -
260B LEU* 4.1 32.7 - - + +
263B GLN* 4.2 9.2 - - + +
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Residues in contact with TYR 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLU* 2.9 23.8 + - + +
258A ASP* 3.9 3.6 - - - +
260A LEU* 1.3 83.2 - - + +
262A ALA* 1.3 61.6 + - - +
264A LYS* 3.2 13.3 + - + +
265A LEU* 3.1 45.5 + - + +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ASP* 2.9 21.2 + - - +
259A GLU* 3.7 15.3 - - - +
261A TYR* 1.3 75.1 - - - +
263A GLN* 1.3 57.0 + - - +
264A LYS 3.0 1.3 - - - -
265A LEU* 3.3 5.1 + - - +
266A LYS* 2.6 49.2 + - + +
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Residues in contact with GLN 263 (chain A).
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* 2.6 41.1 + - - +
260A LEU* 2.6 12.8 + - - +
262A ALA* 1.3 75.8 - - - +
264A LYS* 1.3 48.0 + - - -
266A LYS* 3.6 8.6 - - - +
267A TYR* 2.7 37.8 + - - +
260B LEU* 3.5 1.0 - - - +
263B GLN* 3.7 41.0 - - + +
264B LYS* 2.6 38.1 + - - +
267B TYR* 4.4 31.9 - - + -
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 2.9 52.6 + - + +
261A TYR* 3.3 13.9 - - + +
262A ALA 3.0 0.2 - - - -
263A GLN* 1.3 74.2 - - - +
265A LEU* 1.3 63.1 + - + +
266A LYS 3.0 1.1 - - - -
267A TYR* 2.9 23.8 + - - +
268A LYS* 3.0 15.1 + - - +
259B GLU* 3.3 30.5 + - - +
263B GLN* 3.1 24.2 + - - +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A TYR* 3.1 38.6 + - + +
262A ALA* 4.1 4.0 - - - +
264A LYS* 1.3 80.4 - - + +
266A LYS* 1.3 51.1 + - - +
268A LYS* 4.0 10.0 - - - +
269A ALA* 2.8 38.5 + - - +
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ALA* 2.6 34.1 + - - +
263A GLN* 4.0 8.7 - - - +
265A LEU* 1.3 73.4 - - - +
267A TYR* 1.3 55.7 + - - +
269A ALA* 4.0 7.2 - - + -
270A ILE* 2.7 47.0 + - + +
267B TYR* 4.4 33.7 + - + -
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Residues in contact with TYR 267 (chain A).
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 2.7 21.4 + - - +
264A LYS* 3.1 10.8 - - - +
266A LYS* 1.3 79.7 - - - +
268A LYS* 1.3 70.2 + - + +
270A ILE* 3.0 22.7 - - - +
271A SER* 3.0 23.0 + - - -
263B GLN* 4.6 15.7 - - + -
266B LYS* 4.0 38.7 - - + -
270B ILE* 4.8 9.1 - - + +
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Residues in contact with LYS 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LYS 3.0 12.9 + - - +
265A LEU* 4.4 9.9 - - - +
267A TYR* 1.3 87.0 - - + +
269A ALA* 1.3 64.4 + - - +
270A ILE 3.2 0.4 - - - -
271A SER* 3.9 4.9 - - - -
272A GLU* 3.0 52.3 + - + +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LEU 2.8 23.7 + - - +
266A LYS* 4.0 9.9 - - + +
268A LYS* 1.3 82.6 - - - +
270A ILE* 1.3 52.0 + - - +
272A GLU* 4.3 2.6 - - - +
273A GLU* 2.8 41.1 + - - +
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LYS* 2.7 31.2 + - + +
267A TYR* 3.0 16.6 - - - +
269A ALA* 1.3 77.9 - - - +
271A SER* 1.3 67.8 - - - +
273A GLU* 3.6 8.0 - - - +
274A LEU* 2.6 38.2 + - - +
267B TYR* 5.0 12.8 - - + -
270B ILE* 3.6 41.5 - - + -
271B SER* 4.4 13.2 - - - +
274B LEU* 3.3 26.9 - - + +
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Residues in contact with SER 271 (chain A).
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* 3.0 24.1 + - - -
268A LYS* 3.9 7.6 - - - -
269A ALA 3.5 0.2 - - - -
270A ILE* 1.3 84.3 - - - +
272A GLU* 1.3 57.6 + - - +
274A LEU* 3.5 5.8 - - - +
275A ASP* 3.0 30.1 + - - +
270B ILE* 4.5 12.9 - - - +
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LYS* 3.0 37.8 + - + +
269A ALA* 4.3 2.5 - - - +
271A SER* 1.3 73.1 - - - +
273A GLU* 1.3 55.1 + - - +
274A LEU 2.9 4.7 + - - -
275A ASP* 3.1 6.1 + - + +
276A HIS* 2.7 52.4 + - + +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA 2.8 25.0 + - - +
270A ILE* 3.9 9.4 - - - +
272A GLU* 1.3 77.4 - - - +
274A LEU* 1.3 49.8 + - - +
276A HIS* 4.1 5.5 - - - +
277A ALA* 2.6 39.7 + - + +
274B LEU* 5.0 4.7 - - + +
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Residues in contact with LEU 274 (chain A).
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 2.6 22.3 + - - +
271A SER* 3.5 6.1 - - - +
273A GLU* 1.3 71.2 - - - +
275A ASP* 1.3 71.6 + - - +
276A HIS 3.0 0.7 - - - -
277A ALA* 2.7 26.2 + - + +
278A LEU* 2.9 18.6 + - + +
270B ILE* 4.2 19.5 - - + +
273B GLU* 4.4 7.2 - - + -
274B LEU* 3.3 50.7 - - + +
277B ALA* 4.5 14.6 - - + -
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Residues in contact with ASP 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A SER 3.0 13.8 + - - +
272A GLU* 3.7 5.8 - - + +
274A LEU* 1.3 89.4 - - - +
276A HIS* 1.3 56.1 + - + +
278A LEU* 3.4 4.7 + - - +
279A LYS* 2.7 44.6 + - + +
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLU* 2.7 33.0 + - + +
273A GLU* 4.1 5.6 - - - +
275A ASP* 1.3 78.2 - - + +
277A ALA* 1.3 58.1 + - - +
278A LEU 3.1 0.4 - - - -
279A LYS* 3.9 12.0 - - + +
280A ASP* 2.7 38.7 + - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLU* 2.6 28.4 + - + +
274A LEU* 2.7 14.0 + - + +
276A HIS* 1.3 74.8 - - - +
278A LEU* 1.3 54.2 + - - -
280A ASP* 4.0 5.3 - - - +
281A MET* 3.3 22.5 + - - +
274B LEU* 5.4 8.1 - - + -
278B LEU* 4.7 23.9 - - + +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 2.9 17.6 + - + +
275A ASP* 3.9 4.7 - - - +
277A ALA* 1.3 75.0 - - - +
279A LYS* 1.3 65.2 + - - +
280A ASP 3.0 2.0 - - - -
281A MET* 2.7 6.8 + - + +
282A THR* 2.5 37.0 + - - +
277B ALA* 3.5 43.3 - - + +
278B LEU* 5.4 3.4 - - + -
281B MET* 3.7 28.3 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ASP* 2.7 29.0 + - + +
276A HIS* 3.9 16.8 - - + +
278A LEU* 1.3 83.8 - - - +
280A ASP* 1.3 60.8 + - - +
282A THR* 3.9 16.8 + - - +
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A HIS* 2.7 24.2 + - - +
277A ALA* 4.0 5.6 - - - +
279A LYS* 1.3 73.1 - - - +
281A MET* 1.3 63.1 + - - +
282A THR* 4.5 2.8 - - - +
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Residues in contact with MET 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA 3.3 13.8 + - - +
278A LEU* 2.7 10.1 + - + +
280A ASP* 1.3 79.7 - - - +
282A THR* 1.3 84.0 + - - +
284A ILE* 3.1 36.6 - - + +
278B LEU* 2.9 37.5 - - + -
281B MET* 3.1 27.8 - - + -
282B THR 3.1 25.8 - - - +
283B SER* 4.7 2.7 - - - -
284B ILE 4.6 2.5 - - - +
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Residues in contact with THR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 2.5 19.4 + - - -
279A LYS* 3.9 16.2 - - - +
280A ASP 4.5 3.1 - - - +
281A MET* 1.3 101.5 - - - +
283A SER* 1.3 62.9 + - - +
284A ILE* 2.5 24.8 + - + +
281B MET* 2.7 12.4 - - - +
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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