Contacts of the helix formed by residues 260 - 285 (chain D) in PDB entry 2GPV
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 SER 260 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257D VAL* 5.4 1.7 - - - +
258D PRO* 3.3 7.9 + - - -
259D ASP* 1.3 76.5 - - - +
261D ASP* 1.3 74.5 + - - +
262D ILE* 3.4 6.9 + - - +
263D LYS* 3.3 24.4 + - - +
264D ALA* 3.4 19.1 + - - +
339D LEU* 4.8 12.6 - - - +
340D ALA* 5.3 0.3 - - - -
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Residues in contact with ASP 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D SER* 1.3 81.4 + - - +
262D ILE* 1.3 84.8 + - + +
263D LYS 3.2 0.2 + - - -
264D ALA* 3.3 10.2 + - - +
265D LEU* 3.3 23.0 + - + +
339D LEU* 3.7 23.3 + - - +
340D ALA* 4.4 8.6 - - - +
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Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D SER* 3.4 4.4 + - - +
261D ASP* 1.3 91.9 + - + +
263D LYS* 1.3 54.3 + - - +
265D LEU* 3.0 17.3 + - + +
266D THR* 2.6 51.7 + - - +
441D GLU 5.8 8.1 - - - -
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Residues in contact with LYS 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D PRO* 4.8 10.3 - - - +
254D ASP* 3.1 30.1 + - + +
255D PRO* 4.7 4.4 - - - +
257D VAL* 2.8 42.4 + - + +
258D PRO 3.9 2.0 - - - +
259D ASP* 3.7 36.4 + - - +
260D SER* 3.3 20.1 + - - +
262D ILE* 1.3 77.5 - - - +
264D ALA* 1.3 67.1 + - - +
266D THR* 2.9 8.5 + - - -
267D THR* 2.8 32.9 + - - +
330D TYR* 5.4 5.6 - - + +
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D SER 3.4 8.1 + - - +
261D ASP 3.3 10.1 + - - +
263D LYS* 1.3 78.9 - - - +
265D LEU* 1.3 57.0 + - - +
267D THR* 3.5 2.9 + - - -
268D LEU* 3.1 37.6 + - + +
330D TYR* 3.2 28.6 + - + +
332D MET* 4.8 5.8 - - + -
336D GLN 5.8 0.2 - - - +
340D ALA* 3.7 26.5 - - + -
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D ASP* 3.4 24.2 - - + +
262D ILE* 3.0 17.0 + - + +
264D ALA* 1.3 73.7 - - + +
266D THR* 1.3 66.2 + - - +
267D THR 3.1 1.6 - - - -
268D LEU* 3.2 4.2 + - + +
269D CYS* 2.9 36.8 + - - -
340D ALA 4.4 19.3 - - - +
342D LEU* 4.4 13.5 - - + -
434D HIS* 5.8 0.7 - - - +
438D ILE* 4.1 23.3 - - + -
441D GLU* 6.1 1.3 - - - +
503D OHT 3.9 27.4 - - + -
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Residues in contact with THR 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ILE* 2.6 38.4 + - - +
263D LYS* 3.5 7.4 - - - -
265D LEU* 1.3 72.0 - - - +
267D THR* 1.3 62.0 + - - +
269D CYS* 3.9 5.0 - - - +
270D ASP* 3.1 35.4 + - - +
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Residues in contact with THR 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ALA* 3.6 40.9 - - + +
253D PRO* 4.3 21.4 - - + +
254D ASP 5.0 1.6 + - - -
263D LYS* 2.8 25.4 + - - +
264D ALA* 3.7 6.7 - - - -
266D THR* 1.3 75.8 - - - +
268D LEU* 1.3 55.8 + - + +
269D CYS 3.2 0.2 - - - -
270D ASP* 3.4 4.6 + - - +
271D LEU* 2.7 35.4 + - + +
330D TYR* 4.5 15.3 - - + -
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Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264D ALA* 3.1 25.0 + - + +
265D LEU* 3.2 5.8 + - - +
267D THR* 1.3 75.8 - - - +
269D CYS* 1.3 53.2 + - - +
271D LEU* 3.5 10.6 - - + +
272D ALA* 2.8 35.7 + - - +
326D TYR* 3.7 43.1 - - + -
330D TYR* 4.2 14.1 - - + -
332D MET* 4.5 9.2 - - - -
342D LEU* 3.8 28.7 - - + -
503D OHT 3.6 38.0 - - + -
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Residues in contact with CYS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D LEU* 2.9 30.3 + - - +
266D THR* 3.9 6.5 - - - +
268D LEU* 1.3 74.8 - - - +
270D ASP* 1.3 59.6 + - - +
272D ALA* 3.7 1.7 - - - +
273D ASP* 2.8 41.5 + - - +
435D PHE* 3.9 29.4 - - - -
438D ILE* 6.3 1.6 - - - -
503D OHT 3.9 26.3 - - - -
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Residues in contact with ASP 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D ALA 6.1 0.2 - - - +
266D THR* 3.1 29.2 + - - +
267D THR* 3.8 4.0 - - - +
269D CYS* 1.3 79.2 - - - +
271D LEU* 1.3 59.0 + - - +
273D ASP* 3.4 11.1 + - - +
274D ARG* 3.0 47.5 + - + +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 4.0 27.6 - - + +
250D TYR 4.5 1.1 - - - +
251D ALA* 4.3 28.5 - - + +
267D THR 2.7 22.1 + - - +
268D LEU* 3.5 10.5 - - + +
270D ASP* 1.3 69.8 - - - +
272D ALA* 1.3 55.7 + - - +
274D ARG* 3.1 13.1 + - - +
275D GLU* 2.8 56.9 + - + +
326D TYR* 3.5 43.1 - - + +
503D OHT 3.9 9.0 - - + -
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D LEU 2.8 21.2 + - - +
269D CYS 3.7 3.8 - - - +
271D LEU* 1.3 72.5 - - - +
273D ASP* 1.3 54.4 + - - +
275D GLU* 3.1 8.0 + - - +
276D LEU* 2.8 40.4 + - + +
309D LEU* 4.1 9.5 - - + +
503D OHT 3.5 49.1 - - + -
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Residues in contact with ASP 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LEU* 6.0 1.9 - - - +
269D CYS* 2.8 28.0 + - - +
270D ASP* 3.5 12.8 - - - +
272D ALA* 1.3 74.7 - - - +
274D ARG* 1.3 62.4 + - + +
276D LEU* 3.7 17.3 + - - +
277D VAL* 3.7 14.6 + - - +
503D OHT 3.1 37.4 + - - +
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 3.4 34.4 - - + +
250D TYR 3.1 27.5 + - - +
251D ALA* 3.5 19.8 + - - +
252D MET* 4.9 16.8 - - - +
267D THR 5.2 0.2 + - - -
270D ASP* 3.0 27.9 + - + +
271D LEU* 3.7 16.5 - - - +
273D ASP* 1.3 74.5 - - + +
275D GLU* 1.3 67.1 + - - +
277D VAL* 3.4 19.7 + - - +
278D VAL* 3.8 5.2 + - - +
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ILE* 3.9 23.8 - - + +
271D LEU* 2.8 44.5 + - + +
272D ALA 3.5 4.0 - - - +
274D ARG* 1.3 74.5 - - - +
276D LEU* 1.3 66.0 + - - +
278D VAL* 3.0 11.1 + - + +
279D ILE* 2.9 26.7 + - + +
309D LEU* 3.8 20.4 - - + +
312D GLY* 5.7 0.7 - - - -
316D ARG* 3.9 19.5 + - - -
326D TYR 5.1 0.4 - - - -
503D OHT 2.8 30.6 + - - -
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B MET* 4.7 14.4 - - - -
450B PHE* 4.5 15.3 - - + -
272D ALA 2.8 24.1 + - - +
273D ASP* 3.7 18.6 - - - +
274D ARG 3.4 0.2 - - - -
275D GLU* 1.3 72.5 - - - +
277D VAL* 1.3 65.1 + - + +
279D ILE* 2.9 22.2 + - + +
280D ILE* 2.8 33.2 + - + +
305D TRP* 3.7 50.7 - - + +
309D LEU* 5.0 5.2 - - + -
503D OHT 5.1 5.2 - - - +
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B MET* 2.9 49.9 - - + +
273D ASP 3.7 10.9 + - - +
274D ARG* 3.4 11.5 + - - +
275D GLU 3.2 0.6 + - - -
276D LEU* 1.3 80.5 - - + +
278D VAL* 1.3 70.9 + - + +
280D ILE* 4.8 1.8 - - + -
281D GLY* 3.3 8.5 + - - -
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Residues in contact with VAL 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO* 3.8 28.1 - - + +
247D GLU 6.1 0.2 - - - +
249D ILE* 3.7 28.3 - - + -
274D ARG 3.8 5.1 + - - +
275D GLU* 3.0 15.8 + - + +
277D VAL* 1.3 80.8 - - + +
279D ILE* 1.3 58.1 - - + +
281D GLY* 4.4 2.5 - - - +
282D TRP* 2.7 34.9 + - - +
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO* 5.5 3.4 - - + -
275D GLU* 2.9 21.5 + - + +
276D LEU* 2.9 22.0 + - + +
278D VAL* 1.3 78.9 - - + +
280D ILE* 1.3 59.6 + - + +
282D TRP* 3.3 14.7 - - + +
283D ALA* 2.8 25.3 + - - +
301D LEU* 4.5 10.8 - - + -
305D TRP* 4.7 1.6 - - - +
308D ILE* 3.6 49.6 - - + +
309D LEU* 3.8 32.1 - - + +
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Residues in contact with ILE 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449B LEU* 4.4 2.7 - - + +
450B PHE* 3.7 39.5 - - + +
453B MET* 3.5 46.0 - - + -
454B LEU* 3.5 29.1 - - + +
276D LEU* 2.8 24.8 + - + +
277D VAL* 3.7 6.7 - - - +
279D ILE* 1.3 75.7 - - + +
281D GLY* 1.3 65.3 + - - +
283D ALA* 3.1 21.2 + - - +
284D LYS* 3.3 11.0 + - - +
301D LEU* 4.0 6.5 - - + -
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Residues in contact with GLY 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B MET* 4.3 4.8 - - - +
277D VAL 3.3 11.0 + - - -
278D VAL* 3.9 3.6 - - - -
280D ILE* 1.3 78.8 - - - +
282D TRP* 1.3 59.3 + - - +
284D LYS* 3.4 22.4 + - - +
285D HIS* 3.0 24.9 + - - -
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Residues in contact with TRP 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LEU* 4.6 9.6 + - + +
244D ALA* 3.5 34.3 - - + +
245D GLU* 4.6 8.7 + - - +
246D PRO* 3.9 19.3 - - + -
278D VAL 2.7 23.7 + - - +
279D ILE* 3.3 33.7 - - + +
281D GLY* 1.3 72.7 - - - +
283D ALA* 1.3 69.2 + - + +
285D HIS* 2.9 27.8 + - - +
286D ILE* 3.5 35.2 + - + +
308D ILE* 3.7 28.5 - - + -
367D VAL* 4.5 6.5 + - - +
370D LYS* 3.8 48.4 - - + +
371D ALA* 4.0 6.1 - - + -
374D LEU* 4.2 5.4 - - + -
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ILE 2.8 16.6 + - - +
280D ILE* 3.1 13.9 + - - +
282D TRP* 1.3 82.3 - - + +
284D LYS* 1.3 62.0 + - - +
286D ILE* 3.1 17.2 + - - +
289D PHE* 3.0 45.3 - - + +
301D LEU* 4.3 9.0 - - + -
374D LEU* 4.0 11.9 - - + -
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Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B MET 3.3 27.4 + - - -
454B LEU* 3.5 33.6 + - + +
455B GLU 4.2 8.7 - - - -
280D ILE* 3.3 12.0 + - - +
281D GLY* 3.6 15.0 - - - +
282D TRP 3.1 0.8 + - - -
283D ALA* 1.3 78.4 - - - +
285D HIS* 1.3 65.9 + - + +
286D ILE 3.2 8.2 + - - +
289D PHE* 4.0 3.1 - - + -
290D SER* 3.0 31.6 + - - +
297D GLN* 5.1 3.4 - - - +
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Residues in contact with HIS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D HIS* 3.0 38.0 + - - +
241D LEU* 5.2 0.4 - - - +
244D ALA* 3.8 30.0 - - + +
281D GLY* 3.0 29.2 + - - -
282D TRP* 2.9 13.6 + - - +
284D LYS* 1.3 78.9 - - + +
286D ILE* 1.3 61.6 + - - +
287D PRO* 3.3 0.9 - - - +
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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