Contacts of the helix formed by residues 250 - 273 (chain D) in PDB entry 2Y0N
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 ASN 250 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D PHE* 4.0 4.0 - - - -
246D PRO 5.1 5.5 + - - -
247D ALA 3.8 16.1 - - - +
248D GLU 3.3 2.6 - - - -
249D LYS* 1.3 74.8 - - - +
251D VAL* 1.3 63.7 + - - +
252D ASP* 3.1 23.6 + - - +
253D LEU* 3.1 17.9 + - + +
254D CYS* 3.0 20.6 + - - +
483D HIS* 4.1 1.2 + - - -
553E VAL 4.1 3.2 + - - -
554E THR* 3.4 45.3 + - - +
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Residues in contact with VAL 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D VAL* 5.0 7.4 - - + +
217D PHE* 3.6 21.1 - - + -
218D ALA* 4.2 26.7 - - + -
221D ALA* 5.7 3.8 - - + -
249D LYS 3.5 6.5 + - - +
250D ASN* 1.3 73.4 + - - +
252D ASP* 1.3 72.7 + - - +
254D CYS* 3.3 2.6 - - + +
255D LYS* 3.1 40.8 + - + +
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Residues in contact with ASP 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASN* 3.1 13.3 + - - +
251D VAL* 1.3 83.1 - - - +
253D LEU* 1.3 65.0 + - - +
255D LYS* 3.3 21.4 + - - +
256D GLU* 3.3 25.7 + - - +
554E THR 4.8 7.4 - - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ALA 3.6 23.6 - - - +
248D GLU* 4.1 6.3 - - - +
250D ASN* 3.1 20.7 + - + +
252D ASP* 1.3 75.3 - - - +
254D CYS* 1.3 64.2 + - - +
256D GLU* 3.4 8.6 + - - +
257D MET* 3.3 18.0 + - - +
479D ALA* 4.4 7.9 - - + -
483D HIS* 3.7 15.4 - - + +
553E VAL* 4.2 15.7 - - + +
554E THR* 3.3 27.8 + - - +
555E SER* 3.7 5.8 - - - +
556E PHE* 3.4 47.8 - - + +
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Residues in contact with CYS 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR* 3.5 34.5 - - - -
214D VAL* 4.7 9.9 - - - -
217D PHE* 3.6 37.0 - - + -
250D ASN 3.0 11.4 + - - +
251D VAL 3.3 10.3 - - - +
253D LEU* 1.3 76.7 - - - +
255D LYS* 1.3 63.1 + - - +
257D MET* 3.0 14.7 + - - +
258D VAL* 3.1 20.1 + - - +
483D HIS* 3.8 13.1 + - - +
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Residues in contact with LYS 255 (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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441B PHE* 3.3 21.0 - - - +
442B ASP* 3.2 38.1 + - + +
443B GLN* 3.9 16.7 + - - +
214D VAL* 4.1 26.5 - - + -
251D VAL* 3.1 27.2 + - - +
252D ASP* 3.3 22.1 + - - +
254D CYS* 1.3 77.0 - - - +
256D GLU* 1.3 60.8 + - - +
258D VAL* 3.5 9.8 + - - +
259D ASP* 3.1 24.4 + - - +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLN* 4.7 10.1 - - - +
252D ASP* 3.3 13.4 + - - +
253D LEU* 3.6 11.4 - - - +
254D CYS 3.2 1.0 - - - -
255D LYS* 1.3 74.7 - - - +
257D MET* 1.3 66.2 + - - +
259D ASP* 3.4 6.2 + - - +
260D GLY* 2.9 20.6 + - - -
554E THR 4.8 1.2 - - - +
555E SER* 3.2 24.3 + - - -
556E PHE* 2.9 40.9 + - + -
557E PHE* 3.7 35.8 - - + +
577H PHE* 4.4 5.3 + - - -
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Residues in contact with MET 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR* 4.2 17.9 - - + -
253D LEU 3.3 8.6 + - - +
254D CYS* 3.0 10.8 + - - +
256D GLU* 1.3 79.1 - - - +
258D VAL* 1.3 81.7 + - + +
260D GLY 3.1 2.1 + - - -
261D LEU* 2.9 48.5 + - + +
480D LEU* 4.4 8.5 - - + -
483D HIS* 3.4 40.4 - - + +
484D PHE* 3.5 34.1 - - + -
487D PHE* 4.5 7.9 - - + -
556E PHE* 4.2 4.2 - - + -
577H PHE* 3.2 14.4 - - + -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B PHE* 3.3 17.9 - - + -
210D LEU* 3.2 48.8 - - + +
213D TYR* 4.3 6.3 - - + -
214D VAL* 3.7 21.3 - - + -
254D CYS* 3.1 21.9 + - - +
255D LYS* 3.8 5.4 - - - +
256D GLU 3.3 0.2 - - - -
257D MET* 1.3 93.3 - - + +
259D ASP* 1.3 62.3 + - - +
261D LEU* 3.3 7.8 + - - +
262D ARG* 3.2 17.5 + - - +
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Residues in contact with ASP 259 (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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441B PHE* 3.6 17.0 - - + -
443B GLN* 3.5 32.1 - - - +
255D LYS 3.1 17.3 + - - +
256D GLU* 3.8 3.8 - - - +
258D VAL* 1.3 72.9 - - - +
260D GLY* 1.3 66.1 + - - +
262D ARG* 2.3 42.0 + - - +
263D ILE* 3.1 37.4 + - - +
557E PHE* 5.7 5.4 - - - -
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Residues in contact with GLY 260 (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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256D GLU 2.9 12.4 + - - -
259D ASP* 1.3 76.3 + - - +
261D LEU* 1.3 49.5 + - - +
263D ILE* 3.2 5.2 + - - +
264D THR* 2.6 39.7 + - - -
576H ALA* 4.0 6.5 - - - +
577H PHE* 3.3 38.8 - - - -
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ILE* 6.2 0.2 - - - -
210D LEU* 4.4 17.3 - - + -
257D MET* 2.9 52.0 + - + +
258D VAL* 3.3 10.1 - - - +
260D GLY* 1.3 74.3 - - - +
262D ARG* 1.3 57.1 + - - +
264D THR* 3.8 2.3 - - - -
265D PHE* 2.8 33.2 + - - +
456D LEU* 4.3 7.9 - - + -
459D LEU* 3.9 23.7 - - + +
460D PHE* 3.6 35.0 - - + -
463D LEU* 4.7 5.8 - - + -
484D PHE* 4.4 6.5 - - + -
487D PHE* 4.6 4.0 - - + -
577H PHE* 3.2 12.1 - - + -
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Residues in contact with ARG 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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440B GLU* 3.9 21.1 + - - +
441B PHE* 3.7 21.4 - - + -
206D ILE* 5.1 2.2 - - + -
207D ILE* 3.8 19.5 - - + +
210D LEU* 3.8 21.3 - - + -
258D VAL 3.2 4.0 + - - +
259D ASP* 2.3 41.1 + - - +
261D LEU* 1.3 76.7 - - - +
263D ILE* 1.3 80.7 + - - +
265D PHE* 4.4 2.2 - - - -
266D ASP* 2.9 50.0 + - - +
448D SER* 3.1 13.4 + - - +
449D TYR* 5.6 2.6 - - - -
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Residues in contact with ILE 263 (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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259D ASP* 3.1 36.8 + - - +
260D GLY* 3.6 7.6 - - - +
262D ARG* 1.3 95.6 - - - +
264D THR* 1.3 67.0 + - - +
265D PHE 3.2 0.2 + - - -
266D ASP* 3.3 9.2 + - - +
267D TYR* 3.2 20.1 + - + +
557E PHE* 6.3 2.0 - - + -
574H VAL* 3.8 28.3 - - + -
575H VAL 3.8 20.6 - - - +
576H ALA* 4.3 7.0 - - + -
581H LEU* 4.4 3.4 - - + -
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Residues in contact with THR 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 GLY 2.6 29.7 + - - -
261D LEU* 3.8 4.0 - - - -
263D ILE* 1.3 73.9 - - - +
265D PHE* 1.3 52.1 + - - +
267D TYR* 3.3 2.1 + - - +
268D THR* 2.3 46.0 + - - +
459D LEU* 4.3 15.0 - - + -
463D LEU* 4.8 4.7 - - + -
466D ILE* 4.7 13.9 - - + -
470D MET* 5.2 0.9 - - + -
576H ALA* 3.5 8.8 - - - +
577H PHE* 3.2 25.4 - - + -
581H LEU* 4.1 24.6 - - + +
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Residues in contact with PHE 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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206D ILE* 3.4 33.4 - - + -
261D LEU 2.8 22.4 + - - +
262D ARG* 4.1 4.9 - - - +
264D THR* 1.3 70.5 - - - +
266D ASP* 1.3 68.2 + - - +
267D TYR 3.0 0.2 + - - -
268D THR* 4.2 2.9 - - - -
269D LEU* 2.9 55.2 + - + +
273D LEU* 4.0 14.1 - - + -
447D PRO* 3.6 31.2 - - + -
448D SER* 3.9 11.9 - - - -
451D TYR* 3.7 9.0 - - + -
455D HIS* 3.7 25.8 - - + -
456D LEU* 4.3 12.6 - - + -
459D LEU* 4.1 13.4 - - + +
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Residues in contact with ASP 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 ARG* 2.9 31.0 + - - +
263D ILE* 3.3 7.3 + - - +
265D PHE* 1.3 79.6 - - - +
267D TYR* 1.3 60.2 + - - +
270D PRO* 3.8 6.4 - - - +
446D PRO* 3.3 17.0 - - + +
447D PRO* 3.1 33.7 - - + +
448D SER* 2.8 41.2 + - - -
449D TYR* 6.0 0.5 - - - -
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Residues in contact with TYR 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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263D ILE* 3.2 8.8 + - + +
264D THR* 3.8 5.2 - - + +
265D PHE 3.1 0.8 - - - -
266D ASP* 1.3 78.0 - - - +
268D THR* 1.3 72.5 + - - +
269D LEU 3.6 0.2 - - - -
270D PRO* 3.6 10.7 - - - +
271D LEU* 3.6 31.6 - - + +
572F LEU* 3.6 35.1 - - + +
568G ILE* 5.7 0.3 - - - +
574H VAL* 6.0 0.9 - - + -
581H LEU* 3.6 24.5 - - + -
582H PRO 3.3 21.3 - - - -
583H LYS* 3.1 13.8 - - - +
584H LEU* 2.9 37.5 + - + -
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Residues in contact with THR 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 THR* 2.3 38.3 + - - +
265D PHE 3.9 1.6 - - - -
267D TYR* 1.3 82.8 - - - +
269D LEU* 1.3 67.4 + - - +
271D LEU* 2.8 17.0 + - - +
272D VAL* 2.9 47.8 + - + -
273D LEU* 3.8 12.7 + - + -
459D LEU* 3.9 16.9 - - + +
466D ILE* 4.0 12.5 - - + +
584H LEU* 4.5 4.8 - - + +
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Residues in contact with LEU 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 PHE* 2.9 47.5 + - + +
268D THR* 1.3 77.0 - - - +
270D PRO* 1.4 65.5 - - + +
271D LEU 3.0 5.4 + - - -
273D LEU* 3.2 30.7 + - + +
274D LEU* 3.6 16.1 + - + +
282D TYR* 3.8 20.0 - - + -
447D PRO* 3.9 9.6 - - + -
451D TYR* 3.4 36.8 - - + +
455D HIS* 4.0 26.2 - - + -
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Residues in contact with PRO 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ASP 3.8 11.7 - - - +
267D TYR 3.6 12.1 - - - +
268D THR 3.5 3.6 - - - -
269D LEU* 1.4 99.2 - - + +
271D LEU* 1.3 65.8 + - + +
274D LEU* 4.5 16.2 - - + +
279D GLN* 5.0 6.2 + - - +
282D TYR* 3.3 43.5 - - + +
447D PRO* 4.5 1.8 - - + -
586H PRO* 5.6 1.2 - - - +
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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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267D TYR* 3.6 46.4 - - + +
268D THR* 2.8 8.7 + - - +
270D PRO* 1.3 88.8 - - + +
272D VAL* 1.3 64.4 + - + +
273D LEU 3.9 0.2 - - - -
274D LEU* 5.3 1.1 - - - -
568G ILE* 6.5 0.2 - - + -
584H LEU* 3.4 28.5 - - + +
586H PRO* 3.4 31.1 - - + +
587H GLN 2.8 30.2 + - - +
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D THR* 2.9 42.9 + - + +
271D LEU* 1.3 81.1 - - + +
273D LEU* 1.3 59.8 + - + +
274D LEU 3.7 0.2 - - - -
462D LYS* 3.5 42.0 - - + +
465D GLU* 4.9 5.2 - - - +
466D ILE* 4.9 0.7 - - + -
584H LEU* 4.4 16.2 - - + -
585H ALA 5.0 4.5 - - - +
587H GLN* 3.3 29.9 - - + +
589H PHE* 3.6 21.8 - - - +
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Residues in contact with LEU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D PHE* 4.0 20.6 - - + -
268D THR* 3.8 15.0 - - + -
269D LEU* 3.2 33.2 + - + +
272D VAL* 1.3 80.9 - - + +
274D LEU* 1.3 63.1 + - - +
455D HIS* 4.2 3.1 - - + +
458D ARG* 3.1 35.9 + - + +
459D LEU* 3.7 47.1 - - + +
462D LYS* 3.8 27.6 - - + -
589H PHE* 3.8 10.8 - - + +
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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