Contacts of the helix formed by residues 245 - 272 (chain D) in PDB entry 6DWN
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 245 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ALA* 5.0 8.3 - - - +
240D LEU* 3.7 22.4 + - - +
243D LEU 2.9 11.5 + - - +
244D PRO* 1.3 73.3 - - - +
246D PRO* 1.3 63.9 - - - +
247D SER* 3.4 12.3 + - - -
248D LEU* 3.1 37.9 + - + +
249D ASN* 2.8 38.3 + - - +
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Residues in contact with PRO 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D PRO* 3.8 7.2 - - + +
245D ASN* 1.3 87.8 - - - +
247D SER* 1.3 64.5 + - - +
249D ASN* 4.1 5.3 - - + +
250D ALA* 3.0 27.2 + - - +
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Residues in contact with SER 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ASN* 2.9 37.4 + - - +
226D GLU* 4.0 18.5 + - - +
227D VAL* 3.6 14.8 - - - +
245D ASN* 3.2 9.5 + - - -
246D PRO* 1.3 84.0 - - - +
248D LEU* 1.3 61.2 + - - +
250D ALA* 4.8 0.4 - - - -
251D PHE* 3.1 12.8 + - - +
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Residues in contact with LEU 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 4.0 28.3 - - + -
111D THR* 4.5 17.0 - - + -
114D LEU* 4.4 9.6 - - + -
227D VAL* 5.4 4.5 - - + -
232D ASN* 5.4 3.1 - - - +
234D ALA* 4.7 11.2 - - + -
240D LEU 4.4 0.4 - - - +
241D ARG* 3.8 30.5 - - - +
245D ASN* 3.1 30.1 + - + +
247D SER* 1.3 77.3 - - - +
249D ASN* 1.3 68.2 + - - +
251D PHE* 3.1 18.7 + - + +
252D LYS* 3.2 33.9 + - - +
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Residues in contact with ASN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D LEU 5.0 1.0 - - - +
244D PRO* 5.0 1.6 - - - +
245D ASN* 2.8 34.6 + - - +
246D PRO* 4.1 4.7 - - + +
248D LEU* 1.3 74.3 - - - +
250D ALA* 1.3 64.9 + - - +
252D LYS* 3.2 29.8 + - - +
253D ASP* 3.2 21.1 + - - +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ASN 5.7 3.6 - - - +
223D ASN* 4.5 13.9 - - - +
246D PRO 3.0 18.8 + - - +
247D SER* 4.0 3.8 - - - +
249D ASN* 1.3 77.1 - - - +
251D PHE* 1.3 62.7 + - - +
253D ASP* 3.4 14.4 + - - +
254D LEU* 3.5 16.1 + - - +
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Residues in contact with PHE 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D THR* 3.5 22.4 - - - -
114D LEU* 3.7 28.5 - - + -
115D ILE* 3.9 13.7 - - + -
223D ASN* 4.2 9.6 + - - +
224D PHE* 3.5 37.5 - + - -
227D VAL* 3.7 30.1 - - + -
228D VAL* 3.8 19.3 - - + -
247D SER 3.1 14.4 + - - +
248D LEU* 3.2 15.3 - - + +
249D ASN 3.1 0.4 - - - -
250D ALA* 1.3 78.3 - - - +
252D LYS* 1.3 59.8 + - - +
254D LEU* 3.8 1.1 + - - +
255D ASN* 2.6 46.2 + - - -
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Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 3.6 24.0 + - - -
114D LEU* 3.8 27.1 - - + -
241D ARG 4.9 4.8 + - - -
248D LEU* 3.2 29.1 + - - +
249D ASN* 3.2 26.9 + - - +
251D PHE* 1.3 77.7 - - - +
253D ASP* 1.3 64.9 + - - +
255D ASN* 3.5 5.6 + - - +
256D GLU* 3.1 36.2 + - + +
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Residues in contact with ASP 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ASN 3.2 10.8 + - - +
250D ALA* 3.8 11.7 - - - +
251D PHE 3.3 0.4 - - - -
252D LYS* 1.3 78.6 - - - +
254D LEU* 1.3 65.6 + - + +
256D GLU* 3.2 12.3 + - - +
257D LYS* 2.7 57.9 + - - +
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Residues in contact with LEU 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL 6.0 3.8 - - - +
220D LEU* 4.0 39.0 - - + +
221D ASN 5.2 0.9 - - - +
222D ASN* 3.2 32.8 - - + +
250D ALA 3.5 11.9 + - - +
251D PHE 4.7 1.3 - - - +
252D LYS 3.4 0.2 - - - -
253D ASP* 1.3 84.3 - - + +
255D ASN* 1.3 59.7 + - - +
257D LYS* 3.4 15.2 - - + +
258D PHE* 2.5 54.4 + - + +
602D AQ4 5.6 0.2 - - - +
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Residues in contact with ASN 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D LEU 3.2 29.0 - - - +
115D ILE* 3.4 23.3 - - - +
116D SER 4.1 6.0 + - - +
117D ASN 5.6 1.4 + - - +
224D PHE* 4.5 8.9 - - - -
251D PHE* 2.6 50.8 + - - +
252D LYS* 3.8 5.2 - - - +
253D ASP 3.3 0.4 - - - -
254D LEU* 1.3 78.5 - - - +
256D GLU* 1.3 60.8 + - + +
258D PHE* 3.9 7.2 - - - +
259D TYR* 3.2 24.8 + - - +
312D LEU* 5.6 0.9 - - - +
602D AQ4 4.8 8.7 + - - -
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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
----------------------------------------------------------
252D LYS* 3.1 23.6 + - + +
253D ASP* 3.5 12.3 - - - +
254D LEU 3.1 0.6 - - - -
255D ASN* 1.3 77.7 - - + +
257D LYS* 1.3 69.2 + - + +
259D TYR* 3.5 5.7 + - - +
260D SER* 3.1 26.5 + - - -
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Residues in contact with LYS 257 (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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253D ASP* 2.7 45.3 + - - +
254D LEU* 3.4 21.5 - - + +
256D GLU* 1.3 79.1 + - - +
258D PHE* 1.3 55.6 + - + +
260D SER* 3.0 8.4 + - - +
261D PHE* 2.7 36.8 + - - +
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Residues in contact with PHE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 5.3 15.5 - - + -
222D ASN* 4.0 12.8 - - - -
254D LEU* 2.5 39.5 + - + +
255D ASN* 3.9 7.9 - - - +
257D LYS* 1.3 72.5 - - + +
259D TYR* 1.3 57.3 + - - +
261D PHE* 3.2 8.1 + + + +
262D MET* 2.8 30.4 + - - +
312D LEU* 3.7 32.8 - - + +
315D PHE* 4.5 24.2 - + - -
316D GLY* 5.6 1.8 - - - -
319D PHE* 4.9 10.3 - + - -
602D AQ4 3.2 44.0 - + + -
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Residues in contact with TYR 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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116D SER* 3.3 43.0 + - - -
117D ASN* 3.5 19.5 - - + +
255D ASN 3.2 15.1 + - - +
256D GLU* 3.8 7.0 - - - +
257D LYS 3.2 0.6 - - - -
258D PHE* 1.3 79.4 - - - +
260D SER* 1.3 59.2 + - - +
262D MET* 3.5 27.2 - - + +
263D GLN* 3.4 36.7 + - - +
305D GLU* 2.7 42.2 + - + +
309D ASN* 3.6 17.2 + - + +
312D LEU* 3.8 11.0 - - + -
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Residues in contact with SER 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D GLU 3.1 13.8 + - - -
257D LYS* 3.0 12.4 + - - -
259D TYR* 1.3 75.7 - - - +
261D PHE* 1.3 65.8 + - - +
262D MET 3.1 1.3 - - - -
263D GLN* 3.2 22.1 + - - +
264D LYS* 3.2 11.8 + - - +
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Residues in contact with PHE 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 4.8 12.8 - + - -
207D TYR* 4.2 21.1 - + - -
257D LYS 2.7 18.7 + - - +
258D PHE* 3.6 9.2 - + + +
260D SER* 1.3 71.9 - - - +
262D MET* 1.3 64.1 + - - +
264D LYS* 3.2 30.1 + - + +
265D MET* 3.2 48.2 + - + +
315D PHE* 6.4 2.0 - + - -
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Residues in contact with MET 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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203D PHE* 6.4 2.0 - - + -
258D PHE 2.8 17.0 + - - +
259D TYR* 3.5 48.5 - - + +
260D SER 3.1 0.2 - - - -
261D PHE* 1.3 81.1 - - - +
263D GLN* 1.3 70.8 + - + +
265D MET* 3.0 8.2 + - + +
266D VAL* 2.9 38.1 + - + +
305D GLU* 6.1 0.4 - - + -
308D ILE* 4.4 8.3 - - + +
309D ASN* 3.6 33.4 - - + +
311D VAL* 4.5 11.0 - - + -
312D LEU* 4.4 23.3 - - + -
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Residues in contact with GLN 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D TYR* 3.4 28.4 + - - +
260D SER* 3.2 15.7 + - - +
262D MET* 1.3 84.2 - - + +
264D LYS* 1.3 56.9 + - - +
266D VAL* 3.7 7.0 - - - +
267D LYS* 2.8 60.9 + - - +
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Residues in contact with LYS 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 3.2 8.2 + - - +
261D PHE* 3.2 37.0 + - + +
263D GLN* 1.3 78.5 - - - +
265D MET* 1.3 64.0 + - - +
267D LYS* 3.7 8.6 - - - +
268D GLU* 2.9 59.6 + - + +
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Residues in contact with MET 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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203D PHE* 3.4 54.7 - - + +
205D ARG* 5.4 9.0 - - - +
207D TYR* 3.9 14.8 - - - +
261D PHE* 3.2 41.0 + - + +
262D MET* 3.0 9.2 + - - +
264D LYS* 1.3 81.2 - - - +
266D VAL* 1.3 66.5 + - + +
268D GLU* 3.3 23.8 + - - +
269D HIS* 2.8 41.1 + - + -
282D THR* 5.0 2.2 - - - +
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Residues in contact with VAL 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 MET* 2.9 30.2 + - + +
263D GLN* 3.8 6.1 - - - +
265D MET* 1.3 77.4 - - + +
267D LYS* 1.3 58.5 + - + +
269D HIS* 3.4 2.9 + - - +
270D TYR* 3.0 26.4 + - + +
282D THR* 4.2 18.2 - - + +
286D ILE* 4.1 12.5 - - + +
308D ILE* 3.4 44.9 - - + -
311D VAL* 5.3 4.3 - - + -
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Residues in contact with LYS 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 GLN* 2.8 59.3 + - - +
264D LYS* 3.7 6.3 - - - +
266D VAL* 1.3 74.6 - - + +
268D GLU* 1.3 67.4 + - + +
269D HIS 3.0 3.0 + - - -
270D TYR* 3.1 17.8 + - - +
271D LYS* 3.1 14.6 + - - +
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Residues in contact with GLU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ARG* 5.0 14.2 + - - +
264D LYS* 2.9 52.0 + - + +
265D MET* 3.3 25.6 + - - +
267D LYS* 1.3 76.3 - - + +
269D HIS* 1.3 64.1 + - - +
271D LYS* 4.3 3.0 - - - +
272D THR* 3.1 29.6 + - - +
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Residues in contact with HIS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.6 15.8 + - + -
205D ARG* 6.1 3.6 - - - -
265D MET* 2.8 40.1 + - + +
266D VAL 3.7 8.3 - - - +
267D LYS 3.0 0.4 - - - -
268D GLU* 1.3 81.9 - - + +
270D TYR* 1.3 54.2 + - - +
271D LYS 3.2 0.2 - - - -
272D THR 3.1 0.7 + - - -
273D PHE* 2.5 41.9 + - - +
279D ARG* 3.7 14.9 + - - +
280D ASP* 2.9 33.9 + - - -
282D THR* 3.5 15.6 - - + -
283D ASP* 3.0 26.9 - - - +
286D ILE* 3.9 10.1 - - + -
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Residues in contact with TYR 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D VAL* 3.0 19.1 + - + +
267D LYS* 3.1 8.3 + - - +
269D HIS* 1.3 76.4 - - - +
271D LYS* 1.3 66.2 + - + +
273D PHE* 3.6 17.4 + + + +
286D ILE* 4.2 18.3 - - + +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LYS 3.1 14.3 + - - +
268D GLU* 4.3 5.6 - - - +
270D TYR* 1.3 83.1 - - + +
272D THR* 1.3 66.1 + - + +
273D PHE 3.4 1.4 + - - +
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Residues in contact with THR 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D GLU 3.1 20.3 + - - +
269D HIS 3.1 1.0 + - - -
271D LYS* 1.3 84.8 - - + +
273D PHE* 1.3 64.1 + - - +
274D GLU* 3.3 5.7 + - - +
279D ARG* 2.8 33.6 + - - -
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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