Contacts of the helix formed by residues 225 - 256 (chain D) in PDB entry 4OQB
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 LYS 225 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D SER* 1.3 76.2 - - - +
226D LYS* 1.3 65.4 - - + +
228D LYS* 4.0 1.3 - - - +
229D ASP* 3.1 38.6 + - - +
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Residues in contact with LYS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D SER 4.7 0.8 - - - +
225D LYS* 1.3 83.6 - - + +
227D GLU* 1.3 65.1 + - + +
229D ASP* 4.2 4.7 - - - -
230D LYS* 3.1 64.1 + - + +
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D SER* 3.5 33.8 + - - +
225D LYS 3.3 0.6 - - - -
226D LYS* 1.3 79.2 - - + +
228D LYS* 1.3 57.2 + - - +
230D LYS* 4.1 2.2 - - - +
231D ASP* 3.1 28.1 + - - +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D SER* 3.1 18.8 + - - +
225D LYS* 4.3 1.8 - - - +
227D GLU* 1.3 77.4 - - - +
229D ASP* 1.3 59.6 + - - +
231D ASP* 3.6 12.5 - - - +
232D SER* 2.8 36.6 + - - -
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Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D LYS* 3.1 31.0 + - + +
226D LYS* 3.9 7.0 - - - +
227D GLU 3.3 0.4 - - - -
228D LYS* 1.3 74.5 - - - +
230D LYS* 1.3 64.0 + - + +
232D SER* 3.3 4.0 + - - -
233D LYS* 2.7 45.4 + - - +
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LYS* 3.1 48.7 + - + +
227D GLU* 4.3 2.2 - - - +
229D ASP* 1.3 82.9 + - + +
231D ASP* 1.3 56.0 + - - +
233D LYS* 4.5 5.2 - - + -
234D LEU* 3.0 32.6 + - - +
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Residues in contact with ASP 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D GLU 3.1 20.7 + - - +
228D LYS* 3.6 13.3 - - - +
230D LYS* 1.3 78.8 - - - +
232D SER* 1.3 61.8 + - - +
234D LEU* 3.9 6.2 - - - +
235D GLU* 3.5 20.1 + - - +
359D PRO* 5.7 4.7 - - - +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LYS* 2.8 26.9 + - - -
229D ASP* 3.9 4.7 - - - -
231D ASP* 1.3 74.6 - - - +
233D LYS* 1.3 63.3 + - - +
235D GLU* 3.4 11.7 + - - +
236D LYS* 3.2 18.9 + - - +
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Residues in contact with LYS 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ASP* 2.7 32.2 + - - +
230D LYS* 4.4 5.8 - - + +
232D SER* 1.3 70.2 - - - +
234D LEU* 1.3 63.3 + - - +
236D LYS* 3.4 24.0 - - + +
237D ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D LYS 3.0 21.0 + - - +
231D ASP* 3.9 6.5 - - - +
232D SER 3.3 0.2 - - - -
233D LYS* 1.3 73.2 - - - +
235D GLU* 1.3 57.4 + - + +
236D LYS 3.1 1.3 - - - -
237D ALA* 3.0 9.2 + - + +
238D LEU* 2.7 57.1 + - + +
356D ILE* 4.7 15.4 - - + +
357D PHE 4.7 7.4 - - - +
359D PRO* 5.1 13.0 - - + -
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Residues in contact with GLU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 3.9 23.6 - - + -
86D LYS* 4.8 11.1 + - - -
231D ASP 3.5 10.4 + - - +
232D SER* 3.4 12.9 + - - +
234D LEU* 1.3 81.9 - - + +
236D LYS* 1.3 60.8 + - - +
238D LEU* 3.7 9.4 - - + +
239D LYS* 3.2 22.9 + - - +
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D SER 3.2 12.7 + - - +
233D LYS* 3.4 32.8 - - + +
234D LEU 3.1 0.8 - - - -
235D GLU* 1.3 77.7 + - - +
237D ALA* 1.3 56.7 + - - +
239D LYS* 3.7 30.8 - - - +
240D ALA* 3.1 26.2 + - - +
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D LYS 3.2 9.3 + - - +
234D LEU* 3.0 11.3 + - + +
236D LYS* 1.3 76.9 - - - +
238D LEU* 1.3 59.8 + - - +
240D ALA* 3.5 10.3 - - - +
241D GLN* 3.1 26.2 + - - +
356D ILE* 3.6 22.7 - - + +
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Residues in contact with LEU 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 3.7 22.2 - - + -
234D LEU* 2.7 29.5 + - + +
235D GLU* 3.8 10.1 - - + +
236D LYS 3.3 0.2 - - - -
237D ALA* 1.3 73.3 - - - +
239D LYS* 1.3 60.3 + - - +
241D GLN* 3.4 5.0 + - + +
242D ASN* 3.0 27.9 + - - +
356D ILE* 3.3 39.9 - - + +
357D PHE 3.7 14.6 - - - +
358D PRO* 4.6 17.3 - - + -
359D PRO* 5.0 5.4 - - + -
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 3.6 53.5 - - + +
235D GLU 3.2 13.0 + - - +
236D LYS* 3.7 24.2 - - - +
238D LEU* 1.3 76.9 - - - +
240D ALA* 1.3 65.7 + - - +
242D ASN* 3.2 0.5 + - - +
243D ASP* 3.0 48.9 + - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D LYS* 3.1 19.8 + - - +
237D ALA* 3.5 12.1 - - + +
238D LEU 3.3 0.2 - - - -
239D LYS* 1.3 78.2 - - - +
241D GLN* 1.3 57.4 + - - +
243D ASP* 3.5 6.3 - - - +
244D LEU* 3.1 27.8 + - - +
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Residues in contact with GLN 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D ALA 3.1 17.7 + - - +
238D LEU* 3.8 5.4 - - + +
239D LYS 3.2 0.2 - - - -
240D ALA* 1.3 76.6 - - - +
242D ASN* 1.3 67.1 + - - +
244D LEU* 3.5 9.2 + - + +
245D ILE* 3.4 27.6 + - + +
288D VAL* 6.0 0.4 - - + -
289D PHE* 3.6 22.4 - - + -
353D GLN* 3.5 22.3 + - - +
354D ASP 3.4 19.6 + - - -
355D ARG* 3.5 11.9 - - - +
356D ILE* 2.7 44.9 + - + +
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Residues in contact with ASN 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D SER 3.5 9.9 + - - -
76D GLU 5.0 0.2 + - - -
77D LEU 3.1 20.9 + - - +
78D ARG* 3.5 3.1 - - - -
79D TRP* 2.7 45.6 + - + +
82D GLN* 3.2 14.5 - - - +
238D LEU 3.0 16.8 + - - +
239D LYS 3.2 4.2 + - - +
241D GLN* 1.3 79.9 - - - +
243D ASP* 1.3 59.3 + - - +
244D LEU 3.2 0.2 - - - -
245D ILE* 3.5 4.8 + - - +
246D TRP* 3.3 32.4 + - - +
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Residues in contact with ASP 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 4.9 5.0 - - + +
239D LYS* 3.0 50.6 + - - +
240D ALA* 3.5 8.7 - - - +
242D ASN* 1.3 81.6 - - + +
244D LEU* 1.3 61.9 + - - +
246D TRP* 3.9 11.7 - - + -
247D ASN* 3.0 36.5 + - - +
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Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ALA 3.1 19.6 + - - +
241D GLN* 3.6 10.5 - - + +
242D ASN 3.2 0.8 - - - -
243D ASP* 1.3 79.6 + - - +
245D ILE* 1.3 66.7 + - + +
247D ASN* 3.4 7.6 + - + +
248D ILE* 3.0 46.9 + - + +
288D VAL* 4.6 14.8 - - + -
348D LEU* 4.5 19.1 - - + +
349D LYS 5.3 3.1 - - - +
350D VAL* 5.1 11.2 - - + -
353D GLN* 3.7 30.3 - - - +
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Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLN* 3.4 16.6 + - + +
242D ASN* 3.8 7.4 - - - +
244D LEU* 1.3 77.6 - - + +
246D TRP* 1.3 52.1 + - + +
248D ILE* 3.1 9.3 + - - +
249D LYS* 2.6 46.0 + - + +
281D ASP* 5.2 6.3 - - - +
284D ALA* 3.7 24.5 - - + +
285D ASP* 5.1 3.1 - - + +
288D VAL* 4.4 17.7 - - + -
289D PHE* 3.8 29.4 - - + -
355D ARG* 3.8 19.1 - - - +
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Residues in contact with TRP 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.8 32.1 - + - -
76D GLU 3.2 29.0 + - - -
77D LEU 3.2 11.1 + - - -
78D ARG* 3.2 56.5 - - + +
242D ASN* 3.3 30.3 + - - +
243D ASP* 4.0 10.3 - - + -
244D LEU 3.3 0.2 - - - -
245D ILE* 1.3 77.2 - - + +
247D ASN* 1.3 66.3 + - - +
249D LYS* 3.7 42.7 - - + +
250D ASP* 3.0 34.1 + - + +
280D LEU* 6.0 0.4 - - + -
----------------------------------------------------------
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Residues in contact with ASN 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 5.8 1.4 + - - -
243D ASP* 3.0 28.2 + - - +
244D LEU* 3.5 9.3 - - + +
246D TRP* 1.3 76.8 - - - +
248D ILE* 1.3 61.5 + - + +
250D ASP* 3.1 14.7 - - - +
251D GLU* 3.0 27.1 - - + +
348D LEU* 6.2 4.9 - - + +
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D LEU* 3.0 34.0 + - + +
245D ILE* 3.4 7.4 - - - +
247D ASN* 1.3 77.2 - - + +
249D LYS* 1.3 66.1 + - - +
251D GLU* 3.5 7.5 + - - +
252D LEU* 3.2 20.4 + - + +
284D ALA* 4.1 13.2 - - + -
287D MET* 3.2 34.3 - - + -
288D VAL* 3.4 29.6 - - + -
345D LEU* 5.3 13.2 - - + +
348D LEU* 5.8 4.7 - - + -
350D VAL* 5.6 7.4 - - + -
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Residues in contact with LYS 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU 5.5 0.4 + - - -
245D ILE* 2.6 32.9 + - + +
246D TRP* 3.7 49.5 - - + +
247D ASN 3.4 0.6 - - - -
248D ILE* 1.3 73.4 - - - +
250D ASP* 1.3 58.6 + - - +
252D LEU* 3.1 9.5 + - - +
253D LYS 3.1 19.6 + - - -
277D SER* 4.0 9.7 + - - -
280D LEU* 3.2 43.7 - - + +
281D ASP* 3.3 37.2 + - - +
284D ALA* 3.8 18.8 - - + -
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Residues in contact with ASP 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ARG* 2.7 36.9 + - - +
246D TRP* 3.0 19.0 - - + +
247D ASN* 3.1 13.3 - - - +
249D LYS* 1.3 73.8 - - + +
251D GLU* 1.3 61.3 + - - +
253D LYS* 3.7 15.6 - - + +
254D LYS* 3.2 27.7 + - - +
280D LEU* 5.0 0.7 - - - -
----------------------------------------------------------
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Residues in contact with GLU 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ASN* 3.0 23.9 + - + +
248D ILE* 3.5 9.6 - - + +
249D LYS 3.2 0.6 - - - -
250D ASP* 1.3 82.6 + - - +
252D LEU* 1.3 62.8 + - + +
254D LYS* 3.3 24.9 + - - +
255D VAL* 3.2 37.7 + - - +
344D TYR* 5.2 7.8 - - - +
345D LEU* 5.3 18.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D ILE* 3.2 13.9 + - + +
249D LYS* 3.1 9.4 + - - +
251D GLU* 1.3 77.1 - - + +
253D LYS* 1.3 59.7 + - - +
255D VAL* 3.9 7.6 - - + -
256D CYS* 2.7 55.0 + - - +
261D LEU* 4.0 20.8 - - + +
264D LEU* 5.0 5.4 - - + -
280D LEU* 5.0 7.4 - - + +
283D VAL* 3.6 31.0 - - + -
284D ALA* 4.7 3.4 - - - +
287D MET* 3.7 28.0 - - + -
345D LEU* 5.9 7.0 - - + -
----------------------------------------------------------
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Residues in contact with LYS 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LYS 3.1 7.0 + - - +
250D ASP* 3.9 21.5 - - + +
251D GLU 3.3 0.4 - - - -
252D LEU* 1.3 76.6 - - - +
254D LYS* 1.3 60.4 + - - +
256D CYS 4.0 9.4 - - - +
261D LEU* 5.7 4.9 - - - -
276D GLU* 3.6 32.5 + - - +
277D SER* 4.9 4.9 - - - +
280D LEU* 3.6 35.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASP 3.2 14.8 + - - +
251D GLU* 3.5 28.5 + - - +
252D LEU 3.2 0.4 - - - -
253D LYS* 1.3 79.1 - - - +
255D VAL* 1.3 64.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D GLU* 3.4 26.2 - - - +
252D LEU* 3.9 10.8 - - + -
254D LYS* 1.3 90.5 - - + +
256D CYS* 1.3 81.5 + - - +
257D SER 4.2 0.3 + - - -
260D ASP* 5.4 0.3 - - - +
341D GLU* 4.7 24.5 - - + -
----------------------------------------------------------
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Residues in contact with CYS 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D LEU* 2.7 39.2 + - - +
253D LYS* 4.0 11.6 - - - +
255D VAL* 1.3 91.6 - - - +
257D SER* 1.3 67.9 + - - +
260D ASP* 4.1 22.2 - - + -
261D LEU* 4.2 16.5 - - + +
264D LEU* 5.0 6.5 - - - -
----------------------------------------------------------
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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