Contacts of the helix formed by residues 237 - 267 (chain D) in PDB entry 3U1K
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 LEU 237 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ASN 6.0 0.2 - - - +
236D ILE* 1.3 78.2 - - - +
238D GLN* 1.3 65.0 + - - +
239D GLN* 4.3 6.1 - - + +
240D ASP* 3.1 31.8 + - - +
241D PHE* 2.9 20.3 + - - +
552D LYS* 3.8 20.4 - - + +
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Residues in contact with GLN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D ILE 3.6 2.0 + - - -
237D LEU* 1.3 72.1 - - - +
239D GLN* 1.3 60.8 + - + +
241D PHE* 3.1 1.2 + - - +
242D CYS* 2.8 50.3 + - - -
552D LYS 5.2 2.0 + - - -
553D GLY* 5.3 1.0 - - - -
554D ILE* 3.9 18.7 - - + +
572D MET 5.2 1.4 + - - -
575D ILE* 3.9 15.9 - - + +
576D GLN* 3.2 36.1 + - - +
579D SER* 3.5 25.5 + - - +
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Residues in contact with GLN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D LEU* 3.2 6.1 - - + +
238D GLN* 1.3 82.6 - - + +
240D ASP* 1.3 65.8 + - - +
242D CYS* 4.0 6.3 - - + +
243D HIS* 3.1 24.6 + - - +
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Residues in contact with ASP 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ILE* 4.1 8.7 - - + +
200D TYR* 3.2 29.8 + - - +
236D ILE* 4.4 14.2 - - + +
237D LEU* 3.1 34.6 + - + +
239D GLN* 1.3 82.2 - - - +
241D PHE* 1.3 62.4 + - - +
244D ALA* 3.2 18.9 + - - +
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Residues in contact with PHE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D LEU* 3.7 26.0 - - + -
216D LEU* 4.8 6.1 - - + -
231D ALA* 3.6 33.4 - - + -
233D ALA* 4.6 3.1 - - + -
236D ILE* 4.0 13.6 - - + +
237D LEU 2.9 12.3 + - - +
238D GLN 3.4 7.4 - - - +
240D ASP* 1.3 77.2 - - - +
242D CYS* 1.3 61.2 + - - +
244D ALA* 3.2 7.0 + - - +
245D ILE* 3.1 36.7 + - + +
547D ILE* 4.7 1.3 - - + -
554D ILE* 3.8 42.2 - - + -
556D ALA* 5.9 0.4 - - - -
557D LEU* 3.6 32.1 - - + -
575D ILE* 3.8 17.0 - - + -
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Residues in contact with CYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D GLN* 2.8 46.0 + - - +
239D GLN* 4.0 7.4 - - + +
241D PHE* 1.3 74.1 - - - +
243D HIS* 1.3 60.4 + - - +
245D ILE* 3.4 6.4 + - - +
246D LYS* 3.1 31.0 + - - +
572D MET* 3.4 34.6 - - - +
575D ILE* 3.9 22.0 - - - -
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Residues in contact with HIS 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D TYR* 3.1 50.2 - + + +
239D GLN 3.1 18.4 + - - +
241D PHE 3.2 0.2 - - - -
242D CYS* 1.3 74.6 - - - +
244D ALA* 1.3 61.0 + - - +
246D LYS* 3.2 16.3 + - + +
247D VAL* 2.9 38.7 + - + +
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Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ILE* 3.8 12.8 - - + +
200D TYR* 3.6 11.8 - - + -
214D LEU* 3.4 33.0 - - + -
216D LEU* 3.8 7.9 - - + +
240D ASP 3.2 12.3 + - - +
241D PHE 3.5 7.6 - - - +
243D HIS* 1.3 77.6 - - - +
245D ILE* 1.3 56.2 + - - +
247D VAL* 3.0 12.3 - - - +
248D GLY* 2.9 26.7 + - - -
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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
----------------------------------------------------------
216D LEU* 3.8 21.5 - - + -
218D VAL* 4.5 3.3 - - + +
226D ILE* 3.8 28.5 - - + -
229D LEU* 4.2 17.7 - - + -
241D PHE* 3.1 27.4 + - + +
242D CYS* 3.5 7.2 - - - +
243D HIS 3.2 0.2 - - - -
244D ALA* 1.3 77.7 - - - +
246D LYS* 1.3 56.8 + - - +
248D GLY* 3.2 1.4 + - - -
249D VAL* 2.9 30.8 + - + +
568D ILE* 5.0 0.4 - - + -
571D VAL* 4.1 10.5 - - + -
572D MET* 3.9 14.6 - - + -
575D ILE* 3.6 31.2 - - + -
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Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D CYS* 3.1 15.4 + - - +
243D HIS* 3.2 18.4 + - + +
245D ILE* 1.3 78.6 - - - +
247D VAL* 1.3 61.7 + - - +
249D VAL* 3.4 7.4 + - - +
250D LYS* 3.2 20.3 + - - +
568D ILE* 4.2 24.0 - - + +
572D MET* 4.0 29.2 - - + +
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Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ILE* 4.3 12.3 - - + -
200D TYR* 4.2 22.4 - - + +
243D HIS* 2.9 23.1 + - + +
244D ALA* 3.0 26.2 - - - +
246D LYS* 1.3 72.7 - - - +
248D GLY* 1.3 64.7 - - - +
250D LYS* 3.3 25.9 + - - +
251D TYR* 3.2 40.5 + - + +
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Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D VAL* 3.9 8.9 - - - +
193D ILE* 3.7 20.0 - - - -
218D VAL* 4.1 9.0 - - - -
244D ALA 2.9 17.1 + - - -
245D ILE 3.2 4.2 + - - -
247D VAL* 1.3 77.1 - - - +
249D VAL* 1.3 62.8 + - - +
250D LYS 3.1 0.9 + - - -
251D TYR* 3.2 10.9 + - - -
252D THR* 3.2 17.9 + - - +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 4.0 10.2 - - + +
220D GLY* 5.7 1.1 - - - -
224D SER* 3.8 43.7 - - - +
225D GLN 5.2 1.3 - - - +
226D ILE* 3.7 34.3 - - + -
245D ILE* 2.9 24.4 + - + +
246D LYS 3.8 5.2 - - - +
247D VAL 3.4 0.2 - - - -
248D GLY* 1.3 71.8 - - - +
250D LYS* 1.3 63.4 + - - +
252D THR* 2.8 29.2 + - - +
253D GLN* 3.3 7.8 - - - +
568D ILE* 4.0 14.1 - - + -
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Residues in contact with LYS 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D SER* 6.0 0.2 - - - -
246D LYS 3.2 9.9 + - - +
247D VAL* 3.3 31.9 - - - +
248D GLY 3.1 0.6 - - - -
249D VAL* 1.3 78.8 - - - +
251D TYR* 1.3 78.2 + - + +
253D GLN* 3.1 18.5 + - - +
254D GLN* 3.5 35.6 + - - +
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Residues in contact with TYR 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D LEU* 3.9 21.0 - - + +
52D GLY* 3.8 21.1 + - - -
191D VAL* 3.9 20.9 - - + -
193D ILE* 4.4 2.5 - - + -
202D VAL* 3.7 35.1 - - + +
247D VAL* 3.2 42.7 + - + +
248D GLY 3.2 4.5 + - - +
250D LYS* 1.3 89.7 - - + +
252D THR* 1.3 62.4 + - - +
254D GLN* 3.2 27.2 + - - +
255D ILE* 3.2 22.9 + - - +
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Residues in contact with THR 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D GLY* 3.3 30.2 - - - +
190D ALA* 3.9 3.8 - - - -
191D VAL* 4.2 5.8 - - + +
218D VAL* 3.7 20.0 - - + +
220D GLY* 3.6 13.5 - - - +
248D GLY 3.2 17.6 + - - +
249D VAL* 2.8 21.0 + - - -
251D TYR* 1.3 76.0 - - - +
253D GLN* 1.3 70.7 + - - +
255D ILE* 3.2 10.6 + - - +
256D ILE* 3.0 32.6 + - - +
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Residues in contact with GLN 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLY 4.4 1.4 - - - -
221D ALA 3.0 19.5 + - - +
222D PRO* 3.7 2.3 - - - +
223D LYS* 3.2 11.6 + - - -
224D SER* 2.8 44.5 + - - +
249D VAL* 3.3 14.8 + - - +
250D LYS* 3.1 10.4 + - - +
252D THR* 1.3 95.4 + - - +
254D GLN* 1.3 66.1 + - + +
256D ILE* 3.5 14.5 + - - +
257D GLN* 3.2 21.5 + - - +
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Residues in contact with GLN 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 3.8 18.0 - - + +
50D ASP 3.3 21.8 - - - +
51D LEU* 4.2 2.2 - - + -
250D LYS* 3.6 35.6 + - - +
251D TYR* 3.2 27.9 + - - +
252D THR 3.2 0.4 - - - -
253D GLN* 1.3 75.8 - - + +
255D ILE* 1.3 65.8 + - + +
257D GLN* 3.2 13.2 + - - +
258D GLY 3.2 16.3 + - - -
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Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D VAL* 4.3 9.8 - - + +
51D LEU* 4.0 18.4 - - + -
56D LEU* 4.1 16.6 - - + -
58D ILE* 4.8 6.3 - - + +
171D ASN* 3.5 19.7 - - - +
189D GLY* 3.9 7.6 - - - -
190D ALA 3.2 36.3 - - - +
191D VAL* 3.6 16.4 - - + -
251D TYR 3.2 11.2 + - - +
252D THR* 3.4 7.6 - - - +
254D GLN* 1.3 76.7 - - - +
256D ILE* 1.3 64.7 + - - +
258D GLY* 3.0 5.0 + - - -
259D ILE* 3.0 34.3 + - + +
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Residues in contact with ILE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 3.6 21.5 - - + +
188D VAL 4.0 1.1 - - - -
189D GLY 3.6 14.6 - - - +
220D GLY 3.5 11.9 - - - +
221D ALA 3.3 37.0 - - - +
222D PRO* 3.3 9.9 - - + -
252D THR 3.0 17.0 + - - +
253D GLN* 3.6 19.1 - - - +
255D ILE* 1.3 75.9 - - - +
257D GLN* 1.3 57.5 + - - +
259D ILE* 3.1 8.8 + - - +
260D GLN* 2.8 50.7 + - - +
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Residues in contact with GLN 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D GLN 3.2 11.2 + - - +
254D GLN* 3.5 14.0 - - - +
255D ILE 3.2 0.4 - - - -
256D ILE* 1.3 79.2 - - - +
258D GLY* 1.3 57.4 - - - +
260D GLN* 3.3 16.7 + - - +
261D GLN* 3.0 29.0 + - - +
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Residues in contact with GLY 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.9 21.4 - - - +
48D ALA 5.6 0.2 - - - -
49D VAL* 5.1 8.7 - - - -
58D ILE* 5.1 4.5 - - - -
254D GLN 3.2 6.2 + - - -
255D ILE 3.0 8.0 + - - -
257D GLN* 1.3 78.1 - - - +
259D ILE* 1.3 55.7 + - - +
261D GLN* 3.3 7.9 + - - +
262D LEU* 2.9 26.2 + - - +
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Residues in contact with ILE 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ILE* 3.7 18.6 - - + -
171D ASN* 4.7 2.5 - - + +
174D SER* 3.8 7.0 - - - +
175D VAL* 3.8 28.3 - - + -
178D SER* 4.1 13.5 - - - +
187D PRO* 3.5 23.8 - - + -
188D VAL 3.6 24.5 - - - +
255D ILE* 3.0 28.9 + - + +
256D ILE 3.5 6.7 - - - +
258D GLY* 1.3 73.7 - - - +
260D GLN* 1.3 58.8 + - - +
262D LEU* 3.2 7.6 + - + +
263D VAL* 2.8 34.3 + - + +
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Residues in contact with GLN 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 3.8 21.1 - - + +
222D PRO* 4.6 11.1 - - - +
256D ILE* 2.8 33.9 + - - +
257D GLN* 3.3 20.9 + - + +
259D ILE* 1.3 72.7 - - - +
261D GLN* 1.3 57.4 + - - +
263D VAL* 3.3 8.3 + - - +
264D LYS* 3.0 29.9 + - - +
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Residues in contact with GLN 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 3.5 29.7 - - + +
257D GLN 3.0 14.0 + - - +
258D GLY* 3.3 9.6 - - - +
260D GLN* 1.3 73.4 - - - +
262D LEU* 1.3 67.5 + - - +
264D LYS* 3.2 12.2 + - - +
265D GLU* 2.9 49.6 + - - +
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 3.3 26.9 - - - +
46D ALA* 3.7 29.2 - - - +
47D VAL* 4.0 9.4 - - + -
58D ILE* 3.6 33.9 - - + +
59D SER 4.8 3.8 - - - +
175D VAL* 3.8 17.3 - - + -
179D LEU* 3.8 14.6 - - + -
258D GLY 2.9 14.1 + - - +
259D ILE* 3.2 11.0 + - + +
261D GLN* 1.3 75.8 - - - +
263D VAL* 1.3 57.9 + - + +
265D GLU* 3.8 3.5 - - - +
266D THR* 2.9 39.6 + - - +
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Residues in contact with VAL 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D SER* 3.7 33.0 - - - +
179D LEU* 3.9 16.4 - - + -
187D PRO* 5.2 2.7 - - + -
259D ILE* 2.8 27.5 + - + +
260D GLN* 3.6 8.7 - - - +
261D GLN 3.2 0.2 - - - -
262D LEU* 1.3 73.2 - - + +
264D LYS* 1.3 59.6 + - - +
267D GLY* 2.9 27.5 + - - -
268D VAL* 3.6 23.4 + - + +
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Residues in contact with LYS 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D GLN 3.0 17.1 + - - +
261D GLN* 3.2 12.3 + - - +
263D VAL* 1.3 79.6 - - - +
265D GLU* 1.3 68.2 + - + +
267D GLY* 3.4 11.0 + - - -
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Residues in contact with GLU 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 5.4 6.4 - - - -
46D ALA 4.0 17.2 + - - +
47D VAL* 4.0 6.6 - - - +
261D GLN* 2.9 46.5 + - - +
262D LEU* 3.9 6.0 - - + +
264D LYS* 1.3 83.2 - - + +
266D THR* 1.3 62.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D MET* 3.8 36.2 - - + +
45D SER* 2.9 30.7 + - - +
60D SER* 6.2 1.3 - - - +
179D LEU* 3.9 24.7 - - + +
262D LEU* 2.9 20.1 + - - +
263D VAL 4.2 0.7 - - - -
265D GLU* 1.3 77.2 - - - +
267D GLY* 1.3 68.6 + - - +
268D VAL* 5.3 0.7 - - + -
----------------------------------------------------------
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Residues in contact with GLY 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D MET* 5.4 0.7 - - - +
179D LEU 5.2 0.9 - - - +
263D VAL 2.9 11.1 + - - -
264D LYS 3.4 7.3 + - - -
265D GLU 3.3 2.6 - - - -
266D THR* 1.3 88.6 - - - +
268D VAL* 1.3 63.7 + - - +
269D THR* 5.5 0.2 - - - -
----------------------------------------------------------
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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