Contacts of the helix formed by residues 237 - 267 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ASN 5.8 0.7 - - - +
236B ILE* 1.3 77.4 - - - +
238B GLN* 1.3 66.2 + - - +
239B GLN* 4.3 8.1 - - + +
240B ASP* 3.0 28.8 + - - +
241B PHE* 3.0 19.9 + - - +
552B LYS* 3.9 19.1 - - + +
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE 3.6 2.0 + - - -
237B LEU* 1.3 74.3 - - - +
239B GLN* 1.3 58.7 + - - +
241B PHE* 3.3 1.4 + - - +
242B CYS* 2.9 36.6 + - - -
552B LYS 5.1 2.2 + - - -
553B GLY* 5.2 0.8 - - - -
554B ILE* 3.7 19.0 - - + +
572B MET 5.5 0.4 + - - -
575B ILE* 3.9 24.8 - - + +
576B GLN* 2.8 32.5 + - - +
579B SER* 3.4 30.3 + - - -
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 3.2 7.3 - - + +
238B GLN* 1.3 80.5 - - - +
240B ASP* 1.3 65.4 + - - +
242B CYS* 3.5 5.6 + - - +
243B HIS* 3.0 29.3 + - + +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ILE* 4.9 5.4 - - + -
200B TYR* 3.3 25.1 + - - +
236B ILE* 4.2 14.4 - - + +
237B LEU* 3.0 36.6 + - - +
239B GLN* 1.3 82.6 + - - +
241B PHE* 1.3 66.0 + - - +
243B HIS* 3.4 0.4 + - - -
244B ALA* 3.1 23.7 + - - +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.9 21.8 - - + -
216B LEU* 4.6 6.5 - - + +
231B ALA* 3.7 32.8 - - + -
232B SER 5.6 0.2 - - - -
233B ALA* 4.5 4.5 - - + -
236B ILE* 3.7 15.6 - - + +
237B LEU 3.0 12.1 + - - +
238B GLN 3.6 7.0 - - - +
240B ASP* 1.3 76.9 - - - +
242B CYS* 1.3 62.0 + - - +
244B ALA* 3.4 7.3 + - - +
245B ILE* 3.2 42.9 + - + +
547B ILE* 4.7 2.5 - - + -
554B ILE* 3.8 41.1 - - + -
556B ALA 5.7 0.4 - - - -
557B LEU* 3.7 26.7 - - + -
575B ILE* 4.2 10.1 - - + -
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Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLN* 2.9 37.6 + - - +
239B GLN* 3.9 6.7 - - + +
241B PHE* 1.3 77.7 - - - +
243B HIS* 1.3 61.9 + - - +
245B ILE* 3.2 14.1 + - - +
246B LYS* 3.2 18.9 + - - +
572B MET* 3.6 30.5 - - - +
575B ILE* 3.7 29.8 - - - -
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Residues in contact with HIS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B TYR* 3.1 37.1 - + - +
239B GLN* 3.0 19.0 + - + +
240B ASP* 3.8 4.5 - - - +
241B PHE 3.3 0.2 - - - -
242B CYS* 1.3 74.5 - - - +
244B ALA* 1.3 63.3 + - - +
246B LYS* 3.0 21.1 + - + +
247B VAL* 3.0 41.5 + - + +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 3.8 11.6 - - + +
200B TYR* 3.8 18.8 - - + -
214B LEU* 3.4 33.2 - - + -
216B LEU* 3.8 7.7 - - + +
240B ASP 3.1 13.1 + - - +
241B PHE 3.5 9.2 - - - +
242B CYS 3.3 0.2 - - - -
243B HIS* 1.3 77.0 - - - +
245B ILE* 1.3 55.0 + - - +
247B VAL* 3.4 4.5 + - - +
248B GLY* 2.9 26.3 + - - -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.7 22.9 - - + -
218B VAL* 4.5 2.6 - - - +
226B ILE* 3.8 29.2 - - + -
229B LEU* 4.3 22.7 - - + -
241B PHE* 3.2 37.7 + - + +
242B CYS* 3.2 7.9 + - - +
243B HIS 3.2 0.6 - - - -
244B ALA* 1.3 75.8 - - - +
246B LYS* 1.3 59.8 + - - +
248B GLY* 3.3 1.6 + - - -
249B VAL* 2.9 35.0 + - + +
557B LEU* 4.8 0.2 - - + -
568B ILE* 5.3 2.0 - - + -
571B VAL* 4.4 0.4 - - + -
572B MET* 3.9 15.7 - - + -
575B ILE* 3.6 21.5 - - + -
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B CYS* 3.2 12.1 + - - +
243B HIS* 3.0 21.6 + - + +
245B ILE* 1.3 78.5 - - - +
247B VAL* 1.3 62.7 + - + +
249B VAL* 3.4 8.1 + - - +
250B LYS* 3.1 22.0 + - - +
568B ILE* 4.3 26.4 - - + +
572B MET* 4.0 26.1 - - + +
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 4.1 11.0 - - + -
200B TYR* 4.6 19.1 - - + +
202B VAL 6.3 0.2 - - - +
243B HIS* 3.0 44.3 + - + +
244B ALA* 3.7 9.2 - - - +
246B LYS* 1.3 71.9 - - + +
248B GLY* 1.3 66.7 + - - +
250B LYS* 3.1 14.1 + - - +
251B TYR* 3.1 53.3 + - + -
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Residues in contact with GLY 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 3.7 11.0 - - - +
193B ILE* 3.7 24.4 - - - +
218B VAL* 4.2 9.2 - - - -
244B ALA 2.9 12.0 + - - -
245B ILE 3.7 3.4 - - - -
247B VAL* 1.3 76.8 - - - +
249B VAL* 1.3 61.7 + - - +
251B TYR 3.2 2.8 + - - -
252B THR* 3.0 27.1 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 4.1 9.6 - - + +
220B GLY* 5.4 3.4 - - - -
224B SER* 3.9 30.1 - - - +
226B ILE* 3.9 30.3 - - + -
245B ILE* 2.9 20.8 + - + +
246B LYS 3.4 2.2 + - - +
248B GLY* 1.3 75.8 - - - +
250B LYS* 1.3 64.7 + - - +
252B THR* 2.7 28.4 + - - +
253B GLN* 3.1 9.1 + - - +
568B ILE* 3.7 26.9 - - + -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LYS 3.1 13.4 + - - +
247B VAL* 3.1 17.1 + - - +
249B VAL* 1.3 79.0 - - - +
251B TYR* 1.3 93.1 + - - +
253B GLN* 3.3 17.8 + - - +
254B GLN* 3.5 27.0 - - - +
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.8 34.2 + - + +
52B GLY* 5.4 2.5 - - - -
191B VAL* 3.9 20.2 - - + -
193B ILE* 4.7 1.3 - - + -
202B VAL* 4.1 24.7 - - + +
247B VAL* 3.1 47.6 + - + -
248B GLY 3.2 5.4 + - - +
250B LYS* 1.3 93.0 + - - +
252B THR* 1.3 64.7 + - - +
254B GLN* 3.1 43.0 + - - +
255B ILE* 3.3 14.7 + - - +
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLY* 3.2 34.6 - - - +
190B ALA* 4.1 2.9 - - - -
191B VAL* 4.2 5.1 - - + +
218B VAL* 3.5 18.8 - - + +
220B GLY* 3.7 14.1 - - - +
248B GLY 3.0 16.6 + - - +
249B VAL* 2.7 23.3 + - - -
251B TYR* 1.3 75.4 - - - +
253B GLN* 1.3 69.9 + - - +
255B ILE* 3.2 6.7 + - - +
256B ILE* 2.9 31.2 + - - +
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B GLY* 4.6 0.6 - - - -
221B ALA 3.0 21.0 + - - +
222B PRO* 3.7 2.4 - - - +
223B LYS* 3.2 12.1 + - - -
224B SER* 2.9 45.0 + - - +
249B VAL* 3.1 13.6 + - - +
250B LYS* 3.6 10.8 - - - +
251B TYR 3.2 0.6 - - - -
252B THR* 1.3 104.0 + - - +
254B GLN* 1.3 56.4 + - + +
256B ILE* 3.4 11.7 + - - +
257B GLN* 3.0 28.4 + - - +
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.3 9.2 - - + +
50B ASP 3.1 22.8 - - - +
51B LEU* 3.6 14.5 - - + +
250B LYS* 3.5 30.9 + - + +
251B TYR* 3.1 30.5 + - - +
253B GLN* 1.3 73.9 - - + +
255B ILE* 1.3 64.9 + - - +
257B GLN* 3.4 11.7 + - - +
258B GLY* 3.2 17.3 + - - -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.1 9.1 - - + +
51B LEU* 4.1 13.9 - - + -
56B LEU* 3.6 30.1 - - + -
58B ILE* 4.7 6.1 - - + -
171B ASN* 3.4 21.1 - - - +
189B GLY* 3.7 9.4 - - - -
190B ALA 3.3 30.3 - - - +
191B VAL* 3.7 17.5 - - + -
203B ASN* 5.8 0.2 - - - +
251B TYR 3.3 8.7 + - - +
252B THR 3.2 7.3 + - - +
254B GLN* 1.3 75.3 - - - +
256B ILE* 1.3 59.0 + - - +
258B GLY* 3.1 4.5 + - - -
259B ILE* 2.9 38.8 + - + +
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Residues in contact with ILE 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO* 3.7 19.5 - - + +
188B VAL 3.9 1.1 - - - -
189B GLY 3.5 15.5 - - - +
220B GLY 3.5 13.9 - - - +
221B ALA* 3.3 36.1 - - - +
222B PRO* 3.7 9.4 - - + -
252B THR 2.9 20.1 + - - +
253B GLN* 3.6 18.4 - - - +
255B ILE* 1.3 77.0 - - - +
257B GLN* 1.3 58.2 + - - +
259B ILE* 3.1 7.8 + - - +
260B GLN* 2.8 52.4 + - - +
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLN 3.0 17.3 + - - +
254B GLN* 3.6 10.5 - - - +
256B ILE* 1.3 77.5 - - - +
258B GLY* 1.3 61.7 - - - +
260B GLN* 3.3 15.9 + - - +
261B GLN* 3.1 25.5 + - - +
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Residues in contact with GLY 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.8 27.8 - - - +
48B ALA 5.8 0.2 - - - -
49B VAL* 4.6 11.4 - - - -
58B ILE* 5.6 1.6 - - - -
254B GLN 3.2 7.4 + - - -
255B ILE 3.1 8.2 + - - -
257B GLN* 1.3 80.4 - - - +
259B ILE* 1.3 61.3 + - - +
261B GLN* 3.2 10.4 - - - +
262B LEU* 3.2 16.5 + - - +
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 4.4 8.1 - - + -
171B ASN* 4.7 2.2 - - + +
174B SER* 3.7 10.1 - - - +
175B VAL* 3.8 33.4 - - + -
178B SER* 3.9 19.5 - - - +
179B LEU* 6.0 0.4 - - + -
187B PRO* 3.6 22.4 - - + -
188B VAL 3.4 25.1 - - - +
255B ILE* 2.9 32.2 + - + +
256B ILE* 3.1 5.4 + - - +
258B GLY* 1.3 73.0 - - - +
260B GLN* 1.3 62.5 + - - +
262B LEU* 3.1 8.9 + - + +
263B VAL* 2.8 28.7 + - + +
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO* 3.9 21.4 - - + +
222B PRO* 4.3 13.1 - - - +
256B ILE* 2.8 31.2 + - - +
257B GLN* 3.6 19.4 - - - +
259B ILE* 1.3 75.1 - - - +
261B GLN* 1.3 57.7 - - - +
263B VAL* 3.3 9.8 + - - +
264B LYS* 2.9 34.7 + - + +
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Residues in contact with GLN 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 5.6 0.4 + - - -
47B VAL* 3.8 28.2 - - + +
257B GLN* 3.1 14.7 + - - +
258B GLY* 3.2 14.4 - - - +
260B GLN* 1.3 73.8 - - - +
262B LEU* 1.3 65.4 + - - +
264B LYS* 3.1 9.9 + - - +
265B GLU* 3.0 34.8 + - - +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 3.5 32.8 - - - +
46B ALA 3.9 5.8 - - - +
47B VAL* 3.7 27.3 - - + +
58B ILE* 3.7 35.9 - - + +
59B SER* 4.9 3.1 - - - +
175B VAL* 3.9 17.0 - - + -
179B LEU* 4.1 15.7 - - + -
258B GLY 3.2 4.3 + - - +
259B ILE* 3.1 11.3 + - + +
261B GLN* 1.3 80.0 - - - +
263B VAL* 1.3 57.5 + - - +
265B GLU* 3.2 10.4 + - - +
266B THR* 2.9 37.8 + - + +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER* 3.7 41.1 - - - +
179B LEU* 4.1 8.1 - - + -
187B PRO* 5.2 2.9 - - + -
259B ILE* 2.8 23.2 + - + +
260B GLN* 3.5 11.0 - - - +
262B LEU* 1.3 73.4 - - - +
264B LYS* 1.3 69.6 + - + +
265B GLU 3.0 1.3 - - - -
267B GLY* 2.9 31.2 + - - +
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Residues in contact with LYS 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLN* 2.9 19.3 + - + +
261B GLN* 3.1 9.6 + - - +
263B VAL* 1.3 79.0 - - + +
265B GLU* 1.3 59.0 - - - +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 3.9 20.2 - - - -
46B ALA 4.0 11.7 + - - +
47B VAL* 4.8 0.9 - - - +
261B GLN* 3.0 31.9 + - - +
262B LEU* 3.3 17.1 - - - +
264B LYS* 1.3 79.6 - - - +
266B THR* 1.3 63.0 + - - +
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Residues in contact with THR 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B MET* 4.3 22.9 + - - +
45B SER* 3.6 31.2 + - - +
60B SER* 5.6 0.4 - - - -
179B LEU* 3.7 22.7 - - + +
262B LEU* 2.9 24.2 + - + +
263B VAL 3.3 0.4 + - - -
265B GLU* 1.3 80.4 - - - +
267B GLY* 1.3 67.7 + - - +
268B VAL* 3.5 8.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B SER 4.8 1.1 - - - -
179B LEU* 3.7 22.9 - - - -
263B VAL* 2.9 26.2 + - - +
266B THR* 1.3 81.5 - - - +
268B VAL* 1.3 65.0 + - - -
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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