Contacts of the helix formed by residues 250 - 279 (chain T) in PDB entry 4BOG
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 250 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243P MET* 3.8 8.3 - - + -
244P THR* 5.1 1.1 - - - -
300P HIS* 4.5 8.1 - - - +
306P HIS* 2.7 27.2 + - - +
242T LEU* 4.8 0.2 - - + -
243T PRO* 5.6 2.0 - - + -
246T ALA* 2.9 19.9 - - + +
247T GLY 2.5 57.5 - - - +
248T GLY 2.6 9.1 + - - -
249T GLN* 1.3 108.7 - - - +
251T CYS* 1.3 53.4 + - - -
252T THR 3.1 2.2 - - - -
253T LEU* 2.8 38.1 - - + +
254T SER* 2.6 33.8 + - - -
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Residues in contact with CYS 251 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241S GLU 5.4 2.5 - - - -
242S LYS* 4.9 3.8 - - + -
245S LEU* 4.5 8.9 - - + +
247T GLY 4.8 0.2 + - - -
248T GLY 3.5 8.7 + - - +
250T LYS* 1.3 78.1 - - - +
252T THR* 1.3 94.7 + - - +
254T SER* 3.2 18.5 - - - -
255T ILE* 3.3 12.9 + - - +
304T LEU* 4.7 3.6 - - + +
307T SER* 4.7 15.4 + - - +
313T THR 5.4 0.2 - - - +
314T HIS* 3.0 44.4 - - + +
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Residues in contact with THR 252 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P THR* 5.5 1.8 + - - +
242S LYS* 5.8 0.4 - - - -
244S THR* 5.8 5.8 - - + -
245S LEU* 4.0 19.0 - - - +
249T GLN* 4.2 16.6 - - + +
251T CYS* 1.3 94.4 - - - +
253T LEU* 1.3 67.6 + - - +
254T SER 3.1 0.4 - - - -
255T ILE* 3.0 11.8 + - - +
256T SER* 2.8 23.0 + - - -
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Residues in contact with LEU 253 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244P THR* 4.0 16.4 - - - +
247P ILE* 3.1 37.0 - - + -
300P HIS* 3.8 18.2 - - + +
242T LEU* 2.9 37.0 - - + -
249T GLN 3.7 4.9 - - - +
250T LYS* 2.8 49.6 + - + +
252T THR* 1.3 80.7 + - - +
254T SER* 1.3 65.3 + - - +
256T SER* 2.8 26.8 + - - -
257T VAL* 3.3 9.1 + - + +
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Residues in contact with SER 254 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239T VAL* 2.5 41.3 + - - +
242T LEU* 5.3 2.9 - - - -
243T PRO* 5.9 2.4 - - - +
250T LYS 2.6 14.2 + - - -
251T CYS* 3.2 13.9 - - - -
253T LEU* 1.3 79.9 - - - +
255T ILE* 1.3 66.2 + - - +
257T VAL* 3.0 21.0 + - - +
258T LEU* 3.1 10.9 + - - +
303T VAL* 4.1 6.7 - - - +
307T SER* 5.0 7.1 + - - -
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Residues in contact with ILE 255 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245S LEU* 2.9 50.3 - - + -
248S SER* 3.8 14.8 - - - +
249S VAL* 3.8 10.1 - - + -
251T CYS 3.4 9.0 - - - +
252T THR* 3.0 8.0 + - - +
254T SER* 1.3 75.1 - - - +
256T SER* 1.3 69.5 + - - +
257T VAL 2.9 1.8 - - - -
258T LEU* 2.7 23.4 + - + +
259T LEU* 2.9 14.4 + - + +
303T VAL* 6.1 0.9 - - + -
304T LEU* 3.2 45.3 - - + -
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Residues in contact with SER 256 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P ILE* 3.2 35.8 - - - +
248P SER* 5.7 0.4 - - - -
251P LEU* 2.7 27.9 - - - +
248S SER* 5.7 1.8 - - - -
252T THR* 2.8 13.0 + - - -
253T LEU* 2.8 15.9 + - - -
255T ILE* 1.3 77.1 - - - +
257T VAL* 1.3 54.2 + - - +
259T LEU* 3.5 9.6 + - - +
260T ALA 3.0 15.4 + - - -
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Residues in contact with VAL 257 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247P ILE* 3.9 18.8 - - + -
251P LEU* 4.1 8.5 - - + -
235T LEU* 2.9 48.7 - - + -
239T VAL* 4.4 15.5 - - + -
242T LEU* 5.1 6.7 - - + -
253T LEU* 3.4 20.2 - - + +
254T SER* 3.1 13.0 - - - +
255T ILE 2.8 1.6 + - - -
256T SER* 1.3 80.2 + - - +
258T LEU* 1.3 56.7 + - - +
260T ALA 3.0 1.2 + - - -
261T GLN* 2.3 42.6 + - + +
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Residues in contact with LEU 258 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228S LEU* 3.3 34.1 - - + -
231S LEU* 5.9 1.3 - - + -
249S VAL* 4.3 2.2 - - + -
239T VAL* 5.6 1.5 - - + +
254T SER 3.1 8.6 + - - +
255T ILE* 2.7 26.2 + - + +
257T VAL* 1.3 70.0 - - - +
259T LEU* 1.3 76.8 + - + +
261T GLN* 3.5 6.9 - - - +
262T THR* 3.0 34.1 + - - +
297T VAL* 5.4 3.8 - - + +
300T CYS* 3.2 35.0 - - + +
301T VAL* 3.9 23.8 - - + +
304T LEU* 6.1 4.5 - - + -
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Residues in contact with LEU 259 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248S SER* 2.8 47.6 - - - +
249S VAL* 3.2 22.4 - - + -
251S LEU* 5.8 0.2 - - + -
252S SER* 2.8 34.5 - - - +
256S PHE* 3.6 6.4 - - + -
255T ILE* 2.9 15.8 + - + +
256T SER* 3.7 9.4 - - - +
258T LEU* 1.3 87.3 - - + +
260T ALA* 1.3 58.5 + - - +
263T ILE* 2.9 36.5 + - + +
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Residues in contact with ALA 260 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P LEU* 2.5 62.1 - - + +
256T SER 3.0 4.5 + - - +
257T VAL 3.0 0.6 + - - +
259T LEU* 1.3 79.0 - - - +
261T GLN* 1.3 57.8 + - - +
263T ILE* 3.2 5.5 + - - -
264T PHE* 2.5 45.8 + - + -
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Residues in contact with GLN 261 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P LEU* 4.8 0.2 - - - +
232T ILE* 3.4 26.7 - - + +
235T LEU* 5.0 3.4 - - + -
236T VAL* 2.9 33.1 - - + +
257T VAL* 2.3 40.2 + - + +
258T LEU* 3.1 8.3 + - - +
260T ALA* 1.3 67.1 - - - +
262T THR* 1.3 63.4 + - - +
264T PHE* 3.5 7.3 - - - +
265T LEU* 2.8 45.7 + - + +
296T ILE* 2.7 37.5 - - - +
297T VAL* 5.2 0.4 - - - +
300T CYS* 4.1 17.7 - - - -
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Residues in contact with THR 262 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224S LEU* 5.5 6.7 - - + +
256S PHE* 3.2 27.8 - - + -
258T LEU* 3.0 20.7 + - - +
261T GLN* 1.3 79.3 - - - +
263T ILE* 1.3 67.3 + - - +
264T PHE 2.8 1.8 - - - -
265T LEU* 2.3 42.0 - - + +
266T PHE* 2.9 21.2 + - + +
297T VAL* 4.0 10.1 - - + +
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Residues in contact with ILE 263 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P VAL* 4.2 11.2 - - + -
255S VAL* 5.2 8.5 - - + -
256S PHE* 3.1 24.1 - - + -
259T LEU* 2.9 25.0 + - + +
260T ALA* 3.5 4.5 - - - +
262T THR* 1.3 78.4 - - - +
264T PHE* 1.3 85.5 + - + +
266T PHE* 5.1 1.0 - - - +
267T LEU* 3.2 25.2 + - + +
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Residues in contact with PHE 264 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250P LEU 5.3 0.2 - - - -
251P LEU* 3.2 23.6 - - + -
254P THR* 3.7 18.8 - - + -
255P VAL* 2.7 39.3 - - + -
258P LEU* 3.2 29.5 - - + +
231T LEU* 6.4 1.6 - - + -
232T ILE* 5.3 12.1 - - + -
235T LEU* 5.6 6.7 - - + -
260T ALA* 2.5 40.2 - - + +
261T GLN* 3.5 8.7 - - - +
263T ILE* 1.3 92.4 - - + +
265T LEU* 1.3 50.4 + - - +
267T LEU* 3.3 8.6 - - - +
268T ILE* 2.8 37.7 + - + +
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Residues in contact with LEU 265 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224S LEU* 5.7 0.2 - - + -
232T ILE* 5.8 2.0 - - + -
261T GLN* 2.8 38.6 + - - +
262T THR* 2.3 44.2 + - + +
264T PHE* 1.3 73.0 - - - +
266T PHE* 1.3 64.0 + - - +
267T LEU 3.0 0.7 - - - -
268T ILE* 2.6 39.1 + - + +
269T ALA* 2.7 8.2 + - - +
293T SER* 4.6 11.9 - - - +
296T ILE* 3.0 19.7 - - + -
297T VAL* 3.9 21.3 - - + -
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Residues in contact with PHE 266 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217S ASN* 6.1 2.9 - - - -
256S PHE* 5.2 17.0 - + + -
259S VAL* 4.5 13.7 - - + -
260S ILE* 5.5 4.0 - - + -
263S LEU* 2.9 41.7 - - + -
262T THR* 2.9 17.2 + - + +
263T ILE 5.7 0.4 - - - -
265T LEU* 1.3 80.7 - - - +
267T LEU* 1.3 54.7 + - - +
269T ALA* 2.6 21.7 + - + -
270T GLN* 2.6 67.3 + - + +
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Residues in contact with LEU 267 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255P VAL* 4.9 13.0 - - + -
258P LEU* 5.0 10.8 - - + -
259P VAL* 4.6 17.3 - - + -
262P GLU* 4.0 25.1 - - - +
263T ILE* 3.2 26.2 + - + +
264T PHE* 3.3 7.9 - - - +
265T LEU 3.0 0.8 - - - -
266T PHE* 1.3 77.4 - - - +
268T ILE* 1.3 60.9 + - - +
270T GLN* 2.7 58.2 - - - +
271T LYS* 2.9 17.7 + - - +
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Residues in contact with ILE 268 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225T ILE* 4.8 17.7 - - + -
264T PHE* 2.8 20.9 + - + +
265T LEU* 2.6 36.8 + - + +
267T LEU* 1.3 71.5 - - - +
269T ALA* 1.3 68.9 + - + +
271T LYS* 3.0 22.0 + - + +
272T VAL* 3.2 30.0 + - + +
273T PRO* 3.5 0.9 - - - +
289T VAL* 4.8 16.8 - - + -
293T SER* 6.6 0.2 - - - -
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Residues in contact with ALA 269 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265T LEU 2.7 6.3 + - - +
266T PHE* 2.6 40.9 + - + +
268T ILE* 1.3 79.5 - - + +
270T GLN* 1.3 47.6 + - - -
272T VAL* 5.5 0.7 - - - -
273T PRO* 2.6 32.6 - - - +
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Residues in contact with GLN 270 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262P GLU* 4.1 6.4 - - - +
259S VAL* 4.6 11.7 - - - +
263S LEU* 4.3 12.3 - - + +
266T PHE* 2.6 55.4 + - + +
267T LEU* 2.7 53.8 - - - +
269T ALA* 1.3 71.4 - - - +
271T LYS* 1.3 57.0 + - - +
273T PRO* 2.5 26.2 - - - +
274T GLU* 3.5 10.2 + - - +
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Residues in contact with LYS 271 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258P LEU 5.3 1.3 - - - -
261P VAL* 5.0 11.7 - - + -
262P GLU* 2.7 51.1 + - - +
224T ASN* 5.6 6.5 - - - +
267T LEU* 2.9 18.8 + - - +
268T ILE* 3.0 11.8 + - + +
270T GLN* 1.3 71.1 + - - +
272T VAL* 1.3 68.5 + - + +
273T PRO* 2.9 4.3 - - - -
274T GLU* 3.1 27.7 - - - +
275T THR* 3.4 6.8 + - - +
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Residues in contact with VAL 272 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221T TYR* 6.0 7.6 - - + -
225T ILE* 5.7 9.4 - - + -
268T ILE* 3.2 27.3 + - + +
269T ALA* 5.5 0.4 - - - -
271T LYS* 1.3 78.8 - - + +
273T PRO* 1.3 72.8 - - + +
274T GLU 3.1 1.6 - - - -
275T THR* 2.9 35.1 - - + +
276T SER* 3.2 8.0 + - - +
289T VAL* 6.1 2.9 - - + -
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Residues in contact with PRO 273 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268T ILE 3.5 1.1 - - - +
269T ALA 2.6 31.4 - - - +
270T GLN* 2.5 35.0 - - - +
271T LYS 3.1 0.4 - - - +
272T VAL* 1.3 90.1 - - + +
274T GLU* 1.3 65.3 + - - +
276T SER* 3.1 11.4 + - - -
277T LEU* 2.9 29.2 + - + +
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Residues in contact with GLU 274 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270T GLN 3.7 8.8 - - - +
271T LYS* 3.1 14.8 - - - +
273T PRO* 1.3 83.4 - - - +
275T THR* 1.3 64.7 + - - +
277T LEU* 3.0 23.9 + - + +
278T ASN* 2.9 35.1 + - - +
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Residues in contact with THR 275 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221T TYR* 5.6 17.0 - - + -
271T LYS* 3.4 5.2 + - - +
272T VAL* 2.9 43.3 - - + +
274T GLU* 1.3 81.3 - - - +
276T SER* 1.3 56.3 + - - +
278T ASN* 3.3 3.9 + - - +
279T VAL* 2.6 41.9 + - + +
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Residues in contact with SER 276 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T LYS* 4.7 0.5 - - - +
134T PHE* 5.3 8.7 - - - -
272T VAL* 3.2 6.2 + - - +
273T PRO* 3.1 9.5 + - - -
275T THR* 1.3 83.0 - - - +
277T LEU* 1.3 55.8 + - - +
279T VAL* 2.1 32.1 - - - +
280T PRO 2.4 16.5 + - - +
281T LEU* 3.3 34.6 - - - +
286T LEU* 5.7 1.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 277 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T LYS* 2.4 43.9 + - - +
273T PRO* 2.9 25.8 - - + +
274T GLU* 3.0 16.3 + - + +
276T SER* 1.3 81.6 - - - +
278T ASN* 1.3 53.1 + - - +
281T LEU* 4.9 12.8 - - + -
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Residues in contact with ASN 278 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T ASN* 3.5 13.3 - - - +
45T LYS* 3.3 19.2 - - - +
274T GLU* 2.9 42.6 + - - +
275T THR* 4.1 5.1 - - - +
277T LEU* 1.3 78.7 - - - +
279T VAL* 1.3 62.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 279 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T LEU 4.9 9.0 - - - +
43T ASN* 5.1 1.8 - - - +
44T GLU 5.6 0.2 - - - +
45T LYS* 3.1 18.6 - - - +
134T PHE* 5.2 7.0 - - + -
216T ARG* 4.8 14.8 - - - +
275T THR* 2.6 39.5 - - + +
276T SER* 2.1 26.9 - - - +
277T LEU 3.2 0.2 - - - -
278T ASN* 1.3 80.0 - - + +
280T PRO* 1.4 75.7 - - + +
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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