Contacts of the helix formed by residues 250 - 279 (chain O) 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 O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K MET* 3.8 8.1 - - + -
244K THR* 5.1 0.9 - - - -
300K HIS* 4.5 8.2 - - - +
306K HIS* 2.7 26.8 + - - +
242O LEU* 4.8 0.2 - - + -
243O PRO* 5.6 2.7 - - + -
246O ALA* 2.9 21.0 - - + +
247O GLY 2.5 57.1 - - - +
248O GLY 2.6 9.7 + - - -
249O GLN* 1.3 109.8 - - - +
251O CYS* 1.3 53.6 + - - +
252O THR 3.1 2.7 - - - -
253O LEU* 2.8 35.8 - - + +
254O SER* 2.6 33.4 + - - -
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Residues in contact with CYS 251 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241N GLU 5.4 2.2 - - - -
242N LYS* 4.9 3.8 - - + -
245N LEU* 4.6 9.0 - - + -
248O GLY 3.5 9.5 + - - +
250O LYS* 1.3 77.6 - - - +
252O THR* 1.3 96.1 + - - +
254O SER* 3.2 18.1 - - - -
255O ILE* 3.3 12.8 + - - +
304O LEU* 4.7 3.8 - - + +
307O SER* 4.7 15.4 + - - +
314O HIS* 3.0 45.1 - - + +
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Residues in contact with THR 252 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244K THR* 5.5 1.1 + - - +
242N LYS* 5.8 0.2 - - - -
244N THR* 5.8 6.2 - - + +
245N LEU* 4.0 19.6 - - - +
249O GLN* 4.2 17.0 - - + +
251O CYS* 1.3 94.5 - - - +
253O LEU* 1.3 68.1 + - - +
254O SER 3.1 0.4 - - - -
255O ILE* 3.0 11.5 + - - +
256O SER* 2.8 23.0 + - - -
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Residues in contact with LEU 253 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244K THR* 4.0 17.0 - - - +
247K ILE* 3.1 37.2 - - + -
300K HIS* 3.8 18.8 - - + +
242O LEU* 2.9 37.2 - - + -
249O GLN 3.7 5.8 + - - +
250O LYS* 2.8 49.5 - - + +
252O THR* 1.3 80.7 - - - +
254O SER* 1.3 64.7 + - - +
256O SER* 2.8 26.5 + - - -
257O VAL* 3.3 9.4 + - + +
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Residues in contact with SER 254 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239O VAL* 2.5 41.9 + - - +
242O LEU* 5.3 2.2 - - - -
243O PRO* 5.9 2.9 - - - +
250O LYS 2.6 14.0 + - - -
251O CYS* 3.2 14.1 - - - -
253O LEU* 1.3 80.7 - - - +
255O ILE* 1.3 65.5 + - - -
257O VAL* 3.0 21.6 + - - +
258O LEU* 3.1 10.7 + - - +
303O VAL* 4.1 7.1 - - - +
307O SER* 5.0 7.4 - - - -
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Residues in contact with ILE 255 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245N LEU* 2.9 50.9 - - + -
248N SER* 3.8 14.4 - - - +
249N VAL* 3.8 10.1 - - + -
251O CYS 3.4 8.1 - - - +
252O THR 3.0 8.0 + - - +
254O SER* 1.3 74.7 - - - +
256O SER* 1.3 68.5 + - - +
257O VAL 2.9 2.0 - - - -
258O LEU* 2.7 24.1 + - + +
259O LEU* 2.9 14.9 + - + +
303O VAL* 6.1 0.9 - - + -
304O LEU* 3.2 45.8 - - + -
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Residues in contact with SER 256 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K ILE* 3.2 36.1 - - - +
248K SER* 5.7 0.9 - - - -
251K LEU* 2.7 27.8 - - - +
248N SER* 5.7 1.6 - - - -
252O THR* 2.8 13.0 + - - -
253O LEU* 2.8 15.7 + - - -
255O ILE* 1.3 78.5 - - - +
257O VAL* 1.3 53.4 + - - +
259O LEU* 3.5 10.4 + - - +
260O ALA 3.0 15.2 + - - -
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Residues in contact with VAL 257 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K ILE* 3.9 18.2 - - + -
251K LEU* 4.1 8.3 - - + -
235O LEU* 2.9 49.8 - - + -
236O VAL* 5.5 0.2 - - + -
239O VAL* 4.4 15.3 - - + -
242O LEU* 5.1 5.8 - - + -
253O LEU* 3.4 20.4 - - + +
254O SER* 3.1 14.1 - - - +
255O ILE 2.8 1.4 + - - -
256O SER* 1.3 79.3 + - - +
258O LEU* 1.3 55.7 + - - +
260O ALA 3.0 0.9 + - - -
261O GLN* 2.3 42.6 + - + +
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Residues in contact with LEU 258 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228N LEU* 3.3 33.7 - - + -
231N LEU* 5.9 1.8 - - + -
249N VAL* 4.3 2.5 - - + -
239O VAL* 5.6 1.7 - - + +
254O SER 3.1 8.0 + - - +
255O ILE* 2.7 27.2 + - + +
257O VAL* 1.3 70.4 - - - +
259O LEU* 1.3 77.0 + - + +
261O GLN* 3.5 6.5 - - - +
262O THR* 3.0 34.2 + - - +
297O VAL* 5.4 3.8 - - + +
300O CYS* 3.2 34.5 - - - +
301O VAL* 3.9 24.0 - - + +
304O LEU* 6.1 4.7 - - + -
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Residues in contact with LEU 259 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248N SER* 2.8 47.8 - - - +
249N VAL* 3.2 22.7 - - + -
252N SER* 2.8 35.2 - - - +
256N PHE* 3.6 6.0 - - + -
255O ILE* 2.9 15.2 + - + +
256O SER* 3.7 9.9 - - - +
258O LEU* 1.3 88.2 - - + +
260O ALA* 1.3 58.7 + - - +
262O THR 3.5 0.2 + - - -
263O ILE* 2.9 36.5 + - + +
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Residues in contact with ALA 260 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K LEU* 2.5 61.7 - - + -
256O SER 3.0 5.1 + - - +
257O VAL 3.0 1.2 + - - +
259O LEU* 1.3 76.4 - - - +
261O GLN* 1.3 58.5 + - - +
263O ILE* 3.2 6.2 + - - -
264O PHE* 2.5 46.2 + - + -
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Residues in contact with GLN 261 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232O ILE* 3.4 27.9 - - + +
235O LEU* 5.0 4.0 - - + +
236O VAL* 2.9 32.3 - - + +
257O VAL* 2.3 41.0 + - + +
258O LEU* 3.5 8.1 - - - +
260O ALA* 1.3 67.0 - - - +
262O THR* 1.3 65.8 + - - +
264O PHE* 3.5 7.7 - - - +
265O LEU* 2.8 43.9 + - - +
296O ILE* 2.7 38.0 - - - +
297O VAL* 5.2 0.6 - - - +
300O CYS* 4.1 17.7 - - - -
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Residues in contact with THR 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N LEU* 5.6 5.8 - - + -
256N PHE* 3.2 28.3 - - + -
258O LEU* 3.0 20.3 + - - +
261O GLN* 1.3 79.0 - - - +
263O ILE* 1.3 68.1 + - - +
264O PHE 2.8 1.8 - - - -
265O LEU* 2.3 41.6 - - + +
266O PHE* 2.9 22.1 + - + +
297O VAL* 4.0 11.0 - - + +
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Residues in contact with ILE 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K VAL* 4.2 10.8 - - + -
255N VAL* 5.2 9.9 - - + -
256N PHE* 3.1 24.3 - - + -
259O LEU* 2.9 24.6 + - + +
260O ALA* 3.2 4.0 + - - +
262O THR* 1.3 78.2 - - - +
264O PHE* 1.3 86.2 + - + +
266O PHE* 5.1 0.7 - - - +
267O LEU* 3.2 24.9 + - + +
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Residues in contact with PHE 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K LEU 5.3 0.2 - - - -
251K LEU* 3.2 22.7 - - + -
254K THR* 3.7 19.1 - - + -
255K VAL* 2.7 39.9 - - + -
258K LEU* 3.2 28.2 - - + +
231O LEU* 6.4 1.8 - - + -
232O ILE* 5.3 11.4 - - + -
260O ALA* 2.5 40.4 - - + +
261O GLN* 3.5 9.6 - - - +
263O ILE* 1.3 90.8 - - + +
265O LEU* 1.3 49.5 + - - +
267O LEU* 3.3 8.6 - - - +
268O ILE* 2.8 37.5 + - + +
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Residues in contact with LEU 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224N LEU* 5.7 0.4 - - + -
232O ILE* 5.8 1.6 - - + -
261O GLN* 2.8 39.7 + - - +
262O THR* 2.3 43.9 + - + +
264O PHE* 1.3 73.2 - - - +
266O PHE* 1.3 63.2 + - - +
267O LEU 3.0 0.7 - - - -
268O ILE* 2.6 38.9 + - + +
269O ALA* 2.7 8.2 + - - +
293O SER* 4.6 11.4 - - - +
296O ILE* 3.0 20.0 - - + -
297O VAL* 3.9 21.1 - - + -
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Residues in contact with PHE 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217N ASN* 6.1 2.9 - - - -
256N PHE* 5.2 16.6 - + + -
259N VAL* 4.5 13.9 - - + -
260N ILE* 5.5 3.8 - - + -
263N LEU* 2.9 42.8 - - + -
262O THR* 2.9 16.9 + - + +
263O ILE 5.1 0.7 - - - +
265O LEU* 1.3 80.5 - - - +
267O LEU* 1.3 54.4 + - - +
269O ALA* 2.6 21.7 + - + -
270O GLN* 2.6 67.5 + - + +
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Residues in contact with LEU 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K VAL* 4.9 12.3 - - + -
258K LEU* 5.0 9.9 - - + -
259K VAL* 4.6 17.5 - - + -
262K GLU* 4.0 26.5 - - - +
263O ILE* 3.2 25.1 + - + +
264O PHE* 3.3 8.7 - - - +
265O LEU 3.0 1.0 - - - -
266O PHE* 1.3 77.1 - - - +
268O ILE* 1.3 61.4 + - - +
270O GLN* 2.7 58.2 - - - +
271O LYS* 2.9 16.7 + - - +
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Residues in contact with ILE 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225O ILE* 4.8 17.5 - - + -
264O PHE* 2.8 22.6 + - + +
265O LEU* 2.6 35.7 + - + +
267O LEU* 1.3 71.9 - - - +
269O ALA* 1.3 69.4 + - + +
271O LYS* 3.0 21.9 + - + +
272O VAL* 3.2 29.9 + - + -
273O PRO* 3.5 1.0 - - - +
289O VAL* 4.8 17.0 - - + -
293O SER* 6.6 0.2 - - - -
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Residues in contact with ALA 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265O LEU 2.7 6.4 + - - +
266O PHE* 2.6 41.4 + - + +
268O ILE* 1.3 80.6 - - + +
270O GLN* 1.3 46.9 - - - -
272O VAL* 5.5 0.4 - - - -
273O PRO* 2.6 31.6 - - - +
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Residues in contact with GLN 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262K GLU* 4.1 6.8 - - - +
259N VAL* 4.6 11.5 - - - +
263N LEU* 4.3 12.7 - - + +
266O PHE* 2.6 54.4 + - + +
267O LEU* 2.7 53.2 - - - +
269O ALA* 1.3 70.8 - - - +
271O LYS* 1.3 55.7 + - - +
273O PRO* 2.5 27.2 - - - +
274O GLU* 3.5 10.4 + - - +
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Residues in contact with LYS 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258K LEU 5.3 1.3 - - - -
261K VAL* 5.0 11.2 - - + -
262K GLU* 2.7 51.2 + - - +
224O ASN* 5.6 6.5 - - - +
267O LEU* 2.9 18.1 + - - +
268O ILE* 3.0 10.9 + - + +
270O GLN* 1.3 71.9 + - - +
272O VAL* 1.3 68.6 + - + +
273O PRO* 2.9 3.4 - - - -
274O GLU* 3.1 27.5 - - - +
275O THR* 3.4 6.6 + - - +
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Residues in contact with VAL 272 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221O TYR* 6.0 7.6 - - + -
225O ILE* 5.7 9.9 - - + -
268O ILE* 3.2 26.9 + - + +
269O ALA* 5.5 0.7 - - - -
271O LYS* 1.3 79.3 - - + +
273O PRO* 1.3 74.2 - - + +
274O GLU 3.1 1.1 - - - -
275O THR* 2.9 35.1 - - + +
276O SER* 3.2 8.4 + - - +
289O VAL* 6.1 2.9 - - + -
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Residues in contact with PRO 273 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268O ILE 3.5 1.3 - - - +
269O ALA* 2.6 31.2 - - - +
270O GLN* 2.5 35.0 - - - +
271O LYS 3.1 0.7 - - - +
272O VAL* 1.3 88.2 - - + +
274O GLU* 1.3 65.1 + - - +
276O SER* 3.1 11.9 + - - -
277O LEU* 2.9 28.1 + - + +
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Residues in contact with GLU 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270O GLN 3.7 8.6 - - - +
271O LYS* 3.1 15.6 - - - +
273O PRO* 1.3 82.9 - - - +
275O THR* 1.3 63.0 + - - +
277O LEU* 3.0 25.2 + - + +
278O ASN* 2.9 34.1 + - - +
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Residues in contact with THR 275 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221O TYR* 5.6 17.3 - - + -
271O LYS* 3.4 5.0 + - - +
272O VAL* 2.9 44.3 - - + +
274O GLU* 1.3 80.1 - - - +
276O SER* 1.3 57.4 + - - +
278O ASN* 3.3 3.4 + - - +
279O VAL* 2.6 40.9 + - + +
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Residues in contact with SER 276 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LYS* 4.7 0.3 - - - +
134O PHE* 5.3 9.1 - - - -
272O VAL* 3.2 7.3 + - - +
273O PRO* 3.1 9.7 + - - -
275O THR* 1.3 81.4 - - - +
277O LEU* 1.3 57.3 + - - +
279O VAL* 2.1 32.4 - - - +
280O PRO 2.4 17.0 + - - +
281O LEU* 3.3 35.0 - - - +
286O LEU* 5.7 1.3 - - - +
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Residues in contact with LEU 277 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O LYS* 2.4 44.3 + - - +
273O PRO* 2.9 26.2 - - + +
274O GLU* 3.0 16.1 + - + +
276O SER* 1.3 82.1 - - - +
278O ASN* 1.3 52.3 + - - +
281O LEU* 4.9 12.8 - - + -
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Residues in contact with ASN 278 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ASN* 3.5 14.0 - - - +
45O LYS* 3.3 20.1 - - - +
274O GLU* 2.9 42.3 + - - +
275O THR* 4.1 5.6 - - - +
277O LEU* 1.3 77.7 - - - +
279O VAL* 1.3 62.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 279 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O LEU 4.9 8.5 - - - +
43O ASN* 5.1 1.8 - - - +
44O GLU 5.6 0.4 - - - +
45O LYS* 3.1 18.6 - - - +
134O PHE* 5.2 7.2 - - + -
216O ARG* 4.8 14.6 - - - +
275O THR* 2.6 41.5 + - + +
276O SER* 2.1 25.7 - - - +
278O ASN* 1.3 81.3 - - + +
280O PRO* 1.4 76.1 - - + +
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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