Contacts of the helix formed by residues 250 - 279 (chain E) in PDB entry 2BG9
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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 3.8 7.9 - - + -
244A THR* 5.1 1.3 - - - -
300A HIS* 4.5 8.6 - - - +
306A HIS* 2.7 27.6 + - - +
243E PRO* 5.6 2.2 - - + +
246E ALA* 2.9 20.0 - - + +
247E GLY 2.5 59.1 - - - +
248E GLY 2.6 9.7 + - - -
249E GLN* 1.3 108.3 - - - +
251E CYS* 1.3 54.3 + - - +
252E THR 3.1 2.2 - - - -
253E LEU* 2.8 35.7 - - + +
254E SER* 2.6 33.8 + - - -
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Residues in contact with CYS 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLU 5.4 2.2 - - - -
242D LYS* 4.9 4.0 - - + -
245D LEU* 4.6 9.0 - - + -
247E GLY 4.8 0.2 + - - -
248E GLY 3.5 8.2 + - - +
250E LYS* 1.3 78.1 - - - +
252E THR* 1.3 97.4 + - - +
254E SER* 3.2 18.6 - - - -
255E ILE* 3.3 13.0 + - - +
304E LEU* 4.7 3.2 - - + +
307E SER* 4.7 15.7 + - - +
314E HIS* 3.0 44.2 - - + +
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Residues in contact with THR 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 5.5 1.8 + - - +
244D THR* 5.8 6.0 - - + +
245D LEU* 4.0 19.2 - - - +
249E GLN* 4.2 17.3 - - + +
251E CYS* 1.3 94.3 - - - +
253E LEU* 1.3 68.2 + - - +
254E SER 3.1 0.7 - - - -
255E ILE* 3.0 12.2 + - - +
256E SER* 2.8 23.4 + - - -
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Residues in contact with LEU 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A THR* 4.0 16.4 - - - +
247A ILE* 3.1 36.8 - - + -
300A HIS* 3.8 18.2 - - + +
242E LEU* 2.9 37.0 - - + -
249E GLN 3.7 5.2 - - - +
250E LYS* 2.8 49.7 - - + +
252E THR* 1.3 80.3 + - - +
254E SER* 1.3 64.6 + - - +
256E SER* 2.8 27.0 + - - -
257E VAL* 3.3 9.3 + - + +
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Residues in contact with SER 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239E VAL* 2.5 41.8 + - - +
242E LEU* 5.3 2.7 - - - -
243E PRO* 5.9 2.8 - - - +
250E LYS 2.6 14.1 + - - -
251E CYS* 3.2 14.1 - - - -
253E LEU* 1.3 79.5 - - - +
255E ILE* 1.3 65.1 + - - -
257E VAL* 3.0 20.8 + - - +
258E LEU* 3.1 10.6 + - - +
303E VAL* 4.1 7.4 - - - +
307E SER* 5.0 7.3 + - - -
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Residues in contact with ILE 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D LEU* 2.9 50.5 - - + -
248D SER* 3.8 14.4 - - - +
249D VAL* 3.8 9.9 - - + -
251E CYS 3.4 8.7 - - - +
252E THR* 3.0 7.7 + - - +
254E SER* 1.3 75.4 - - - +
256E SER* 1.3 68.2 + - - +
257E VAL 2.9 2.0 - - - -
258E LEU* 2.7 24.5 + - + +
259E LEU* 2.9 14.6 + - + +
303E VAL* 6.1 0.7 - - + -
304E LEU* 3.2 45.3 - - + -
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Residues in contact with SER 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.2 35.9 - - - +
248A SER* 5.7 0.9 - - - -
251A LEU* 2.7 27.4 - - - +
248D SER* 5.7 1.3 - - - -
252E THR* 2.8 12.8 + - - -
253E LEU* 2.8 15.6 + - - -
255E ILE* 1.3 78.3 - - - +
257E VAL* 1.3 54.0 + - - +
259E LEU* 3.5 10.0 + - - +
260E ALA 3.0 16.1 + - - -
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Residues in contact with VAL 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.9 18.4 - - + -
251A LEU* 4.1 8.5 - - + -
235E LEU* 2.9 48.2 - - + -
239E VAL* 4.4 15.5 - - + -
242E LEU* 5.1 6.5 - - + -
253E LEU* 3.4 20.2 - - + +
254E SER* 3.1 13.2 - - - +
255E ILE 2.8 1.6 + - - -
256E SER* 1.3 80.2 + - - +
258E LEU* 1.3 55.6 + - - +
260E ALA 3.0 0.7 + - - -
261E GLN* 2.3 42.1 + - + +
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Residues in contact with LEU 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 3.3 34.8 - - + -
231D LEU* 5.9 1.1 - - + -
249D VAL* 4.3 2.5 - - + -
239E VAL* 5.6 1.6 - - + +
254E SER 3.1 8.2 + - - +
255E ILE* 2.7 25.7 + - + +
257E VAL* 1.3 69.8 - - - +
259E LEU* 1.3 77.3 + - + +
261E GLN* 3.5 7.0 - - - +
262E THR* 3.0 33.9 + - - +
297E VAL* 5.4 3.6 - - + +
300E CYS* 3.2 35.7 - - + +
301E VAL* 3.9 23.3 - - + +
304E LEU* 6.1 4.9 - - + -
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Residues in contact with LEU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D SER* 2.8 47.3 - - - +
249D VAL* 3.2 22.2 - - + -
252D SER* 2.8 35.0 - - - +
256D PHE* 3.6 5.7 - - + -
255E ILE* 2.9 15.0 + - + +
256E SER* 3.7 9.6 - - - +
258E LEU* 1.3 88.0 - - + +
260E ALA* 1.3 58.7 + - - +
263E ILE* 2.9 36.3 + - + +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 2.5 60.3 - - + -
256E SER 3.0 5.5 + - - +
257E VAL 3.0 1.1 + - - +
259E LEU* 1.3 77.2 - - - +
261E GLN* 1.3 58.0 + - - +
263E ILE* 3.2 5.7 + - - -
264E PHE* 2.5 46.5 + - + -
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Residues in contact with GLN 261 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 4.8 0.2 - - - +
232E ILE* 3.4 26.1 - - + +
235E LEU* 5.0 3.4 - - + -
236E VAL* 2.9 33.2 - - + +
257E VAL* 2.3 40.2 + - + +
258E LEU* 3.5 8.5 - - - +
260E ALA* 1.3 67.2 - - - +
262E THR* 1.3 65.8 + - - +
264E PHE* 3.5 7.0 - - - +
265E LEU* 2.8 44.2 + - + +
296E ILE* 2.7 37.8 - - - +
297E VAL* 5.2 0.4 - - - +
300E CYS* 4.1 17.7 - - - -
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Residues in contact with THR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 5.6 6.5 - - + -
256D PHE* 3.2 28.0 - - + -
258E LEU* 3.0 20.7 + - - +
261E GLN* 1.3 79.6 - - - +
263E ILE* 1.3 68.5 + - - +
264E PHE 2.8 1.6 - - - -
265E LEU* 2.3 42.0 - - + +
266E PHE* 2.9 22.0 + - + +
297E VAL* 4.0 10.1 - - + +
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Residues in contact with ILE 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.2 11.4 - - + -
255D VAL* 5.2 9.0 - - + -
256D PHE* 3.1 23.6 - - + -
259E LEU* 2.9 24.2 + - + +
260E ALA* 3.5 3.8 - - - +
262E THR* 1.3 77.6 - - - +
264E PHE* 1.3 86.6 + - + +
266E PHE* 5.1 0.5 - - - +
267E LEU* 3.2 25.2 + - + +
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Residues in contact with PHE 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.2 23.3 - - + -
254A THR* 3.7 19.1 - - + -
255A VAL* 2.7 40.2 - - + -
258A LEU* 3.2 30.4 - - + +
231E LEU* 6.4 1.6 - - + -
232E ILE* 5.3 11.2 - - + -
235E LEU* 5.6 6.5 - - + -
260E ALA* 2.5 40.2 - - + +
261E GLN* 3.5 9.0 - - - +
263E ILE* 1.3 91.8 - - + +
265E LEU* 1.3 49.9 + - - +
267E LEU* 3.3 8.6 - - - +
268E ILE* 2.8 37.0 + - + +
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Residues in contact with LEU 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 5.7 0.2 - - + -
232E ILE* 5.8 2.0 - - + -
261E GLN* 2.8 38.3 + - - +
262E THR* 2.3 43.9 + - + +
264E PHE* 1.3 72.8 - - - +
266E PHE* 1.3 64.8 + - - +
267E LEU 3.0 0.9 - - - -
268E ILE* 2.6 38.2 + - + +
269E ALA* 2.7 7.6 + - - +
293E SER* 4.6 11.2 - - - +
296E ILE* 3.0 20.4 - - + -
297E VAL* 3.9 21.5 - - + -
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Residues in contact with PHE 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ASN* 6.1 2.9 - - - -
256D PHE* 5.2 17.3 - + + -
259D VAL* 4.5 13.7 - - + -
260D ILE* 5.5 3.4 - - + -
263D LEU* 2.9 42.6 - - + -
262E THR* 2.9 17.4 + - + +
263E ILE 5.7 0.4 - - - -
265E LEU* 1.3 80.3 - - - +
267E LEU* 1.3 53.2 + - - +
269E ALA* 2.6 21.5 + - + -
270E GLN* 2.6 67.5 + - + +
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Residues in contact with LEU 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 4.9 13.0 - - + -
258A LEU* 5.0 10.5 - - + -
259A VAL* 4.6 17.5 - - + -
262A GLU* 4.0 25.6 - - - +
263E ILE* 3.2 25.1 + - + +
264E PHE* 3.3 7.9 - - - +
265E LEU 3.0 1.0 - - - -
266E PHE* 1.3 78.1 - - - +
268E ILE* 1.3 60.9 + - - +
270E GLN* 2.7 57.8 - - - +
271E LYS* 2.9 16.9 + - - +
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Residues in contact with ILE 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225E ILE* 4.8 17.7 - - + -
264E PHE* 2.8 21.7 + - + +
265E LEU* 2.6 36.6 + - + +
267E LEU* 1.3 72.1 - - - +
269E ALA* 1.3 69.4 + - + +
271E LYS* 3.0 22.3 + - + +
272E VAL* 3.2 30.2 + - + +
273E PRO* 3.5 1.0 - - - +
289E VAL* 4.8 16.4 - - + -
293E SER* 6.6 0.4 - - - -
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU 2.7 5.9 + - - +
266E PHE* 2.6 42.3 + - + +
268E ILE* 1.3 79.7 - - + +
270E GLN* 1.3 47.5 + - - -
272E VAL* 5.5 0.7 - - - -
273E PRO* 2.6 32.2 - - - +
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Residues in contact with GLN 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU* 4.1 6.6 - - - +
259D VAL* 4.6 11.9 - - - +
263D LEU* 4.3 13.4 - - + +
266E PHE* 2.6 54.2 + - + +
267E LEU* 2.7 54.0 - - - +
269E ALA* 1.3 71.2 - - - +
271E LYS* 1.3 57.2 + - - +
273E PRO* 2.5 27.1 - - - +
274E GLU* 3.5 10.4 + - - +
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU 5.3 1.3 - - - -
261A VAL* 5.0 11.7 - - + -
262A GLU* 2.7 51.1 + - - +
224E ASN* 5.6 6.5 - - - +
267E LEU* 2.9 18.8 + - - +
268E ILE* 3.0 11.3 + - + +
270E GLN* 1.3 72.9 + - - +
272E VAL* 1.3 68.9 + - + +
273E PRO* 2.9 3.8 - - - -
274E GLU* 3.1 27.6 - - - +
275E THR* 3.4 6.8 + - - +
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Residues in contact with VAL 272 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E TYR* 6.0 7.6 - - + -
225E ILE* 5.7 8.7 - - + -
268E ILE* 3.2 27.1 + - + +
269E ALA* 5.5 0.7 - - - -
271E LYS* 1.3 78.9 - - + +
273E PRO* 1.3 73.4 - - + +
274E GLU 3.1 1.6 - - - -
275E THR* 2.9 36.2 - - + +
276E SER* 3.2 7.9 + - - +
289E VAL* 6.1 2.9 - - + -
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Residues in contact with PRO 273 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E ILE 3.5 0.9 - - - +
269E ALA 2.6 30.5 - - - +
270E GLN* 2.5 34.8 - - - +
271E LYS 3.1 0.4 - - - +
272E VAL* 1.3 89.5 - - + +
274E GLU* 1.3 65.8 + - - +
276E SER* 3.1 11.2 + - - -
277E LEU* 2.9 29.2 + - + +
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Residues in contact with GLU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E GLN 3.7 8.8 - - - +
271E LYS* 3.1 14.4 - - - +
273E PRO* 1.3 82.7 - - - +
275E THR* 1.3 64.5 + - - +
277E LEU* 3.0 24.5 + - + +
278E ASN* 2.9 35.3 + - - +
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Residues in contact with THR 275 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221E TYR* 5.6 16.8 - - + -
271E LYS* 3.4 5.2 + - - +
272E VAL* 2.9 43.0 - - + +
274E GLU* 1.3 80.1 - - - +
276E SER* 1.3 57.1 + - - +
278E ASN* 3.3 4.4 + - - +
279E VAL* 2.6 41.4 + - + +
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Residues in contact with SER 276 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS* 4.6 0.3 - - - +
134E PHE* 5.3 8.7 - - - -
272E VAL* 3.2 6.8 + - - +
273E PRO* 3.1 9.9 + - - -
275E THR* 1.3 82.0 - - - +
277E LEU* 1.3 57.2 + - - +
279E VAL* 2.1 32.4 - - - +
280E PRO 2.4 16.4 + - - +
281E LEU* 3.3 34.9 - - - +
286E LEU* 5.7 1.1 - - - +
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LYS* 2.4 44.2 + - - +
273E PRO* 2.9 24.0 - - + +
274E GLU* 3.0 16.7 + - + +
276E SER* 1.3 80.8 - - - +
278E ASN* 1.3 52.9 + - - +
281E LEU* 4.9 13.5 - - + -
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Residues in contact with ASN 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ASN* 3.5 14.4 - - - +
45E LYS* 3.3 18.8 - - - +
274E GLU* 2.9 43.2 + - - +
275E THR* 4.1 5.1 - - - +
277E LEU* 1.3 77.7 - - - +
279E VAL* 1.3 62.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E LEU 4.9 8.7 - - - +
43E ASN* 5.1 2.0 - - - +
44E GLU 5.6 0.4 - - - +
45E LYS* 3.1 18.0 - - - +
134E PHE* 5.2 7.6 - - + -
216E ARG* 4.8 14.6 - - - +
275E THR* 2.6 40.6 + - + +
276E SER* 2.1 27.1 - - - +
277E LEU 3.2 0.2 - - - -
278E ASN* 1.3 81.3 - - + +
280E PRO* 1.4 76.5 - - + +
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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