Contacts of the helix formed by residues 242 - 271 (chain A) 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 242 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 2.9 49.5 - - + +
239A SER 4.5 0.7 - - - +
240A GLY 3.2 1.0 - - - -
241A GLU* 1.3 81.6 - - + +
243A MET* 1.3 60.0 + - - +
244A THR* 3.3 2.2 - - - -
245A LEU* 3.2 31.0 - - + -
246A SER* 2.9 26.2 + - - -
249B MET* 5.7 2.7 - - + -
250B SER* 5.4 2.2 - - - -
253B ILE* 4.4 11.8 - - - +
302B LEU* 4.3 4.4 + - - +
305B HIS* 4.3 4.9 - - - +
306B HIS* 4.1 10.1 - - - +
312B HIS* 2.6 59.3 + - + +
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 5.3 0.4 - - - -
239A SER 5.8 0.2 - - - -
240A GLY* 2.9 24.8 + - - +
241A GLU* 2.8 24.9 - - - +
242A LYS* 1.3 74.0 - - - +
244A THR* 1.3 89.7 + - + +
246A SER* 3.0 9.7 + - - -
247A ILE* 3.0 14.6 + - - +
250A LEU* 5.4 1.0 - - - +
296A ILE* 5.8 0.9 - - - +
299A HIS* 4.2 24.9 - - - +
300A HIS* 5.1 10.2 + - + -
306A HIS* 2.7 37.7 - - + +
249E GLN* 2.9 40.8 - - + +
250E LYS* 3.8 7.2 - - - -
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 5.1 0.2 - - - -
243A MET* 1.3 97.4 - - + +
245A LEU* 1.3 73.5 + - + +
247A ILE* 2.4 59.6 + - - +
300A HIS* 5.7 0.7 - - - -
250B SER* 6.4 0.9 - - - -
249E GLN* 3.5 24.3 + - + +
250E LYS* 5.1 0.9 - - - -
252E THR* 5.5 1.7 + - - +
253E LEU* 4.0 21.0 - - - -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 3.1 48.0 + - + +
243A MET 3.1 0.2 - - - -
244A THR* 1.3 84.8 - - + +
246A SER* 1.3 53.8 + - - +
248A SER* 2.2 38.4 + - - +
249B MET 3.6 3.4 - - - +
250B SER* 3.0 55.6 - - - +
253B ILE* 3.2 35.7 - - + +
254B SER* 4.7 4.0 - - - +
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.1 25.1 - - - +
235A LEU* 4.4 18.5 - - - +
242A LYS* 2.9 12.8 + - - +
243A MET 3.4 10.1 - - - -
244A THR 3.0 0.4 - - - -
245A LEU* 1.3 72.3 - - - +
247A ILE* 1.3 66.4 + - - +
248A SER 2.9 2.2 - - - -
249A VAL* 2.7 23.0 + - - +
250A LEU* 2.8 21.4 + - - +
296A ILE* 5.8 0.2 - - - -
299A HIS* 4.7 11.9 - - - -
253B ILE* 5.4 2.7 - - - -
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET 3.0 7.7 + - - +
244A THR* 2.4 58.6 + - - +
246A SER* 1.3 68.5 - - - +
248A SER* 1.3 84.1 + - - +
250A LEU* 3.2 16.5 + - + +
251A LEU* 3.1 27.8 + - + +
300A HIS* 5.3 5.4 - - + +
235E LEU* 6.2 0.4 - - + -
253E LEU* 3.1 30.1 - - + -
256E SER* 3.2 33.9 - - - +
257E VAL* 3.9 15.3 - - + -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 2.2 28.0 + - - +
247A ILE* 1.3 93.1 - - - +
249A VAL* 1.3 67.1 + - - +
251A LEU* 3.0 10.7 + - - +
252A SER 2.8 13.2 + - - -
253B ILE* 3.3 14.0 - - - +
254B SER* 5.6 4.5 - - - -
257B LEU* 2.8 29.2 - - - +
256E SER* 5.7 0.9 - - - -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 3.1 32.1 - - + -
232A VAL* 4.6 7.2 - - + -
246A SER* 2.7 27.4 + - - +
248A SER* 1.3 81.2 + - - +
250A LEU* 1.3 62.2 + - + +
252A SER* 2.9 5.1 + - - +
253A LEU* 2.6 57.9 + - + +
253B ILE* 5.0 12.6 - - + -
257B LEU* 3.2 22.0 - - + -
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.7 10.8 - - + -
243A MET 5.4 0.4 - - - +
246A SER* 2.8 30.4 + - - +
247A ILE* 3.6 18.2 - - + +
249A VAL* 1.3 85.7 - - + +
251A LEU* 1.3 64.6 + - + +
253A LEU* 4.2 6.5 - - + +
254A THR* 3.2 23.7 + - - -
292A THR* 3.1 36.8 - - + -
296A ILE* 3.1 44.0 - - + -
300A HIS* 6.0 2.0 - - + +
264E PHE* 5.3 0.3 - - - -
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Residues in contact with LEU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 3.1 21.7 + - + +
248A SER* 3.0 10.2 + - - +
249A VAL 2.9 0.4 - - - -
250A LEU* 1.3 76.3 - - + +
252A SER* 1.3 67.2 + - - +
253A LEU 3.2 0.5 + - - -
255A VAL* 3.2 9.1 + - - +
257B LEU* 5.6 0.4 - - + -
235E LEU* 4.8 9.4 - - + -
256E SER* 2.7 46.9 - - - +
257E VAL* 4.1 14.4 - - + -
259E LEU* 5.7 0.2 - - + -
260E ALA* 2.5 29.8 - - + +
264E PHE* 3.2 28.1 - - + -
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 5.3 0.2 - - - +
248A SER 2.8 9.5 + - - -
249A VAL* 2.9 11.8 + - - +
251A LEU* 1.3 73.7 - - - +
253A LEU* 1.3 52.8 + - - +
255A VAL* 4.0 4.0 - - - -
256A PHE* 2.1 61.1 + - - -
257B LEU* 2.5 53.1 - - - +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 4.9 16.2 - - + -
228A LEU* 3.6 27.6 - - + -
229A THR* 4.4 16.4 - - - +
232A VAL* 5.1 2.9 - - + -
249A VAL* 2.6 48.7 + - + +
250A LEU* 4.2 6.5 - - + +
252A SER* 1.3 73.7 + - - +
254A THR* 1.3 68.9 + - - +
255A VAL 3.0 1.1 - - - -
256A PHE* 2.9 14.4 + - + +
257A LEU* 2.7 33.1 + - + +
288A SER* 4.4 17.7 - - - +
292A THR* 5.4 9.6 - - + -
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU 3.2 17.3 + - - -
253A LEU* 1.3 84.7 - - - +
255A VAL* 1.3 53.5 + - - +
257A LEU* 3.0 11.0 + - + +
258A LEU* 2.6 61.2 + - + +
288A SER* 5.1 1.4 + - - -
289A ILE* 3.2 31.4 - - + +
292A THR* 5.8 2.6 - - - +
231E LEU* 5.1 12.4 - - + +
264E PHE* 3.7 17.3 - - + -
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU 3.2 8.5 + - - +
252A SER* 3.5 13.9 - - - +
253A LEU 3.0 0.6 - - - -
254A THR* 1.3 80.9 - - - +
256A PHE* 1.3 70.9 + - + +
258A LEU* 2.8 14.7 + - + +
259A VAL* 2.7 43.8 + - + +
261B VAL* 5.1 4.9 - - + -
263E ILE* 4.2 13.0 - - + -
264E PHE* 2.7 47.3 - - + -
267E LEU* 4.9 4.9 - - + -
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.6 7.6 - - + -
228A LEU* 6.6 0.2 - - + -
252A SER* 2.1 45.3 - - - -
253A LEU* 2.9 16.9 + - + +
255A VAL* 1.3 84.4 - - + +
257A LEU* 1.3 58.3 + - + +
259A VAL* 3.5 6.7 + - + +
260A ILE* 3.0 30.0 + - - +
257B LEU* 3.7 10.1 - - + -
260B THR* 3.3 28.3 - - + -
261B VAL* 3.0 46.9 - - + -
264B LEU* 3.2 22.4 - - + -
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 5.7 4.0 - - + +
222A CYS* 5.9 4.3 - - - -
225A PHE* 4.4 28.5 - - + -
253A LEU* 2.7 21.5 + - + +
254A THR* 3.3 16.2 - - + +
256A PHE* 1.3 74.4 - - + +
258A LEU* 1.3 64.9 + - + +
260A ILE* 3.0 28.9 - - + +
261A VAL* 3.3 12.1 + - - +
285A VAL* 2.9 45.9 - - + +
288A SER* 4.6 13.5 - - - +
289A ILE* 5.7 2.7 - - + -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 2.6 39.5 + - + +
255A VAL* 2.8 21.7 + - + +
257A LEU* 1.3 76.4 - - + +
259A VAL* 1.3 59.2 + - + +
261A VAL* 2.9 30.2 + - + +
262A GLU* 3.5 8.2 + - - +
228E PRO* 6.0 4.9 - - + -
231E LEU* 5.6 7.2 - - + -
264E PHE* 3.2 44.0 - - + +
267E LEU* 5.0 9.4 - - + -
271E LYS* 5.3 1.2 - - - -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A VAL* 2.7 31.9 + - + +
256A PHE* 4.1 6.1 - - + +
258A LEU* 1.3 71.3 - - + +
260A ILE* 1.3 62.7 + - - +
261A VAL 3.0 1.8 - - - -
262A GLU* 2.9 30.4 + - - +
263A LEU* 2.9 32.0 + - + +
268B ASP* 4.8 13.7 - - - +
267E LEU* 4.6 13.9 - - + -
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 4.5 18.8 - - - +
218A VAL* 5.0 13.0 - - + -
221A PRO* 5.0 15.9 - - + -
256A PHE 3.0 16.3 + - - +
257A LEU* 3.0 32.5 - - + +
258A LEU 3.2 0.2 - - - -
259A VAL* 1.3 77.5 - - - +
261A VAL* 1.3 60.8 + - + +
263A LEU* 3.3 14.9 + - + +
264A ILE* 2.9 53.2 + - + +
285A VAL* 6.2 1.1 - - + -
264B LEU* 6.4 2.2 - - + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU 3.3 14.6 - - - +
258A LEU* 2.9 16.7 + - + +
260A ILE* 1.3 84.2 - - + +
262A GLU* 1.3 52.7 + - - +
264A ILE* 4.2 10.8 - - + +
265A PRO* 2.3 41.2 - - + +
281A THR* 5.9 2.9 - - - +
285A VAL* 5.6 8.7 - - + -
224E ASN* 4.1 27.4 - - - +
271E LYS* 5.0 11.0 - - + -
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU 4.1 4.3 - - - +
259A VAL* 2.9 41.2 + - - +
261A VAL* 1.3 71.8 - - - +
263A LEU* 1.3 61.4 - - + +
265A PRO* 2.6 19.7 - - - +
266A SER* 2.4 27.7 + - - -
267E LEU* 4.0 24.4 - - - +
270E GLN* 4.1 4.3 - - - +
271E LYS* 2.7 42.9 + - - +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 2.9 27.1 - - + +
260A ILE* 3.5 17.7 - - + +
261A VAL 3.2 0.2 - - - -
262A GLU* 1.3 86.3 - - + +
264A ILE* 1.3 60.4 + - + +
265A PRO* 3.1 4.7 - - - -
266A SER* 2.6 17.3 + - - +
267A THR* 3.0 14.2 + - - -
268B ASP* 3.0 28.9 - - - +
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 4.8 24.2 - - + -
218A VAL* 5.1 9.9 - - + -
260A ILE* 2.9 38.9 + - + +
261A VAL* 4.2 11.4 - - + +
263A LEU* 1.3 72.9 - - + +
265A PRO* 1.3 64.0 - - + +
266A SER 3.3 1.1 - - - -
267A THR* 3.0 16.5 - - - +
268A SER* 2.7 26.2 + - - -
273A LEU* 5.7 1.7 - - - +
281A THR* 4.8 20.9 - - + +
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Residues in contact with PRO 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 2.3 35.2 - - + +
262A GLU* 2.6 28.0 - - - +
264A ILE* 1.3 81.7 - - + +
266A SER* 1.3 62.3 + - - +
267A THR 3.0 1.3 - - - -
268A SER* 2.7 15.4 + - - +
269A SER* 2.3 37.0 + - - -
224E ASN* 6.2 0.9 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU 2.4 27.8 + - - -
263A LEU* 2.6 17.8 + - - +
265A PRO* 1.3 79.0 - - - +
267A THR* 1.3 54.5 + - - +
269A SER* 3.2 9.3 - - - -
270A ALA* 2.4 37.3 + - - +
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 5.9 1.1 - - + -
213A TYR* 5.7 4.2 + - - +
214A PHE* 4.8 25.4 - - + -
263A LEU 3.0 18.8 + - - -
264A ILE* 3.0 17.9 - - - +
266A SER* 1.3 79.3 - - - +
268A SER* 1.3 52.4 + - - +
270A ALA* 2.7 8.7 + - + -
271A VAL* 2.5 57.3 + - + +
273A LEU* 5.8 3.6 - - + -
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 4.3 0.5 - - - +
264A ILE 2.7 9.6 + - - -
265A PRO* 2.7 26.1 + - - +
267A THR* 1.3 76.3 - - - +
269A SER* 1.3 57.4 + - - +
271A VAL* 2.6 25.8 - - - +
272A PRO* 3.9 4.5 - - - +
273A LEU* 4.4 23.8 - - - +
278A MET* 6.1 3.0 - - - +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 2.8 30.3 - - - +
265A PRO 2.3 29.0 + - - -
266A SER* 3.2 9.9 - - - -
268A SER* 1.3 68.6 + - - +
270A ALA* 1.3 54.5 + - - +
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Residues in contact with ALA 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.9 10.0 - - - +
45A GLU 5.5 0.2 + - - -
46A VAL* 2.9 19.2 + - - +
266A SER 2.4 29.6 + - - +
267A THR* 3.1 14.6 - - + +
269A SER* 1.3 68.3 - - - +
271A VAL* 1.3 67.4 + - + +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 3.9 12.3 - - + +
46A VAL* 3.0 0.9 - - - +
135A PHE* 4.1 22.4 - - + -
175A GLU* 6.0 3.8 - - + -
209A ARG* 4.5 17.0 - - - +
267A THR* 2.5 42.0 + - + +
268A SER* 2.6 24.5 - - - +
270A ALA* 1.3 85.3 - - + +
272A PRO* 1.3 64.3 - - + +
273A LEU* 3.2 9.9 + - + +
----------------------------------------------------------
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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