Contacts of the helix formed by residues 261 - 284 (chain E) in PDB entry 6D6U
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 ALA 261 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D PRO* 4.0 32.8 - - + -
257E ILE* 4.3 4.7 - - + -
258E ASN* 3.5 14.3 + - + +
259E LYS 3.2 2.1 - - - +
260E ASP* 1.3 73.9 - - - +
262E VAL* 1.3 64.4 + - - +
263E PRO* 3.7 3.8 - - + -
264E ALA* 4.4 7.6 - - + +
265E ARG* 3.8 23.6 + - - +
314E TYR* 4.0 1.7 + - - -
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Residues in contact with VAL 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 5.2 10.5 - - + -
253B PRO* 4.3 23.1 - - + -
259E LYS 4.7 2.0 - - - +
260E ASP* 3.1 14.7 + - - +
261E ALA* 1.3 73.4 - - - +
263E PRO* 1.3 77.6 - - + +
264E ALA 3.4 0.3 + - - -
265E ARG 3.8 0.2 + - - -
266E THR* 3.4 22.6 + - + +
314E TYR* 4.0 10.7 + - - +
318E HIS* 4.5 19.7 - - + +
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Residues in contact with PRO 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ALA* 4.2 14.8 - - + +
249C ALA* 4.1 36.6 - - + +
252C ALA* 4.2 9.2 - - + -
261E ALA* 3.9 3.1 - - + -
262E VAL* 1.3 98.4 - - + +
264E ALA* 1.3 58.5 + - - +
266E THR* 2.9 21.5 + - - +
267E SER* 2.9 22.7 + - - +
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Residues in contact with ALA 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ALA* 6.1 2.9 - - + -
252C ALA* 5.1 4.7 - - - -
253D PRO* 4.1 25.6 - - + +
254D ALA* 5.1 1.8 - - - +
257D VAL* 3.6 28.0 - - + +
257E ILE* 5.0 3.1 - - + -
261E ALA* 4.4 10.1 - - + -
262E VAL 3.3 1.2 - - - -
263E PRO* 1.3 84.0 - - + +
265E ARG* 1.3 60.5 + - + +
267E SER* 3.7 3.9 - - - -
268E LEU* 2.9 30.0 + - - +
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Residues in contact with ARG 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E SER* 2.2 59.6 + - - +
255E PHE* 3.1 28.1 + - - +
257E ILE* 3.0 34.9 + - + -
258E ASN 3.8 17.0 - - - -
259E LYS* 5.5 3.7 - - - +
261E ALA 3.8 10.3 + - - +
262E VAL 3.8 1.8 + - - +
263E PRO 3.4 0.2 - - - -
264E ALA* 1.3 75.4 - - - +
266E THR* 1.3 58.3 + - - +
268E LEU* 3.3 5.8 + - - +
269E GLY* 2.9 25.5 + - - -
311E LEU* 4.3 4.3 - - - +
314E TYR* 3.1 59.2 - - + +
317E LEU* 4.8 8.0 - - - +
332E ASP* 4.9 3.2 + - - -
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Residues in contact with THR 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B VAL* 6.1 1.8 - - + -
253B PRO* 3.6 38.1 - - + -
256B THR* 4.7 9.0 - - + +
257B VAL* 6.3 0.7 - - + -
262E VAL* 3.4 16.9 + - + +
263E PRO* 2.9 17.7 + - - +
265E ARG* 1.3 75.9 - - - +
267E SER* 1.3 58.3 + - - +
269E GLY* 3.3 0.7 + - - -
270E ILE* 2.9 42.7 + - - +
311E LEU* 4.3 11.7 - - + +
314E TYR* 3.9 8.1 - - + -
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Residues in contact with SER 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ALA* 3.1 26.7 + - - +
253C LEU* 6.1 0.5 - - - +
256C THR* 3.7 19.8 + - - -
257D VAL* 4.8 9.2 - - - -
263E PRO* 2.9 23.5 + - - +
264E ALA* 3.7 4.3 - - - -
266E THR* 1.3 77.9 + - - +
268E LEU* 1.3 55.3 + - - +
270E ILE* 3.4 8.3 + - - +
271E THR* 2.7 38.5 + - - -
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Residues in contact with LEU 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D VAL* 4.7 14.5 - - + +
260D VAL* 3.7 32.8 - - + -
261D THR* 4.9 6.5 - - - +
264D LEU* 4.4 6.5 - - + -
250E LEU 4.8 2.0 - - - +
251E SER 4.3 5.4 - - - +
253E VAL* 4.3 11.7 - - + -
254E SER* 3.6 39.0 - - - +
257E ILE* 4.6 8.3 - - + -
264E ALA 2.9 16.5 + - - +
265E ARG* 3.7 5.4 - - - +
267E SER* 1.3 77.6 - - - +
269E GLY* 1.3 62.6 + - - +
271E THR* 3.3 3.9 + - - -
272E THR* 2.9 41.7 + - + +
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Residues in contact with GLY 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E SER* 6.0 0.6 - - - -
265E ARG 2.9 11.9 + - - -
266E THR 3.3 0.4 + - - -
268E LEU* 1.3 76.8 - - - +
270E ILE* 1.3 61.9 + - - +
272E THR* 2.7 22.5 + - - -
273E VAL* 3.0 15.1 + - - +
307E VAL 5.5 1.1 - - - -
311E LEU* 3.7 31.6 - - - -
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Residues in contact with ILE 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 5.3 10.8 - - - -
260B VAL* 4.3 33.0 - - + -
409B Y01 5.4 13.7 - - + -
256C THR* 4.8 15.9 - - + -
266E THR* 2.9 29.7 + - - +
267E SER* 3.9 6.3 - - - +
269E GLY* 1.3 74.2 - - - +
271E THR* 1.3 64.1 + - - +
273E VAL* 3.3 6.9 + - - +
274E LEU* 3.0 41.1 + - + +
311E LEU* 4.1 10.9 - - + +
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Residues in contact with THR 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ILE* 5.8 0.5 - - - +
256C THR* 4.3 17.2 + - - +
259C LEU* 3.5 40.2 - - + +
257D VAL* 6.1 0.2 - - - +
261D THR* 3.8 15.0 + - + +
264D LEU* 3.5 19.7 - - + -
267E SER* 2.7 24.1 + - - -
268E LEU* 3.7 6.7 - - - -
269E GLY 3.2 0.2 - - - -
270E ILE* 1.3 79.4 - - - +
272E THR* 1.3 57.5 + - - +
274E LEU* 3.3 5.2 + - - +
275E THR* 2.9 30.8 + - - -
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Residues in contact with THR 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D VAL* 6.0 0.4 - - + -
264D LEU* 4.3 21.3 - - + -
247E ILE* 4.5 9.9 - - + +
250E LEU 5.4 0.7 - - - -
251E SER* 4.0 33.7 - - - +
268E LEU* 2.9 24.4 + - + +
269E GLY* 2.7 24.8 + - - -
271E THR* 1.3 75.7 - - - +
273E VAL* 1.3 57.3 + - - +
275E THR* 3.3 8.1 + - - -
276E MET* 2.9 33.6 + - - +
307E VAL* 4.3 16.0 + - - -
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Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 4.8 16.4 - - + -
264B LEU* 5.2 7.9 - - + -
269E GLY 3.0 22.7 + - - +
270E ILE* 3.7 6.1 - - - +
272E THR* 1.3 76.4 + - - +
274E LEU* 1.3 63.0 + - + +
276E MET* 3.2 8.3 + - - +
277E THR* 2.9 33.8 + - - +
304E PHE* 3.8 23.0 - - + -
307E VAL* 4.3 17.0 - - + +
308E PHE* 4.3 24.9 - - + -
311E LEU* 4.5 9.9 - - + -
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Residues in contact with LEU 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 6.2 3.6 - - + -
264B LEU* 5.5 5.4 - - + -
256C THR* 5.6 0.7 - - + -
259C LEU* 4.5 12.6 - - + -
260C THR* 3.6 36.3 - - + +
263C THR* 4.6 10.1 - - + +
407C Y01 3.8 31.4 - - + -
270E ILE* 3.0 36.0 + - + +
271E THR* 3.7 4.7 - - - +
273E VAL* 1.3 81.0 - - + +
275E THR* 1.3 62.3 + - - +
277E THR* 3.2 12.4 + - - +
278E THR* 3.0 28.4 + - - +
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Residues in contact with THR 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C LEU* 4.3 6.6 - - - +
263C THR* 5.0 0.9 - - - +
264D LEU* 4.1 17.6 - - + +
267D THR* 5.2 4.3 - - + -
268D THR* 3.7 26.6 - - + +
271D ILE* 6.3 1.3 - - + -
247E ILE* 4.0 34.5 - - + -
271E THR 2.9 17.2 + - - -
272E THR* 3.6 8.1 - - - -
273E VAL 3.3 0.2 - - - -
274E LEU* 1.3 77.6 - - - +
276E MET* 1.3 57.7 + - - +
278E THR* 2.6 22.4 + - - +
279E LEU* 2.9 17.3 + - + +
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Residues in contact with MET 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E CYS* 3.8 15.5 - - - +
247E ILE* 3.5 34.8 - - + -
248E VAL* 4.0 0.7 - - + -
272E THR 2.9 17.1 + - - +
273E VAL 3.2 7.8 + - - +
275E THR* 1.3 73.1 - - - +
277E THR* 1.3 60.9 + - - +
279E LEU* 3.4 11.1 + - - +
280E SER* 2.9 31.2 + - - -
300E VAL* 4.9 3.4 - - - +
303E CYS* 3.5 34.1 - - + -
304E PHE* 3.7 24.9 - - + +
307E VAL* 3.5 30.3 - - + -
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Residues in contact with THR 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 3.7 34.4 - - + +
268B THR* 5.6 4.7 - - + -
267C HIS* 6.2 0.7 - - - +
407C Y01 4.1 19.7 - - + -
273E VAL* 2.9 18.0 + - - +
274E LEU* 3.2 14.8 + - + +
276E MET* 1.3 75.5 - - - +
278E THR* 1.3 61.6 + - + +
280E SER* 2.5 24.1 + - - +
281E THR* 3.0 25.3 + - + +
304E PHE* 4.6 5.9 - - - -
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Residues in contact with THR 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C THR* 3.6 37.7 - - + +
266C THR* 4.2 10.8 - - - +
267C HIS* 5.5 5.4 - - + -
268D THR* 3.9 15.1 - - + +
274E LEU 3.0 11.8 + - - +
275E THR* 2.6 26.2 + - - -
277E THR* 1.3 78.8 - - + +
279E LEU* 1.3 61.8 + - - +
281E THR* 3.0 9.6 + - - -
282E ILE* 2.9 37.0 + - - +
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Residues in contact with LEU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D ILE* 3.6 37.7 - - + -
240E THR* 5.4 11.9 - - + +
243E PRO* 4.2 10.3 - - + +
244E CYS* 3.9 44.2 - - + +
247E ILE* 5.5 2.5 - - + -
275E THR* 2.9 19.6 + - + +
276E MET* 3.8 14.1 - - + +
278E THR* 1.3 76.5 + - - +
280E SER* 1.3 58.2 + - - +
282E ILE* 3.4 4.9 + - + +
283E ALA* 2.9 36.4 + - + +
300E VAL* 4.5 10.3 - - + -
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Residues in contact with SER 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E MET 2.9 15.4 + - - -
277E THR* 2.5 27.2 + - - +
279E LEU* 1.3 75.4 - - - +
281E THR* 1.3 61.5 + - - +
283E ALA* 2.6 24.3 + - - -
284E ARG* 2.9 53.0 + - - +
300E VAL* 4.6 6.7 - - - +
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Residues in contact with THR 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B THR* 6.3 2.2 - - + -
271B ILE* 5.9 3.6 - - + -
267C HIS* 3.9 33.8 + - + +
270C GLU* 3.4 16.1 + - - +
277E THR* 3.0 23.8 + - + +
278E THR* 3.0 17.3 + - - -
280E SER* 1.3 83.8 + - - +
282E ILE* 1.3 61.8 + - - +
284E ARG* 4.5 7.6 + - - +
285E LYS* 3.9 17.4 - - - +
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C THR* 5.6 6.5 - - - +
270C GLU* 3.1 22.9 - - - +
268D THR* 4.9 2.7 - - - +
271D ILE* 3.7 36.3 - - + +
272D SER* 4.2 23.1 - - - +
275D ASN* 3.6 25.8 - - + +
278E THR* 2.9 30.4 + - - +
279E LEU* 3.8 4.9 - - + +
281E THR* 1.3 81.4 - - - +
283E ALA* 1.3 63.7 + - - +
285E LYS* 3.5 12.9 + - - +
286E SER* 3.7 10.4 + - - +
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Residues in contact with ALA 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E THR* 5.5 10.1 - - + -
279E LEU* 2.9 23.4 + - + +
280E SER* 2.6 13.0 + - - +
282E ILE* 1.3 70.3 - - - +
284E ARG* 1.3 70.7 + - - +
285E LYS 3.1 2.7 + - - -
286E SER* 3.4 24.4 + - - -
296E MET* 4.7 11.0 - - + +
297E ASP* 4.6 8.5 - - - +
300E VAL* 4.7 12.8 - - + -
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Residues in contact with ARG 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 3.1 48.9 + - + +
270A GLU* 5.6 2.0 + - - +
271A THR* 5.9 1.3 - - + -
280E SER* 2.9 55.6 + - - +
281E THR* 4.2 7.2 - - - +
283E ALA* 1.3 78.4 - - - +
285E LYS* 1.3 62.2 + - + +
286E SER 4.6 1.9 - - - -
297E ASP* 4.7 13.6 + - - +
300E VAL* 3.2 34.1 - - - +
301E SER* 4.6 9.1 - - - +
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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