Contacts of the helix formed by residues 261 - 289 (chain A) in PDB entry 5I4V
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 GLY 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO 3.1 8.3 + - - -
259A ALA 3.0 7.8 + - - -
260A SER* 1.3 78.5 + - - +
262A SER* 1.3 62.9 + - - +
263A ALA* 3.3 3.4 - - - -
264A SER* 3.4 24.0 + - - -
265A GLN* 3.7 12.3 + - - +
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Residues in contact with SER 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 4.1 11.9 + - - +
260A SER* 3.3 19.9 + - - -
261A GLY* 1.3 75.8 - - - +
263A ALA* 1.3 67.0 + - - +
264A SER 3.3 0.2 - - - -
265A GLN* 3.4 19.8 + - - +
266A GLN* 3.0 38.2 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO* 3.4 21.6 - - + +
257A ASP* 3.5 39.7 - - + +
258A PRO* 4.3 12.2 - - + +
261A GLY 3.3 1.3 - - - -
262A SER* 1.3 81.8 + - - +
264A SER* 1.3 57.3 + - - +
266A GLN* 3.2 3.1 + - - -
267A ARG* 2.9 39.3 + - - +
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Residues in contact with SER 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASP* 5.2 1.6 + - - -
261A GLY* 3.4 13.6 + - - -
262A SER 3.3 0.4 - - - -
263A ALA* 1.3 79.2 - - - +
265A GLN* 1.3 63.9 + - - +
267A ARG* 3.3 14.6 + - - +
268A PHE* 3.0 24.7 + - - +
342A ARG 4.6 9.3 + - - +
343A ALA 5.2 0.2 - - - -
447A LYS* 4.7 3.5 + - - -
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Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A SER 5.4 2.0 + - - +
261A GLY 3.7 13.0 + - - +
262A SER* 3.4 19.5 + - - +
263A ALA 3.3 0.4 - - - -
264A SER* 1.3 82.1 - - - +
266A GLN* 1.3 57.6 + - - +
268A PHE* 3.5 3.9 + - - +
269A ALA* 2.9 29.5 + - - +
447A LYS* 4.4 17.9 - - - +
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 4.1 21.0 - - + +
251A PRO* 4.0 15.9 + - - +
253A PRO* 3.9 28.0 - - + +
262A SER* 3.0 32.3 + - - +
263A ALA* 3.5 4.9 - - - +
264A SER 3.2 0.2 - - - -
265A GLN* 1.3 75.8 - - - +
267A ARG* 1.3 54.5 + - - +
269A ALA* 3.2 6.0 + - + +
270A HIS* 2.7 35.8 + - - +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 3.5 45.6 - - + +
253A PRO* 3.5 32.0 + - + +
255A GLY 5.2 2.8 + - - -
257A ASP* 2.9 42.0 + - - -
263A ALA* 2.9 30.8 + - - +
264A SER* 3.7 10.4 + - - +
266A GLN* 1.3 74.8 - - - +
268A PHE* 1.3 63.1 + - - +
270A HIS* 3.3 2.6 + - - +
271A PHE* 3.0 28.9 + - - +
342A ARG* 3.6 38.1 + - - +
343A ALA* 3.8 10.0 - - - +
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Residues in contact with PHE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A SER 3.0 16.8 + - - +
265A GLN 3.7 4.7 - - - +
267A ARG* 1.3 77.4 - - - +
269A ALA* 1.3 59.8 + - + +
271A PHE* 3.5 2.7 + - - +
272A THR* 2.9 49.2 + - + -
343A ALA 3.3 24.1 + - - +
344A GLY* 4.7 6.5 - - - -
442A LEU* 4.1 13.9 - - + -
447A LYS* 3.5 47.1 - - + +
448A LYS 3.7 22.4 - - - -
449A LEU* 4.4 12.6 - - + -
501A 67S 3.7 25.4 - - - -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 4.5 9.0 - - + +
265A GLN 2.9 19.7 + - - +
266A GLN* 3.6 7.0 - - - +
268A PHE* 1.3 78.0 - - + +
270A HIS* 1.3 66.0 + - - +
272A THR* 3.7 6.9 - - - -
273A GLU* 2.9 41.1 + - - +
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Residues in contact with HIS 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 3.4 15.7 - - + +
250A THR* 2.5 31.7 + - - +
251A PRO* 4.5 2.9 - - + +
252A TRP* 3.6 31.6 + + + -
266A GLN 2.7 17.7 + - - +
267A ARG* 3.4 6.3 - - - +
269A ALA* 1.3 75.9 - - - +
271A PHE* 1.3 67.2 + + - +
273A GLU* 3.1 10.0 + - - +
274A LEU* 3.1 34.4 + - + +
333A PHE* 3.7 26.6 - + - -
335A TYR* 2.5 34.4 + + - -
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A TRP* 3.5 29.2 - + - -
267A ARG 3.0 7.9 + - - +
268A PHE* 3.9 2.7 - - - +
270A HIS* 1.3 83.1 - + - +
272A THR* 1.3 63.0 + - - +
274A LEU* 3.2 10.6 + - + +
275A ALA* 2.9 22.7 + - - +
329A PHE* 4.3 6.7 - + - -
335A TYR* 3.9 35.7 - + + -
339A ASP 4.6 0.4 - - - -
340A PHE* 4.1 43.3 - + - -
343A ALA* 3.6 26.7 - - + +
345A LEU* 4.5 11.2 - - + -
501A 67S 3.5 33.9 - - - -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 2.9 37.0 + - + -
269A ALA* 3.7 9.0 - - - +
270A HIS 3.3 0.2 - - - -
271A PHE* 1.3 77.2 - - - +
273A GLU* 1.3 64.6 + - + +
275A ALA* 3.3 4.7 + - - +
276A ILE* 3.0 23.1 + - + +
450A PRO* 3.1 44.0 - - + -
453A LEU* 3.9 5.6 - - + +
501A 67S 3.3 23.2 - - - -
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS 4.9 4.0 - - - +
249A VAL* 3.7 14.2 - - + +
250A THR* 2.7 50.9 + - - -
269A ALA* 2.9 26.3 + - - +
270A HIS 3.1 4.0 + - - +
272A THR* 1.3 75.5 - - + +
274A LEU* 1.3 65.2 + - - +
276A ILE* 3.0 18.4 + - + +
277A ILE* 3.0 27.8 + - + +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 4.1 18.6 - - + -
270A HIS* 3.1 35.9 + - + +
271A PHE* 3.3 13.5 - - + +
273A GLU* 1.3 76.7 - - - +
275A ALA* 1.3 56.3 + - - +
277A ILE* 3.3 7.8 + - + +
278A SER* 2.9 27.7 + - - -
329A PHE* 3.6 35.2 - - + -
330A LEU* 3.8 22.0 - - + -
333A PHE* 4.1 7.9 - - + -
335A TYR* 4.3 4.0 - - + -
501A 67S 3.4 32.8 - - + +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE 2.9 13.3 + - - +
272A THR 3.4 9.6 - - - +
273A GLU 3.2 0.2 - - - -
274A LEU* 1.3 75.5 - - - +
276A ILE* 1.3 62.8 + - - +
278A SER* 3.0 8.5 + - - -
279A VAL* 3.0 26.6 + - - +
312A MET* 4.7 5.6 - - + +
453A LEU* 4.0 20.0 - - + -
457A TRP* 5.0 0.7 - - + -
501A 67S 3.8 35.4 - - + +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 3.0 16.7 + - + +
273A GLU* 3.0 19.0 + - + +
275A ALA* 1.3 75.6 - - - +
277A ILE* 1.3 67.9 + - + +
279A VAL* 3.0 18.6 + - - +
280A GLN* 3.1 32.8 + - - +
450A PRO* 3.7 31.2 - - + -
452A LEU* 4.4 18.1 - - + +
453A LEU* 4.3 15.3 - - + -
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER* 3.8 34.5 - - - +
245A ASP* 3.8 35.0 - - + +
248A LYS* 5.4 3.4 - - + +
249A VAL* 3.9 27.1 - - + -
273A GLU* 3.0 13.9 + - + +
274A LEU* 3.6 10.1 - - + +
276A ILE* 1.3 76.6 - - + +
278A SER* 1.3 59.8 + - - +
280A GLN* 3.1 14.8 + - + +
281A GLU* 2.8 27.0 + - - +
330A LEU* 4.6 9.6 - - + -
501A 67S 4.2 8.1 - - - +
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Residues in contact with SER 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU 2.9 14.0 + - - -
275A ALA* 3.0 15.0 + - - -
277A ILE* 1.3 77.1 - - - +
279A VAL* 1.3 55.1 + - - +
281A GLU* 3.2 4.3 + - - +
282A ILE* 2.9 33.5 + - - +
312A MET* 3.1 31.0 - - - +
315A GLU* 5.8 0.3 - - - +
501A 67S 3.6 36.0 + - - -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ALA 3.0 18.3 + - - +
276A ILE* 3.4 7.0 - - - +
278A SER* 1.3 73.7 - - - +
280A GLN* 1.3 66.9 + - - +
282A ILE* 3.1 9.8 + - - +
283A VAL* 2.9 34.0 + - + +
308A THR* 4.1 22.7 - - + +
312A MET* 4.7 2.7 - - - -
452A LEU* 3.8 29.8 - - + -
453A LEU* 3.8 23.6 - - + -
456A ILE* 4.3 17.0 - - + -
471A LEU* 5.0 3.4 - - + -
474A LEU* 4.9 1.6 - - + -
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 3.8 16.1 - - - +
248A LYS* 5.2 10.0 + - - +
276A ILE* 3.1 28.5 + - + +
277A ILE* 3.4 20.5 - - + +
279A VAL* 1.3 75.9 - - - +
281A GLU* 1.3 56.3 + - - +
283A VAL* 3.3 7.9 + - - +
284A ASP* 2.9 38.0 + - - +
452A LEU* 5.0 3.6 - - + +
474A LEU* 4.1 31.4 - - + +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLN* 5.6 1.4 + - - -
238A CYS* 3.9 21.1 - - + +
239A ASN* 3.0 28.3 + - - -
242A SER* 2.6 33.7 + - - +
277A ILE 2.8 15.9 + - - +
278A SER 3.4 9.4 - - - +
280A GLN* 1.3 72.1 - - - +
282A ILE* 1.3 58.5 + - + +
284A ASP* 3.4 7.9 + - - +
285A PHE* 3.0 29.4 + - + +
315A GLU* 4.7 8.1 - - - +
319A ARG* 4.1 2.9 + - - -
501A 67S 3.2 31.0 + - - +
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 2.9 30.7 + - - +
279A VAL* 3.5 7.4 - - + +
281A GLU* 1.3 77.6 - - + +
283A VAL* 1.3 57.7 + - + +
285A PHE* 3.3 8.7 + - + +
286A ALA* 2.9 28.0 + - + +
304A LEU* 4.8 13.7 - - + -
307A SER* 5.3 0.7 - - - +
308A THR* 3.6 46.9 - - + +
311A ILE* 3.8 42.4 - - + -
312A MET* 4.2 3.4 - - + +
315A GLU* 5.9 2.5 - - + -
378A ILE* 5.7 2.2 - - + -
501A 67S 6.0 0.9 - - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 2.9 26.8 + - + +
280A GLN* 3.7 5.4 - - - +
282A ILE* 1.3 74.8 - - + +
284A ASP* 1.3 68.7 + - - +
286A ALA* 3.2 2.8 + - - +
287A LYS* 3.2 28.5 + - - +
304A LEU* 3.8 16.8 - - + -
471A LEU* 3.6 28.5 - - + -
474A LEU* 4.0 37.2 - - + +
475A LEU* 4.3 16.2 - - + -
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Residues in contact with ASP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A CYS* 3.7 16.1 - - + +
241A ARG* 3.5 33.3 - - - +
280A GLN* 2.9 24.7 + - - +
281A GLU* 3.6 7.3 - - - +
283A VAL* 1.3 79.4 - - - +
285A PHE* 1.3 64.0 + - - +
287A LYS* 3.5 23.0 + - - +
288A GLN* 3.6 18.6 + - - +
474A LEU* 5.6 0.3 - - - +
477A ASP* 5.8 0.2 - - - +
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 3.6 28.7 - - + -
234A ALA* 3.9 16.8 - - + -
235A GLN* 3.5 38.8 - - + -
238A CYS* 3.5 11.4 - - + -
281A GLU 3.0 17.8 + - - +
282A ILE* 3.6 8.5 - - + +
283A VAL 3.2 0.2 - - - -
284A ASP* 1.3 74.1 - - - +
286A ALA* 1.3 69.6 + - - +
288A GLN* 2.9 17.1 + - - +
289A VAL* 3.3 31.1 + - + +
371A ALA* 4.4 12.6 - - + -
374A ILE* 3.6 31.0 - - + -
375A ALA 4.8 2.2 - - - -
378A ILE* 4.5 6.7 - - + -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ILE* 2.9 17.6 + - + +
283A VAL* 3.2 6.9 + - - +
285A PHE* 1.3 77.8 - - - +
287A LYS* 1.3 57.8 + - - +
289A VAL* 2.9 27.6 + - - +
292A PHE* 3.3 47.9 - - + +
304A LEU* 4.1 13.0 - - + -
378A ILE* 4.6 9.6 - - + -
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL* 3.2 18.3 + - - +
284A ASP* 3.7 19.9 + - - +
285A PHE 3.2 0.6 - - - -
286A ALA* 1.3 76.0 - - - +
288A GLN* 1.3 60.9 + - + +
289A VAL 3.7 3.7 + - - +
292A PHE* 4.2 7.2 - - + -
293A LEU* 3.4 41.9 - - + +
474A LEU 3.1 26.2 + - - -
475A LEU* 3.2 38.5 + - + +
477A ASP* 3.3 24.7 + - - +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN* 3.5 26.9 + - - +
231A LEU* 4.9 1.7 - - - +
234A ALA* 3.9 27.4 - - + +
237A GLN* 3.3 35.1 + - - +
238A CYS* 4.1 15.1 - - - -
241A ARG* 4.7 2.3 + - - -
284A ASP* 3.6 15.0 - - - +
285A PHE 2.9 9.3 + - - +
287A LYS* 1.3 78.1 - - + +
289A VAL* 1.3 63.4 + - - +
290A PRO* 3.3 10.2 - - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.1 9.2 - - + -
285A PHE* 3.4 45.1 - - + +
286A ALA* 2.9 15.8 + - - +
287A LYS 4.4 2.9 - - - +
288A GLN* 1.3 77.1 - - - +
290A PRO* 1.3 73.1 - - + +
291A GLY 3.1 3.6 + - - -
292A PHE* 3.1 17.9 + - + +
293A LEU 4.6 0.7 + - - -
375A ALA* 4.3 8.3 - - + -
378A ILE* 4.8 7.4 - - + -
379A PHE* 3.8 24.5 - - + -
399A TYR* 3.6 18.4 - - + +
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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