Contacts of the helix formed by residues 272 - 298 (chain B) in PDB entry 5SY1
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 PRO 272 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE 5.5 0.2 - - - +
83B HIS* 3.4 25.4 - - + +
87B LYS* 5.2 0.2 - - - -
270B ARG 4.3 0.7 - - - +
271B PHE* 1.3 92.5 - - + +
273B LEU* 1.3 64.9 + - - +
274B LYS 3.4 0.9 - - - +
275B LEU* 4.2 12.1 - - + +
276B ALA* 3.1 22.9 + - - +
371B LEU* 3.8 26.7 - - + -
548B TYR* 3.5 21.5 - - + +
549B LEU* 6.0 0.2 - - + -
552B GLU* 3.3 31.4 - - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 4.3 16.4 - - + -
79B ASN 3.5 22.0 - - - +
80B PHE* 3.6 37.8 + - + +
82B ASP 4.1 12.7 + - - +
85B GLN* 5.0 4.9 - - + +
86B HIS 6.1 0.7 - - - +
87B LYS* 3.7 36.6 - - + +
90B ALA* 4.2 12.3 - - + -
271B PHE 3.9 0.6 + - - -
272B PRO* 1.3 70.6 - - - +
274B LYS* 1.3 65.4 + - - +
276B ALA* 3.2 3.2 + - + +
277B ILE* 3.2 45.7 + - + +
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Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 4.3 11.2 + - - -
80B PHE* 3.7 43.2 + - + +
94B TYR* 5.2 3.8 - - + +
272B PRO* 3.4 0.8 - - - +
273B LEU* 1.3 80.1 - - - +
275B LEU* 1.3 61.2 + - - +
277B ILE* 3.9 4.9 + - + -
278B SER* 3.7 5.7 + - - -
399B TRP* 3.6 46.5 + - + +
401B GLY 4.5 5.7 - - - +
402B PHE* 4.7 7.8 - - + -
403B THR* 3.2 52.1 - - + +
548B TYR* 3.8 27.6 - - + +
552B GLU* 5.2 2.0 - - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 5.0 14.1 - - + -
272B PRO* 3.5 24.8 + - + +
273B LEU 3.2 0.6 - - - -
274B LYS* 1.3 76.8 - - - +
276B ALA* 1.3 60.6 + - - +
278B SER* 2.6 24.2 + - - +
279B VAL* 3.7 11.9 + - + +
367B HIS* 3.5 59.0 - - + +
371B LEU* 5.1 4.7 - - + -
402B PHE* 3.9 22.2 - - + -
548B TYR* 3.1 25.9 + - + +
549B LEU* 5.4 2.5 - - + -
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LYS* 3.8 30.3 - - + -
91B VAL* 4.4 7.1 - - + +
271B PHE* 4.4 17.9 - - + +
272B PRO 3.1 19.1 + - - +
273B LEU* 3.2 5.1 + - + +
275B LEU* 1.3 75.1 - - - +
277B ILE* 1.3 64.1 + - - +
279B VAL* 3.7 11.9 + - - +
280B VAL* 4.0 14.9 + - - +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PHE* 6.1 0.2 - - + -
80B PHE* 4.2 8.1 - - + -
90B ALA* 4.1 7.6 - - + +
91B VAL* 3.9 26.0 - - + +
94B TYR* 3.7 44.2 - - + -
273B LEU* 3.2 36.8 + - + +
274B LYS* 4.1 10.3 - - + +
276B ALA* 1.3 78.1 - - - +
278B SER* 1.3 57.6 + - - +
279B VAL 3.1 0.9 + - - -
280B VAL* 3.1 4.7 + - - +
281B VAL* 3.0 44.1 + - + +
403B THR* 4.1 13.5 - - + -
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LYS 3.7 10.4 + - - -
275B LEU* 2.6 35.8 + - - +
277B ILE* 1.3 77.7 - - - +
279B VAL* 1.3 64.0 + - - +
281B VAL* 4.7 4.7 - - - +
282B ALA* 3.3 22.4 + - - +
367B HIS* 5.9 0.3 - - - -
402B PHE* 4.2 6.0 - - - -
403B THR* 3.9 18.6 - - - +
406B GLN* 3.4 29.4 - - - +
407B ALA 5.4 0.2 + - - -
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Residues in contact with VAL 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B PHE* 6.0 4.7 - - + -
275B LEU* 3.7 18.1 + - + +
276B ALA* 4.2 8.7 - - - +
277B ILE 3.1 1.4 + - - -
278B SER* 1.3 80.2 - - - +
280B VAL* 1.3 64.3 + - + +
282B ALA* 3.4 6.6 + - - +
283B PHE* 2.9 26.5 + - + +
360B LEU* 4.6 23.5 - - + +
363B SER 6.2 0.7 - - - -
364B MET* 3.7 37.2 - - + -
367B HIS* 5.6 8.7 - - + +
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Residues in contact with VAL 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B VAL* 3.8 36.3 - - + +
95B GLY* 5.9 0.2 - - - -
276B ALA 4.0 10.1 + - - +
277B ILE 3.1 4.5 + - - +
279B VAL* 1.3 79.5 - - + +
281B VAL* 1.3 60.8 + - + +
283B PHE* 2.8 27.3 + - + +
284B ILE* 2.8 29.4 + - + +
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Residues in contact with VAL 281 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PHE* 4.7 12.3 - - + -
91B VAL* 5.2 2.2 - - + +
94B TYR* 4.0 23.6 - - + +
95B GLY* 4.4 4.9 - - - +
98B PHE* 4.2 26.0 - - + -
277B ILE* 3.0 35.9 + - + +
278B SER* 4.7 4.5 - - - -
280B VAL* 1.3 76.2 - - + +
282B ALA* 1.3 61.4 + - - +
284B ILE* 3.6 9.0 + - - +
285B ALA* 3.1 21.8 + - - +
403B THR* 5.0 5.2 - - - +
407B ALA* 3.9 19.2 - - + +
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER 3.3 21.0 + - - +
279B VAL* 3.5 6.3 - - - +
280B VAL 3.2 0.4 - - - -
281B VAL* 1.3 78.0 - - - +
283B PHE* 1.3 56.3 + - - +
285B ALA* 3.1 5.2 + - - +
286B LEU* 2.9 25.1 + - - +
360B LEU* 3.7 12.6 - - + -
406B GLN* 4.2 17.5 - - + +
407B ALA* 4.5 6.1 - - - +
410B LEU* 3.3 28.9 - - + +
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 2.9 15.3 + - + +
280B VAL* 2.8 17.0 + - + +
282B ALA* 1.3 76.1 - - - +
284B ILE* 1.3 67.7 + - + +
286B LEU* 3.6 19.2 + - + +
287B TYR* 3.3 26.2 + + + +
357B LEU* 4.5 19.7 - - + -
360B LEU* 4.8 7.0 - - + -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLY* 3.7 33.2 - - - +
98B PHE* 3.9 16.4 - - + -
99B CYS* 3.9 22.9 - - - -
188B PRO* 4.4 22.7 - - + -
192B CYS* 5.4 6.7 - - + -
280B VAL* 2.8 28.7 + - + +
281B VAL* 4.0 5.2 - - - +
282B ALA 3.3 0.2 - - - -
283B PHE* 1.3 83.1 - - + +
285B ALA* 1.3 58.9 + - - +
287B TYR* 2.9 21.9 + - - +
288B GLN* 3.0 18.8 + - + +
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 3.6 31.0 - - + -
281B VAL 3.1 14.7 + - - +
282B ALA* 3.1 12.2 + - - +
284B ILE* 1.3 76.6 - - - +
286B LEU* 1.3 62.4 + - - +
288B GLN* 3.3 3.0 + - - +
289B MET* 3.2 29.6 + - - +
407B ALA* 4.2 8.5 - - + +
410B LEU* 4.9 6.1 - - + -
411B CYS* 3.9 15.2 - - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ALA 2.9 15.4 + - - +
283B PHE* 3.7 25.4 - - + +
285B ALA* 1.3 78.0 - - - +
287B TYR* 1.3 60.2 + - - +
289B MET* 3.7 0.9 + - - +
290B ALA* 3.2 23.7 + - - +
353B CYS* 4.0 34.3 - - - +
356B ASN* 4.3 13.2 - - + +
357B LEU* 4.3 21.8 - - + +
360B LEU* 5.3 5.8 - - + -
410B LEU* 4.3 10.5 - - + +
414B MET* 3.7 35.7 - - + -
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Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.7 16.0 + - - +
187B LEU* 3.4 28.1 - - + +
188B PRO* 3.6 30.7 - - + -
283B PHE* 3.3 18.1 + + + +
284B ILE* 2.9 12.0 + - - +
286B LEU* 1.3 80.0 - - - +
288B GLN* 1.3 84.3 + - - +
290B ALA* 3.8 5.2 + - + +
291B LEU* 3.4 29.1 + - + +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.8 0.7 - - + -
99B CYS* 4.9 6.2 - - - -
102B VAL* 3.4 45.4 - - + +
181B TYR* 5.0 5.2 + - - -
185B GLY* 3.9 22.6 + - - +
188B PRO* 3.8 14.1 - - - +
284B ILE* 3.0 22.9 + - + +
285B ALA* 3.3 7.4 + - - +
286B LEU 3.2 0.2 - - - -
287B TYR* 1.3 107.3 - - - +
289B MET* 1.3 63.9 + - + +
291B LEU* 3.9 7.2 - - - +
292B LEU* 3.1 27.4 + - - +
411B CYS* 6.4 0.4 - - - -
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Residues in contact with MET 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ALA 3.2 16.8 + - - +
286B LEU 4.4 0.2 - - - +
288B GLN* 1.3 79.1 - - + +
290B ALA* 1.3 59.5 + - - +
292B LEU* 3.9 18.3 - - + +
293B LEU* 3.0 48.4 + - + +
411B CYS* 3.6 50.3 - - + +
414B MET* 4.0 21.1 - - + -
415B ALA* 4.7 14.8 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU 3.2 18.9 + - - +
287B TYR* 4.2 6.5 - - + +
288B GLN 3.3 0.2 - - - -
289B MET* 1.3 77.3 - - - +
291B LEU* 1.3 57.1 + - - +
293B LEU 4.2 0.4 - - - -
294B ILE* 3.3 29.8 + - - +
349B VAL* 4.5 18.2 - - + +
353B CYS* 4.5 18.6 - - + -
414B MET* 4.9 6.6 - - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B TYR* 3.7 26.5 - - + +
184B PHE* 3.6 46.0 - - + +
185B GLY* 3.8 6.1 - - - -
287B TYR* 3.4 28.0 + - + +
288B GLN* 3.9 10.3 - - - +
289B MET 3.2 0.4 - - - -
290B ALA* 1.3 78.4 - - - +
292B LEU* 1.3 55.4 + - - +
293B LEU 3.3 0.4 - - - -
294B ILE* 4.9 3.6 - - + -
295B SER* 2.4 49.4 + - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 6.4 2.2 - - + -
106B LEU* 4.2 27.4 - - + -
177B ILE* 5.6 7.4 - - + -
181B TYR* 4.0 22.2 - - + +
288B GLN 3.1 18.8 + - - +
289B MET* 3.3 21.9 + - + +
291B LEU* 1.3 76.9 - - - +
293B LEU* 1.3 66.5 + - + +
295B SER* 4.1 5.2 - - - +
296B GLY* 3.4 19.6 + - - -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B MET* 3.0 34.7 + - + +
290B ALA 4.6 2.2 - - - +
292B LEU* 1.3 81.5 - - + +
294B ILE* 1.3 65.6 + - - +
296B GLY 3.6 0.7 + - - -
297B VAL* 3.4 16.2 - - + +
345B TYR* 3.3 30.9 + - - +
349B VAL* 4.4 16.6 - - + -
414B MET* 4.0 17.3 - - + +
415B ALA* 5.4 5.8 - - + -
418B THR* 3.9 32.1 - - + +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 3.3 20.5 + - - +
291B LEU* 3.6 5.9 + - + +
293B LEU* 1.3 79.4 - - - +
295B SER* 1.3 59.4 + - - +
296B GLY 3.1 5.1 + - - -
298B LEU* 3.5 43.1 + - + +
299B PRO* 4.2 0.2 - - - +
345B TYR* 4.9 6.7 - - + -
346B VAL* 4.8 23.6 - - + +
349B VAL* 4.2 29.8 - - + -
350B THR* 6.3 1.1 - - + -
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Residues in contact with SER 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 3.3 22.0 - - - +
178B TYR* 4.5 22.8 - - - +
181B TYR* 3.5 28.4 - - - -
291B LEU* 2.4 32.2 + - - +
292B LEU* 3.9 4.8 - - - +
294B ILE* 1.3 77.3 - - - +
296B GLY* 1.3 54.6 + - - +
299B PRO* 4.3 13.7 - - - +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE* 5.2 3.1 - - - -
292B LEU* 3.4 16.1 + - - -
293B LEU 4.3 0.4 - - - -
294B ILE 3.2 1.2 - - - -
295B SER* 1.3 78.9 - - - +
297B VAL* 1.3 67.3 + - - +
299B PRO* 4.1 8.3 - - - +
300B THR* 4.3 11.8 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU 5.6 0.2 - - - +
293B LEU* 3.4 12.3 - - + +
294B ILE 3.6 0.6 + - - -
296B GLY* 1.3 83.2 - - - +
298B LEU* 1.3 66.1 + - - +
299B PRO* 3.3 1.5 - - - +
300B THR* 3.0 24.7 + - - +
301B LEU* 3.2 26.9 + - + +
345B TYR* 3.3 45.8 - - + +
----------------------------------------------------------
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 6.4 0.4 - - + -
294B ILE* 3.5 33.1 + - + +
297B VAL* 1.3 79.8 - - + +
299B PRO* 1.3 65.3 - - + +
301B LEU* 3.8 16.2 - - + -
302B HIS* 3.0 42.3 + - + +
342B GLU* 3.8 37.9 - - + +
345B TYR* 5.3 6.3 - - + -
346B VAL* 4.6 19.1 - - + -
----------------------------------------------------------
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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