Contacts of the helix formed by residues 272 - 298 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 5.4 0.2 - - - +
83A HIS* 3.4 24.0 - - + +
87A LYS* 5.2 0.4 - - - -
270A ARG 4.3 0.4 - - - +
271A PHE* 1.3 91.8 - - + +
273A LEU* 1.3 65.7 + - - +
274A LYS 4.3 1.3 - - - +
275A LEU* 3.5 13.0 + - + +
276A ALA* 3.1 22.7 + - - +
371A LEU* 3.8 26.0 - - + -
548A TYR* 3.5 20.9 - - + +
549A LEU* 6.0 0.2 - - + -
552A GLU* 3.3 32.3 - - + +
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 4.3 16.6 - - + -
79A ASN 3.5 22.2 - - - +
80A PHE* 3.6 38.0 + - + +
82A ASP 4.1 11.7 + - - +
85A GLN* 5.0 5.8 - - + +
86A HIS 6.1 0.2 - - - +
87A LYS* 3.7 36.1 - - + +
90A ALA* 4.2 12.6 - - + -
91A VAL* 5.2 0.4 - - + -
271A PHE 3.9 0.6 + - - -
272A PRO* 1.3 72.5 - - - +
274A LYS* 1.3 66.9 + - - +
276A ALA* 3.2 3.7 + - + +
277A ILE* 3.2 45.7 + - + +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.7 44.4 + - + +
94A TYR* 5.2 4.0 - - + +
272A PRO* 3.4 1.6 - - - +
273A LEU* 1.3 80.2 - - - +
275A LEU* 1.3 61.1 + - - +
277A ILE* 3.9 4.4 + - + -
278A SER* 3.7 5.0 + - - -
399A TRP* 3.6 45.4 + - + +
401A GLY 4.5 4.0 - - - +
402A PHE* 4.7 9.5 - - + +
403A THR* 3.2 52.1 - - + +
548A TYR* 3.8 27.8 - - + +
552A GLU* 5.2 1.8 - - - +
493B SER* 4.2 14.6 + - - -
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Residues in contact with LEU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 5.0 13.0 - - + -
272A PRO* 3.5 25.0 + - + +
273A LEU 3.2 0.6 - - - -
274A LYS* 1.3 77.5 - - - +
276A ALA* 1.3 62.2 + - - +
278A SER* 2.6 22.7 + - - +
279A VAL* 3.7 12.0 + - + +
367A HIS* 3.5 58.3 - - + +
371A LEU* 5.1 4.9 - - + -
402A PHE* 3.9 21.5 - - + -
548A TYR* 3.1 27.0 + - + +
549A LEU* 5.4 2.9 - - + -
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Residues in contact with ALA 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LYS* 3.8 30.1 - - + -
91A VAL* 4.4 6.7 - - + +
271A PHE* 4.4 17.5 - - + +
272A PRO 3.1 18.2 + - - +
273A LEU* 3.2 4.5 + - + +
275A LEU* 1.3 74.3 - - - +
277A ILE* 1.3 66.1 + - - +
279A VAL* 3.7 11.1 + - - +
280A VAL* 4.0 15.4 + - - +
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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
----------------------------------------------------------
80A PHE* 4.2 8.3 - - + -
90A ALA* 4.1 7.4 - - + +
91A VAL* 3.9 25.1 - - + +
94A TYR* 3.7 44.0 - - + -
273A LEU* 3.2 34.9 + - + +
274A LYS* 4.1 10.5 - - + +
275A LEU 3.3 0.2 - - - -
276A ALA* 1.3 77.2 - - - +
278A SER* 1.3 58.2 + - - +
279A VAL 3.1 1.0 + - - -
280A VAL* 3.1 4.2 + - - +
281A VAL* 3.0 43.4 + - + +
403A THR* 4.1 12.6 - - + -
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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 LYS 3.7 10.4 + - - -
275A LEU* 2.6 35.3 + - - +
277A ILE* 1.3 78.8 - - - +
279A VAL* 1.3 62.0 + - - +
281A VAL* 4.7 4.5 - - - -
282A ALA* 3.3 22.4 + - - +
367A HIS* 5.9 0.3 - - - -
402A PHE* 4.2 6.8 - - - -
403A THR* 3.9 18.2 - - - +
406A GLN* 3.4 30.9 - - - +
407A ALA* 5.8 0.3 - - - +
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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
----------------------------------------------------------
271A PHE* 6.0 4.3 - - + -
275A LEU* 3.7 18.1 + - + +
276A ALA* 4.2 8.1 - - - +
277A ILE 3.2 1.0 - - - -
278A SER* 1.3 80.3 - - - +
280A VAL* 1.3 63.6 + - + +
282A ALA* 3.4 6.5 + - - +
283A PHE* 2.9 25.7 + - + +
360A LEU* 4.6 22.2 - - + +
363A SER 6.0 0.7 - - - +
364A MET* 3.7 37.5 - - + -
367A HIS* 5.6 9.0 - - + +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.8 35.7 - - + +
95A GLY* 5.9 0.2 - - - -
276A ALA 4.1 9.9 - - - +
277A ILE 3.1 4.3 + - - +
279A VAL* 1.3 79.7 - - + +
281A VAL* 1.3 61.7 + - + +
283A PHE* 2.8 26.8 + - + +
284A ILE* 2.8 28.6 + - + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.2 2.9 - - + +
94A TYR* 4.0 23.3 - - + +
95A GLY* 4.4 4.7 - - - +
98A PHE* 4.2 25.4 - - + -
277A ILE* 3.0 35.5 + - + +
278A SER* 4.7 4.3 - - - +
280A VAL* 1.3 77.6 - - + +
282A ALA* 1.3 62.2 + - - +
284A ILE* 3.6 8.2 + - - +
285A ALA* 3.1 21.3 + - - +
403A THR* 5.0 4.9 - - - +
407A ALA* 3.9 19.0 - - + +
497B PHE* 4.5 12.8 - - + -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER 3.3 20.8 + - - +
279A VAL* 3.5 6.5 - - - +
280A VAL 3.2 0.4 - - - -
281A VAL* 1.3 79.3 - - - +
283A PHE* 1.3 56.0 + - - +
285A ALA* 3.1 4.8 + - - +
286A LEU* 2.9 24.8 + - - +
360A LEU* 3.7 12.6 - - + -
406A GLN* 4.2 18.6 - - + +
407A ALA* 4.5 5.9 - - - +
410A LEU* 3.3 28.1 - - + +
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Residues in contact with PHE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 2.9 14.6 + - + +
280A VAL* 2.8 17.2 + - + +
282A ALA* 1.3 76.7 - - - +
284A ILE* 1.3 69.3 + - + +
286A LEU* 3.6 19.0 + - + +
287A TYR* 3.3 25.1 + + + +
357A LEU* 4.5 20.4 - - + -
360A LEU* 4.5 7.6 - - + +
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Residues in contact with ILE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY* 3.7 33.7 - - - +
98A PHE* 3.9 16.8 - - + -
99A CYS* 3.9 22.4 - - - -
188A PRO* 4.4 22.2 - - + -
192A CYS* 5.4 6.7 - - + -
280A VAL* 2.8 28.6 + - + +
281A VAL* 4.0 6.1 - - - +
283A PHE* 1.3 82.7 - - + +
285A ALA* 1.3 57.8 + - - +
287A TYR* 2.9 21.7 + - - +
288A GLN* 3.0 18.8 + - + +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.6 30.3 - - + -
281A VAL 3.1 13.8 + - - +
282A ALA* 3.1 12.4 + - - +
284A ILE* 1.3 77.4 - - - +
286A LEU* 1.3 61.8 + - - +
288A GLN* 3.3 3.6 + - - +
289A MET* 3.2 29.1 + - - +
407A ALA* 4.2 8.5 - - + +
410A LEU* 4.9 5.8 - - + -
411A CYS* 3.9 15.2 - - - -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ALA 2.9 15.1 + - - +
283A PHE* 3.7 24.2 - - + +
285A ALA* 1.3 78.0 - - - +
287A TYR* 1.3 60.4 + - - +
289A MET* 4.3 0.5 - - - +
290A ALA* 3.2 23.9 + - - +
353A CYS* 4.0 33.4 - - - +
356A ASN* 4.3 12.1 - - + +
357A LEU* 4.3 21.8 - - + +
360A LEU* 5.3 6.1 - - + -
410A LEU* 4.3 11.6 - - + +
414A MET* 3.7 36.1 - - + -
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PHE* 3.7 14.2 + - - +
187A LEU* 3.4 28.6 - - + +
188A PRO* 3.6 29.4 - - + -
283A PHE* 3.3 18.6 + + + +
284A ILE* 2.9 12.2 + - - +
286A LEU* 1.3 80.4 - - - +
288A GLN* 1.3 84.4 + - - +
290A ALA* 3.8 4.8 + - + +
291A LEU* 3.4 28.9 + - + +
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Residues in contact with GLN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A CYS* 4.9 6.2 - - - -
102A VAL* 3.4 45.8 - - + +
181A TYR* 5.0 4.9 + - - -
185A GLY* 3.9 22.2 + - - +
188A PRO* 3.8 13.9 - - - +
284A ILE* 3.0 23.9 + - + +
285A ALA* 3.3 7.4 + - - +
286A LEU 3.2 0.4 - - - -
287A TYR* 1.3 107.7 - - - +
289A MET* 1.3 64.2 + - + +
291A LEU* 3.6 8.3 + - - +
292A LEU* 3.1 27.0 + - - +
411A CYS* 6.4 0.4 - - - -
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.2 17.5 + - - +
286A LEU 4.4 0.4 - - - +
288A GLN* 1.3 79.1 - - + +
290A ALA* 1.3 58.7 + - - +
292A LEU* 3.9 18.2 - - + +
293A LEU* 3.0 48.6 + - + +
411A CYS* 3.6 50.5 - - + +
414A MET* 4.0 21.1 - - + -
415A ALA* 4.7 14.8 - - + +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU 3.2 18.8 + - - +
287A TYR* 4.2 5.8 - - + +
289A MET* 1.3 76.2 - - - +
291A LEU* 1.3 59.4 + - - +
293A LEU* 4.2 0.9 - - - -
294A ILE* 3.3 29.5 + - - +
349A VAL* 4.5 17.6 - - + +
353A CYS* 4.5 19.3 - - - -
414A MET* 4.9 6.6 - - + +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.7 25.8 - - + +
184A PHE* 3.6 45.8 - - + +
185A GLY* 3.8 6.7 - - - +
287A TYR* 3.4 28.3 + - + +
288A GLN* 3.6 10.3 + - - +
289A MET 3.2 0.2 - - - -
290A ALA* 1.3 79.3 - - - +
292A LEU* 1.3 55.1 + - - +
293A LEU 3.3 0.7 - - - -
294A ILE* 4.9 3.4 - - + -
295A SER* 2.4 49.8 + - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 6.4 2.5 - - + -
106A LEU* 4.2 26.9 - - + -
177A ILE* 5.6 7.2 - - + -
181A TYR* 4.0 23.1 - - + +
288A GLN 3.1 18.2 + - - +
289A MET* 3.3 22.2 + - + +
291A LEU* 1.3 77.4 - - - +
293A LEU* 1.3 67.6 + - + +
295A SER* 4.1 5.4 - - - +
296A GLY* 3.4 19.2 + - - -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A MET* 3.0 36.8 + - + +
290A ALA 4.6 2.5 - - - +
291A LEU 3.3 0.2 - - - -
292A LEU* 1.3 82.8 - - + +
294A ILE* 1.3 67.1 + - - +
296A GLY 3.6 0.5 + - - -
297A VAL* 3.4 16.4 - - + +
345A TYR* 3.3 29.2 + - - +
349A VAL* 4.4 17.5 - - + -
414A MET* 4.0 18.2 - - + +
415A ALA* 5.4 3.6 - - - -
418A THR* 3.9 31.6 - - + +
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ALA 3.3 20.5 + - - +
291A LEU* 3.6 5.9 + - + +
292A LEU 3.5 0.2 - - - -
293A LEU* 1.3 77.7 - - - +
295A SER* 1.3 61.1 + - - +
296A GLY 3.1 5.2 + - - -
298A LEU* 3.5 43.1 + - + +
345A TYR* 4.9 6.5 - - + -
346A VAL* 4.8 23.6 - - + +
349A VAL* 4.2 29.8 - - + -
350A THR* 6.3 1.3 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 3.3 22.3 - - - +
178A TYR* 4.5 23.0 - - - +
181A TYR* 3.5 28.4 - - - -
291A LEU* 2.4 32.2 + - - +
292A LEU* 3.9 4.1 - - - +
294A ILE* 1.3 77.1 - - - +
296A GLY* 1.3 55.4 + - - +
297A VAL 3.8 0.2 - - - -
299A PRO* 4.3 12.6 - - - +
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Residues in contact with GLY 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ILE* 5.2 3.4 - - - -
292A LEU* 3.4 15.8 + - - -
293A LEU 3.6 0.2 + - - -
294A ILE 3.1 1.2 + - - -
295A SER* 1.3 80.2 - - - +
297A VAL* 1.3 65.7 + - - +
299A PRO* 4.1 6.9 - - - +
300A THR* 4.3 12.5 + - - +
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Residues in contact with VAL 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.4 12.1 - - + +
294A ILE 3.6 0.4 + - - -
296A GLY* 1.3 84.4 - - - +
298A LEU* 1.3 67.7 + - - +
299A PRO 3.3 1.6 - - - -
300A THR* 3.0 25.0 + - - +
301A LEU* 3.2 27.2 + - + +
345A TYR* 3.3 46.4 - - + +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A TYR* 6.4 0.9 - - + -
294A ILE* 3.5 33.0 + - + +
297A VAL* 1.3 80.0 - - + +
299A PRO* 1.3 65.9 - - + +
301A LEU* 3.8 17.3 - - + -
302A HIS* 3.0 42.6 + - + +
342A GLU* 3.8 38.1 - - + +
345A TYR* 5.3 6.7 - - + -
346A VAL* 4.6 18.6 - - + -
----------------------------------------------------------
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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