Contacts of the helix formed by residues 268 - 291 (chain A) in PDB entry 5A86
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 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP 4.4 1.6 - - - +
267A LEU* 1.4 92.6 - - + +
269A ILE* 1.3 66.1 + - - +
270A GLU* 3.3 28.5 - - + +
271A ASP* 3.0 28.7 + - - +
272A GLN* 3.0 10.6 + - - +
357A LEU* 6.2 0.2 - - + -
358A GLN* 3.8 25.1 - - + +
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Residues in contact with ILE 269 (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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267A LEU 3.6 1.4 + - - -
268A PRO* 1.3 72.5 - - + +
270A GLU* 1.3 67.3 + - + +
272A GLN* 3.3 20.0 + - - +
273A ILE* 3.1 31.0 + - + +
684C THR* 4.2 15.7 - - + -
691C HIS* 4.1 22.0 - - + +
694C LEU* 4.0 21.8 - - + -
695C GLN* 3.3 33.9 - - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PRO* 3.2 23.2 - - + +
269A ILE* 1.3 83.8 - - + +
271A ASP* 1.4 68.7 + - - +
273A ILE* 3.4 5.6 + - - -
274A SER* 3.0 31.2 + - - -
355A GLY 5.4 2.0 - - - +
357A LEU* 3.4 31.5 - - + +
683C LEU* 3.3 25.9 - - + +
684C THR* 5.2 4.9 - - + -
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Residues in contact with ASP 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 4.3 11.6 - - + +
268A PRO* 3.0 24.4 + - + +
270A GLU* 1.4 85.0 - - - +
272A GLN* 1.3 59.5 + - - +
274A SER* 3.2 5.5 + - - -
275A LEU* 2.8 38.9 + - + +
355A GLY 4.2 0.7 - - - +
356A VAL* 3.9 11.4 - - + +
357A LEU* 3.1 30.7 + - - +
358A GLN* 3.0 40.0 + - - +
362A VAL* 5.0 0.6 - - + +
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LYS* 5.6 1.6 - - - +
264A PHE* 3.4 57.2 - - + +
265A ARG* 3.2 19.3 - - - +
267A LEU* 3.0 20.1 - - + +
268A PRO 3.0 12.0 + - - +
269A ILE* 3.4 24.2 + - - +
271A ASP* 1.3 74.5 - - - +
273A ILE* 1.3 62.9 + - - +
275A LEU* 3.4 0.6 + - - -
276A LEU* 3.0 28.1 + - - +
694C LEU* 3.7 23.7 + - + +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 3.1 21.2 + - + +
270A GLU* 3.5 8.1 - - - +
272A GLN* 1.3 76.7 - - - +
274A SER* 1.3 62.6 + - - +
276A LEU* 3.3 3.0 + - - +
277A LYS* 3.0 43.2 + - + +
683C LEU* 4.0 13.2 - - + -
684C THR* 4.1 35.9 - - + +
687C HIS* 4.0 23.3 - - + +
690C LEU* 3.8 22.8 - - + +
691C HIS* 4.7 7.0 - - + -
694C LEU* 3.8 17.7 - - + -
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Residues in contact with SER 274 (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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270A GLU 3.0 18.1 + - - -
271A ASP* 3.2 6.0 + - - -
273A ILE* 1.3 77.5 - - - +
275A LEU* 1.3 62.4 + - - +
277A LYS* 3.5 9.5 + - - +
278A GLY* 3.1 19.6 + - - -
353A ARG* 4.3 7.6 - - - +
354A PRO 4.1 11.1 + - - +
355A GLY* 3.4 33.4 + - - -
356A VAL* 4.2 8.5 - - - -
683C LEU* 3.5 12.6 - - - +
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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
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264A PHE* 4.1 17.0 - - + -
267A LEU* 3.5 32.8 - - + -
271A ASP* 2.8 23.9 + - + +
272A GLN 3.9 3.6 - - - +
274A SER* 1.3 72.4 - - - +
276A LEU* 1.3 57.1 + - - +
278A GLY* 3.4 1.9 + - - -
279A ALA* 3.0 31.9 + - - +
348A LEU* 3.4 26.8 - - + +
349A PHE* 4.5 7.4 - - + -
350A SER 3.4 27.4 - - - +
353A ARG* 4.2 5.6 + - + -
356A VAL* 3.9 17.3 - - + -
362A VAL* 4.3 13.7 - - + -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 4.1 16.2 - - + +
255A ILE* 4.1 23.6 - - + -
258A ALA* 3.9 19.5 - - + -
264A PHE* 3.9 10.5 - - + -
272A GLN 3.0 20.4 + - - +
273A ILE 3.3 3.3 + - - +
275A LEU* 1.3 72.0 - - - +
277A LYS* 1.3 59.8 + - - +
279A ALA* 4.5 0.4 - - + +
280A ALA* 2.9 37.0 + - + +
348A LEU* 4.3 9.2 - - + -
428A LEU* 4.3 5.4 - - + -
690C LEU* 3.8 25.4 - - + -
694C LEU* 3.6 31.9 - - + -
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 3.0 32.5 + - + +
274A SER* 3.8 7.6 - - - +
276A LEU* 1.3 76.3 - - - +
278A GLY* 1.3 60.6 + - - +
280A ALA* 4.1 6.8 + - - +
281A PHE 5.4 0.7 + - - -
354A PRO 6.1 1.1 - - - -
404A ASN* 5.3 1.0 + - - -
427A GLU 3.0 22.4 + - - +
428A LEU* 3.5 39.7 + - - +
429A PHE* 4.7 8.2 - - - -
430A GLY* 3.9 13.3 - - - +
683C LEU* 5.1 6.1 - - + -
687C HIS* 3.2 25.8 + - + +
690C LEU* 4.3 9.2 - - + -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A SER 3.1 10.6 + - - -
275A LEU 3.8 2.9 - - - -
277A LYS* 1.3 81.0 - - - +
279A ALA* 1.3 56.6 + - - +
353A ARG* 3.2 33.6 + - - -
354A PRO* 5.9 3.4 - - - -
404A ASN* 3.0 25.8 + - - -
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Residues in contact with ALA 279 (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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254A ILE* 5.3 0.4 - - - -
275A LEU 3.0 15.8 + - - +
276A LEU* 6.3 0.4 - - + -
278A GLY* 1.3 76.2 - - - +
280A ALA* 1.3 65.1 + - - +
281A PHE 3.4 2.7 - - - -
282A GLU* 3.1 6.7 + - - +
283A LEU* 2.9 33.8 + - + +
347A SER* 3.7 16.8 - - - +
348A LEU* 4.0 12.6 - - + -
353A ARG* 3.5 20.6 - - - +
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Residues in contact with ALA 280 (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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251A PHE* 3.7 24.9 - - + +
254A ILE* 4.4 14.5 - - + +
255A ILE* 6.5 0.4 - - + -
276A LEU* 2.9 24.3 + - + +
277A LYS 4.1 4.7 + - - +
278A GLY 3.8 1.0 - - - -
279A ALA* 1.3 70.1 - - - +
281A PHE* 1.3 61.1 + - - +
283A LEU* 4.1 1.2 - - - +
284A CYS* 2.9 31.4 + - - -
428A LEU* 4.3 21.1 - - + -
429A PHE* 5.0 2.7 - - + -
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Residues in contact with PHE 281 (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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251A PHE* 3.9 12.1 - + - -
277A LYS 5.4 0.6 + - - -
279A ALA 3.4 1.0 - - - -
280A ALA* 1.3 76.7 - - - +
282A GLU* 1.3 60.6 + - + +
284A CYS* 3.3 5.4 + - + +
285A GLN* 3.0 60.2 + - + +
323A MET* 4.0 15.0 - - - -
400A LEU* 4.4 4.7 - - + -
403A ILE* 4.2 3.1 - - + -
404A ASN* 3.3 54.0 - - + +
407A HIS* 3.4 41.1 - + + -
429A PHE* 4.5 15.7 - + + -
1433A D7E 3.5 26.0 - - + -
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Residues in contact with GLU 282 (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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278A GLY 4.2 0.4 - - - -
279A ALA 3.1 7.0 + - - +
281A PHE* 1.3 75.1 - - + +
283A LEU* 1.3 65.7 + - - +
285A GLN* 3.3 2.1 + - - +
286A LEU* 3.0 27.5 + - - +
347A SER* 2.8 32.4 + - - +
353A ARG* 2.8 35.8 + - - -
397A LEU* 4.8 3.8 - - - +
400A LEU* 3.7 30.9 - - + +
401A ARG* 3.5 24.8 + - - +
404A ASN* 3.0 27.3 + - + +
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Residues in contact with LEU 283 (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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254A ILE* 3.6 33.4 - - + -
257A PHE* 4.0 22.2 - - + -
279A ALA* 2.9 26.7 + - + +
282A GLU* 1.3 71.9 - - - +
284A CYS* 1.3 62.6 + - - +
286A LEU* 3.3 7.6 + - + +
287A ARG* 3.1 27.2 + - - +
344A GLN* 3.4 48.9 - - + +
347A SER* 3.2 28.3 - - - +
348A LEU* 4.1 9.4 - - + +
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Residues in contact with CYS 284 (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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247A SER* 6.0 0.2 - - - -
250A MET* 3.6 27.8 - - + +
251A PHE* 3.1 33.4 - - + -
254A ILE* 3.7 14.4 - - - -
280A ALA 2.9 26.5 + - - +
281A PHE* 3.4 6.1 - - - +
283A LEU* 1.3 76.9 - - - +
285A GLN* 1.3 60.5 + - - +
287A ARG* 3.3 6.4 + - - +
288A PHE* 2.9 41.7 + - + -
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Residues in contact with GLN 285 (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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281A PHE* 3.0 48.6 + - + +
282A GLU 3.3 4.7 + - - +
284A CYS* 1.3 75.0 - - - +
286A LEU* 1.3 61.0 + - - +
288A PHE* 3.3 16.3 + - - -
289A ASN* 2.9 26.0 + - - +
323A MET* 3.5 18.2 - - + +
326A PHE* 5.2 2.2 - - + -
327A HIS* 2.9 36.8 + - - -
400A LEU* 4.2 8.3 - - + -
1433A D7E 3.3 49.3 + - - +
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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
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282A GLU 3.0 23.0 + - - +
283A LEU* 3.6 8.1 - - - +
285A GLN* 1.3 75.4 - - - +
287A ARG* 1.3 63.0 + - - +
289A ASN* 3.4 17.0 + - - +
290A THR* 3.6 12.5 + - - +
326A PHE* 4.4 2.7 - - + -
330A LEU* 3.9 15.7 - - + -
340A TYR* 3.8 10.4 - - + -
343A MET* 3.5 40.2 - - + +
344A GLN* 3.9 44.6 - - + +
347A SER* 4.6 4.3 - - - -
397A LEU* 4.3 8.1 - - + -
400A LEU* 4.0 15.3 - - + -
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLN* 2.8 27.2 + - - -
161A THR* 2.9 45.3 + - - -
162A PHE* 3.6 50.4 - - + +
250A MET* 3.8 15.9 + - + +
253A GLY* 3.4 20.2 + - - -
254A ILE* 3.4 25.4 - - + +
257A PHE* 3.6 12.1 - - - +
283A LEU 3.1 11.2 + - - +
284A CYS 3.6 7.4 - - - +
285A GLN 3.3 0.2 - - - -
286A LEU* 1.3 74.1 - - - +
288A PHE* 1.3 63.9 + - - +
290A THR* 2.7 25.8 + - - -
291A VAL* 3.7 2.4 + - - +
344A GLN* 3.5 17.0 + - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PHE* 4.3 11.0 - + - -
246A MET* 4.0 19.1 - - + -
247A SER* 6.0 1.8 - - - -
250A MET* 3.4 41.7 - - + -
284A CYS* 2.9 26.5 + - + +
285A GLN* 3.3 23.5 + - - +
287A ARG* 1.3 75.4 - - - +
289A ASN* 1.3 63.1 + - - +
291A VAL* 3.0 29.3 + - + +
292A PHE 3.2 8.5 + - - -
299A TRP* 3.4 12.6 - + + -
301A CYS* 4.3 4.7 - - - -
327A HIS* 4.1 10.1 - - + -
1433A D7E 3.6 48.0 - + + -
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Residues in contact with ASN 289 (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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285A GLN 2.9 13.6 + - - +
286A LEU 3.5 11.2 - - - +
287A ARG 3.2 0.4 - - - -
288A PHE* 1.3 78.6 - - - +
290A THR* 1.3 59.1 + - - +
292A PHE* 3.1 15.3 + - - +
326A PHE* 5.5 0.2 - - + -
327A HIS* 2.9 48.5 + - - +
330A LEU* 3.6 25.7 - - + +
331A LYS* 3.3 21.2 + - - +
340A TYR* 2.5 33.5 + - + -
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Residues in contact with THR 290 (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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158A GLN* 5.8 3.4 - - - +
162A PHE* 3.4 22.5 - - + -
164A THR* 5.7 0.3 - - - +
286A LEU 3.6 14.1 - - - +
287A ARG* 2.7 18.9 + - - +
289A ASN* 1.3 76.0 - - - +
291A VAL* 1.3 61.3 + - - +
331A LYS* 3.5 14.2 + - - +
337A GLU* 4.9 10.5 - - - +
340A TYR* 3.7 38.4 - - + -
344A GLN* 6.0 0.2 - - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PHE* 4.5 7.4 - - + -
164A THR* 4.3 19.5 - - - +
166A PHE* 4.3 10.5 - - + -
287A ARG 4.3 1.8 - - - +
288A PHE* 3.0 28.5 + - + +
290A THR* 1.3 86.7 + - - +
292A PHE* 1.3 60.3 + - - +
293A ASN 3.7 0.5 + - - -
299A TRP* 4.4 3.1 - - + -
300A GLU* 2.8 54.0 + - - +
301A CYS* 4.1 19.7 - - - -
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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