Contacts of the helix formed by residues 268 - 291 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP 3.8 2.2 - - - +
267B LEU* 1.3 89.6 - - + +
269B ILE* 1.3 66.0 + - - +
270B GLU* 4.3 13.9 - - + +
271B ASP* 3.1 25.2 + - - +
272B GLN* 3.1 10.2 + - - +
357B LEU* 6.2 1.6 - - + -
358B GLN* 3.9 32.3 - - + +
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Residues in contact with ILE 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU 3.7 1.4 + - - -
268B PRO* 1.3 71.2 - - - +
270B GLU* 1.3 94.3 + - - +
272B GLN* 3.4 16.0 + - - +
273B ILE* 3.1 25.1 + - + +
684D THR* 3.9 8.7 - - + -
691D HIS* 3.8 28.3 - - + +
694D LEU* 3.6 41.7 - - + -
695D GLN* 5.4 3.4 - - + -
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B PRO* 3.1 10.4 - - + +
269B ILE* 1.3 104.7 + - - +
271B ASP* 1.3 60.5 + - - +
273B ILE* 3.4 8.5 + - - +
274B SER* 3.0 30.7 + - - +
355B GLY 5.4 2.5 - - - +
357B LEU* 5.3 13.0 - - + -
682D SER 5.7 2.2 - - - +
683D LEU* 4.3 30.2 + - + +
684D THR* 3.1 17.3 + - - +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.5 11.1 - - + +
268B PRO* 3.1 21.6 + - + +
270B GLU* 1.3 76.7 - - - +
272B GLN* 1.4 56.9 - - - +
274B SER* 3.7 4.6 - - - -
275B LEU* 2.8 42.2 + - + +
355B GLY 3.7 4.5 - - - +
356B VAL* 3.4 16.2 - - + +
357B LEU* 2.8 30.2 + - - +
358B GLN* 2.9 41.1 + - - +
362B VAL* 5.0 0.4 - - + +
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Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE* 3.2 46.5 + - + +
265B ARG* 3.1 22.6 + - - +
267B LEU* 2.9 25.4 + - + +
268B PRO 3.1 11.4 + - - +
269B ILE* 3.4 23.3 - - - +
270B GLU 3.3 0.2 - - - -
271B ASP* 1.4 73.9 - - - +
273B ILE* 1.3 62.4 + - - +
275B LEU* 3.9 0.4 - - - +
276B LEU* 3.0 31.5 + - - +
694D LEU* 3.7 25.6 - - + +
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Residues in contact with ILE 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 3.1 18.9 + - + +
270B GLU* 3.5 7.6 - - - +
272B GLN* 1.3 77.1 - - - +
274B SER* 1.3 62.7 + - - +
276B LEU* 3.3 5.2 + - - +
277B LYS* 3.0 46.9 + - + +
683D LEU* 4.2 13.9 - - + +
684D THR* 4.0 37.7 - - + +
687D HIS* 4.1 24.9 - - + +
690D LEU* 4.2 12.9 - - + +
691D HIS* 4.7 9.2 - - - +
694D LEU* 3.7 18.6 - - + -
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 3.0 17.5 + - - +
271B ASP* 3.2 5.8 + - - -
273B ILE* 1.3 77.2 - - - +
275B LEU* 1.3 63.5 + - - +
277B LYS* 3.5 9.0 + - - +
278B GLY* 3.2 19.1 + - - -
353B ARG* 4.2 8.1 - - - +
354B PRO 3.9 17.6 + - - +
355B GLY* 3.4 26.8 + - - -
356B VAL* 4.1 8.7 - - - -
683D LEU* 4.3 13.2 - - - +
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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
----------------------------------------------------------
264B PHE* 4.1 17.3 - - + -
267B LEU* 3.5 32.5 - - + -
271B ASP* 2.8 23.5 + - + +
272B GLN 3.9 3.1 - - - +
274B SER* 1.3 72.2 - - - +
276B LEU* 1.3 56.4 + - - +
278B GLY* 3.3 2.4 + - - -
279B ALA* 3.0 32.1 + - - +
348B LEU* 3.5 26.2 - - + +
349B PHE* 4.5 7.2 - - + -
350B SER 3.4 27.4 - - - +
353B ARG* 4.2 6.4 + - + -
356B VAL* 3.8 16.8 - - + -
362B VAL* 4.3 13.0 - - + -
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 4.2 14.4 - - + +
255B ILE* 4.0 33.7 - - + -
258B ALA* 3.9 21.5 - - + -
264B PHE* 3.9 17.7 - - + -
272B GLN 3.0 21.3 + - - +
273B ILE* 3.3 4.9 + - - +
275B LEU* 1.3 73.0 - - - +
277B LYS* 1.3 61.2 + - - +
279B ALA 4.5 0.4 - - - +
280B ALA* 2.9 37.6 + - + +
348B LEU* 4.3 9.4 - - + -
428B LEU* 4.3 10.8 - - + -
690D LEU* 4.9 7.9 - - + -
694D LEU* 3.9 25.1 - - + -
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 3.0 33.1 + - + +
274B SER* 3.8 8.1 - - - +
276B LEU* 1.3 77.4 - - - +
278B GLY* 1.3 62.7 + - - +
279B ALA 3.5 0.2 + - - -
280B ALA* 4.1 5.9 + - - +
281B PHE 5.4 0.5 + - - -
354B PRO 6.1 1.3 - - - -
404B ASN* 5.3 1.2 + - - -
427B GLU 3.0 23.3 + - - +
428B LEU* 3.5 33.6 + - - +
429B PHE* 4.7 7.6 - - - -
430B GLY* 4.0 12.1 - - - +
683D LEU* 4.9 5.6 - - + -
687D HIS* 3.3 26.2 + - + +
690D LEU* 4.1 15.9 - - + -
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER 3.2 9.8 + - - -
275B LEU 3.7 2.9 - - - -
277B LYS* 1.3 81.9 - - - +
279B ALA* 1.3 57.6 + - - +
353B ARG* 3.1 35.2 + - - -
354B PRO* 6.0 2.7 - - - -
404B ASN* 3.0 24.7 + - - -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 5.3 0.7 - - - -
275B LEU 3.0 16.2 + - - +
276B LEU* 4.7 0.7 - - - +
278B GLY* 1.3 78.7 - - - +
280B ALA* 1.3 64.2 + - - +
281B PHE 3.3 2.9 - - - -
282B GLU* 3.1 6.4 + - - +
283B LEU* 2.9 30.2 + - + +
347B SER* 3.7 18.4 - - - +
348B LEU* 4.0 15.5 - - + -
353B ARG* 3.5 18.6 - - - +
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Residues in contact with ALA 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 3.7 24.5 - - + +
254B ILE* 4.4 14.6 - - + +
255B ILE* 6.4 1.3 - - + -
276B LEU* 2.9 21.0 + - + +
277B LYS 4.1 4.4 + - - +
278B GLY 3.8 1.2 - - - -
279B ALA* 1.3 73.5 - - - +
281B PHE* 1.3 62.3 + - - +
283B LEU* 3.6 1.0 + - - +
284B CYS* 3.0 29.1 + - - -
428B LEU* 4.1 21.8 - - + -
429B PHE* 5.1 2.0 - - + -
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PHE* 4.0 12.0 - + - -
277B LYS 5.4 0.8 + - - -
279B ALA 3.3 0.6 - - - -
280B ALA* 1.3 76.5 - - - +
282B GLU* 1.3 62.8 + - + +
284B CYS* 3.3 3.9 + - + +
285B GLN* 3.0 56.6 + - + +
323B MET* 4.0 20.2 - - + -
400B LEU* 4.4 4.5 - - + -
403B ILE* 4.2 3.4 - - + -
404B ASN* 3.3 54.2 - - + +
407B HIS* 3.3 42.2 - + + -
429B PHE* 4.4 15.6 - + + -
1432B D7E 3.4 23.1 - - + -
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLY 4.2 0.2 - - - -
279B ALA 3.1 5.1 + - - +
281B PHE* 1.3 78.1 - - + +
283B LEU* 1.3 62.6 + - - +
285B GLN* 3.3 1.6 + - - -
286B LEU* 3.0 27.9 + - - +
347B SER* 2.8 35.0 + - - +
353B ARG* 2.8 36.1 + - - -
397B LEU* 4.9 3.8 - - - +
400B LEU* 3.7 30.2 - - + +
401B ARG* 3.5 25.2 + - - +
404B ASN* 3.0 27.2 + - + +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 3.6 33.7 - - + -
257B PHE* 3.9 23.6 - - + -
279B ALA* 2.9 23.7 + - + +
280B ALA 4.2 0.2 - - - +
282B GLU* 1.3 72.0 - - - +
284B CYS* 1.3 62.2 + - - +
286B LEU* 3.3 8.3 + - + +
287B ARG* 3.1 26.5 + - - +
344B GLN* 3.4 48.5 - - + +
347B SER* 3.3 25.6 - - - +
348B LEU* 4.0 12.8 - - + +
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Residues in contact with CYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B SER* 5.9 0.2 - - - -
250B MET* 3.6 27.1 - - + +
251B PHE* 2.9 42.2 - - + -
254B ILE* 3.6 15.7 - - - -
280B ALA 3.0 19.2 + - - +
281B PHE* 3.4 5.6 - - - +
283B LEU* 1.3 75.6 - - - +
285B GLN* 1.3 59.6 + - - +
287B ARG* 3.2 7.0 + - - +
288B PHE* 2.8 40.5 + - + -
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.0 44.8 + - + +
282B GLU 3.3 4.5 + - - +
284B CYS* 1.3 76.3 - - - +
286B LEU* 1.3 60.7 + - - +
288B PHE* 3.3 19.0 + - - -
289B ASN* 2.9 26.0 + - - +
323B MET* 3.6 17.9 - - + +
326B PHE* 5.2 2.8 - - + -
327B HIS* 2.9 37.0 + - - -
400B LEU* 4.4 8.3 - - + -
1432B D7E 3.2 48.2 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLU 3.0 21.9 + - - +
283B LEU* 3.6 9.6 - - + +
284B CYS 3.3 0.2 - - - -
285B GLN* 1.3 74.6 - - - +
287B ARG* 1.3 62.7 + - - +
289B ASN* 3.3 16.8 + - - +
290B THR* 3.6 13.0 - - - +
326B PHE* 4.4 2.0 - - + -
330B LEU* 3.9 15.9 - - + -
340B TYR* 3.8 10.6 - - + -
343B MET* 3.5 39.9 - - + +
344B GLN* 3.8 45.3 - - + +
347B SER* 4.7 1.6 - - - -
397B LEU* 4.4 7.9 - - + -
400B LEU* 4.0 17.3 - - + -
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 2.8 27.0 + - - -
161B THR* 2.9 44.1 + - - -
162B PHE* 3.6 46.4 - - + +
250B MET* 3.7 19.1 + - + +
253B GLY* 3.4 21.6 + - - -
254B ILE* 3.3 24.3 - - + +
257B PHE* 3.6 11.9 - - - +
283B LEU 3.1 11.2 + - - +
284B CYS 3.2 8.3 + - - +
286B LEU* 1.3 73.2 - - - +
288B PHE* 1.3 63.3 + - - +
290B THR* 2.7 26.9 + - - -
291B VAL* 3.8 2.6 + - - +
344B GLN* 3.5 17.5 + - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 4.4 3.6 - + - -
246B MET* 4.0 17.5 - - + -
247B SER* 5.7 4.3 - - - -
250B MET* 3.4 42.6 - - + -
284B CYS* 2.8 26.7 + - + +
285B GLN* 3.3 22.6 + - - +
287B ARG* 1.3 75.4 - - - +
289B ASN* 1.3 64.0 + - - +
291B VAL* 3.0 29.6 + - + +
292B PHE 3.2 8.5 + - - -
299B TRP* 3.4 17.1 - + + +
301B CYS* 4.3 12.1 - - - -
327B HIS* 4.0 6.7 - - + -
1432B D7E 3.5 46.4 - + + -
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN 2.9 13.8 + - - +
286B LEU 3.5 11.4 - - - +
287B ARG 3.2 0.4 - - - -
288B PHE* 1.3 77.4 - - - +
290B THR* 1.3 59.8 + - - +
292B PHE* 3.1 16.0 + - - +
326B PHE* 5.5 0.2 - - + -
327B HIS* 2.9 55.4 + - + +
330B LEU* 3.4 28.3 - - + +
331B LYS* 3.3 21.9 + - - +
340B TYR* 2.6 26.1 + - + -
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Residues in contact with THR 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLN* 5.8 3.4 - - - +
162B PHE* 3.4 20.8 - - + -
164B THR* 5.8 0.2 - - - +
286B LEU 3.6 15.3 - - - +
287B ARG* 2.7 18.7 + - - +
289B ASN* 1.3 75.0 - - - +
291B VAL* 1.3 61.1 + - - +
331B LYS* 3.6 14.4 + - - +
337B GLU* 5.0 11.9 - - - +
340B TYR* 3.7 38.8 - - + -
344B GLN* 6.0 0.4 - - - +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 4.5 9.4 - - + -
164B THR* 4.4 12.8 - - - +
166B PHE* 4.4 15.7 - - + -
287B ARG 4.3 0.4 - - - +
288B PHE* 3.0 28.1 + - + +
290B THR* 1.3 87.7 + - - +
292B PHE* 1.3 60.6 + - - +
293B ASN 3.7 1.2 + - - -
299B TRP* 4.4 2.9 - - + -
300B GLU* 2.8 54.9 + - - +
301B CYS* 4.1 19.7 - - - -
331B LYS* 4.9 0.2 - - - -
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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