Contacts of the helix formed by residues 325 - 354 (chain B) in PDB entry 7A62
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 ASP 325 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 2.5 55.7 + - - +
320B VAL 4.8 2.8 + - - +
323B LYS* 3.2 13.0 - - + +
324B GLY* 1.3 74.8 - - - +
326B ALA* 1.3 58.7 + - - +
327B GLY 2.9 17.5 + - - -
328B LEU* 3.1 22.4 + - + +
329B ARG* 2.9 33.6 + - - +
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Residues in contact with ALA 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLY 4.0 1.6 + - - -
325B ASP* 1.3 70.4 + - - +
327B GLY* 1.3 60.9 + - - +
329B ARG* 3.5 30.4 - - - +
330B GLU* 2.8 31.7 + - - +
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Residues in contact with GLY 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 3.8 6.2 - - - +
197B LEU* 3.2 22.4 - - - +
325B ASP* 2.9 9.2 + - - -
326B ALA* 1.3 79.3 - - - +
328B LEU* 1.3 60.6 + - - +
330B GLU* 3.4 7.1 + - - +
331B ALA* 3.2 17.8 + - - +
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ARG* 4.2 15.9 - - + +
196B LEU* 3.8 30.5 - - + -
197B LEU* 3.5 37.9 - - + +
200B LEU* 4.4 7.3 - - + +
319B PHE* 4.5 12.3 - - + -
320B VAL* 3.7 17.3 - - + +
323B LYS* 4.7 10.5 - - + -
325B ASP* 3.1 37.3 + - + +
327B GLY* 1.3 72.1 - - - +
329B ARG* 1.3 67.5 + - - +
331B ALA* 3.3 2.0 + - - +
332B TYR* 2.9 24.3 + - - +
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Residues in contact with ARG 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 3.7 22.2 - - + +
321B LEU* 5.5 3.6 - - - +
324B GLY* 3.8 9.6 - - - -
325B ASP 2.9 30.4 + - - +
326B ALA* 3.5 40.4 - - - +
328B LEU* 1.3 74.8 - - - +
330B GLU* 1.3 58.4 + - - +
332B TYR* 3.3 1.6 + - - +
333B ASP* 2.8 35.0 + - - +
400B LEU* 3.3 32.1 - - + +
401B LYS 3.7 6.5 + - - +
402B GLU* 3.3 47.8 + - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 5.9 4.9 - - + +
326B ALA 2.8 18.7 + - - +
327B GLY* 3.7 6.8 - - - +
328B LEU 3.2 0.2 - - - -
329B ARG* 1.3 77.9 - - - +
331B ALA* 1.3 56.7 + - - +
333B ASP* 3.3 7.1 + - - +
334B ALA* 2.8 27.8 + - + +
337B LYS* 5.9 3.3 + - - +
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LEU* 4.1 11.0 - - + +
200B LEU* 3.7 23.1 - - + +
201B LEU* 3.6 33.0 - - + -
327B GLY 3.2 13.7 + - - +
328B LEU 3.9 3.4 - - - +
330B GLU* 1.3 76.2 - - - +
332B TYR* 1.3 66.8 + - - +
334B ALA* 3.1 11.9 + - - +
335B CYS* 3.1 17.7 + - - -
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Residues in contact with TYR 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.3 8.8 - - + +
277B LEU* 2.6 51.1 + - + +
279B ILE* 4.7 1.9 - - - +
316B VAL* 4.4 13.9 - - + -
317B ARG* 3.0 44.6 + - + +
320B VAL* 4.1 18.4 - - + -
328B LEU 2.9 16.8 + - - +
329B ARG 3.6 2.9 - - - +
331B ALA* 1.3 77.5 - - - +
333B ASP* 1.3 69.8 + - - +
335B CYS* 3.1 10.5 + - - +
336B VAL* 3.0 39.0 + - + +
398B SER 3.9 3.5 + - - -
400B LEU* 3.4 29.4 - - + -
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Residues in contact with ASP 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ARG 2.8 17.0 + - - +
330B GLU* 3.6 7.1 - - + +
332B TYR* 1.3 84.7 - - - +
334B ALA* 1.3 57.6 + - - +
336B VAL* 3.0 1.8 + - - +
337B LYS* 2.7 50.7 + - - +
399B LEU* 3.7 20.2 - - + +
400B LEU* 2.7 49.0 + - - +
401B LYS* 4.0 6.9 + - - +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 4.4 10.5 - - + -
204B ALA* 3.6 18.8 - - + +
208B GLU* 5.3 0.3 - - - +
330B GLU* 2.8 16.4 + - + +
331B ALA* 3.1 14.5 + - - +
333B ASP* 1.3 75.0 - - - +
335B CYS* 1.3 63.1 + - - +
337B LYS* 4.0 10.7 - - - +
338B ALA* 3.1 23.6 + - - +
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Residues in contact with CYS 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 3.2 42.6 - - - -
203B ILE* 3.8 15.7 - - + -
204B ALA* 3.8 16.6 - - - +
207B LEU* 4.3 5.4 - - + +
276B LEU* 6.5 0.2 - - - -
277B LEU* 3.8 24.1 - - + +
331B ALA 3.1 13.7 + - - -
332B TYR 3.1 8.8 + - - +
334B ALA* 1.3 74.6 - - - +
336B VAL* 1.3 66.2 + - - +
338B ALA* 3.3 3.7 + - - +
339B LEU* 3.1 22.2 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B LEU* 4.0 18.2 - - + -
279B ILE* 4.6 6.7 - - + -
332B TYR* 3.0 40.6 + - + +
333B ASP 3.0 7.0 + - - +
335B CYS* 1.3 74.4 - - - +
337B LYS* 1.3 63.3 + - - +
339B LEU* 3.3 5.5 + - - +
340B VAL* 2.9 22.4 + - + +
395B THR* 3.5 31.6 - - + +
398B SER* 4.5 3.4 - - - +
399B LEU* 3.7 27.1 - - + +
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Residues in contact with LYS 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 4.9 1.8 - - - +
330B GLU* 5.9 3.2 + - - +
333B ASP* 2.7 35.2 + - - +
334B ALA* 4.0 7.8 - - - +
336B VAL* 1.3 73.7 - - - +
338B ALA* 1.3 58.0 + - - +
340B VAL* 3.0 10.6 + - - +
341B SER* 2.8 33.4 + - - +
399B LEU* 3.8 22.9 - - + -
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Residues in contact with ALA 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ALA* 4.1 8.7 - - - +
207B LEU* 3.8 27.0 - - + +
208B GLU* 3.5 28.0 + - + +
211B LEU* 5.6 0.5 - - - +
334B ALA 3.1 17.4 + - - +
335B CYS 3.7 5.2 - - - +
337B LYS* 1.3 75.2 - - - +
339B LEU* 1.3 62.9 - - - +
341B SER* 3.2 5.0 + - - -
342B LEU* 3.0 28.2 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 4.5 7.0 - - + +
269B VAL 5.6 0.2 - - - +
270B PHE* 4.1 31.0 - - + +
273B PHE* 4.0 19.1 - - + +
274B ASP* 3.7 37.2 - - - +
277B LEU* 4.5 9.4 - - + -
279B ILE* 4.9 1.6 - - + -
335B CYS 3.1 11.7 + - - +
336B VAL* 3.6 8.3 - - - +
337B LYS 3.2 0.2 - - - -
338B ALA* 1.3 74.6 - - - +
340B VAL* 1.3 65.7 + - - +
342B LEU* 3.3 15.1 + - + +
343B ARG* 3.2 38.8 + - - +
395B THR* 4.2 10.3 - - + -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL* 2.9 20.9 + - + +
337B LYS* 3.0 11.2 + - - +
339B LEU* 1.3 75.9 - - - +
341B SER* 1.3 65.3 + - - +
343B ARG* 3.1 7.5 + - - +
344B SER* 2.9 30.6 + - - +
392B ARG* 4.4 10.6 - - + +
395B THR* 3.7 21.8 - - + -
396B GLU* 3.7 41.3 - - + +
399B LEU* 5.5 2.5 - - + -
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 4.4 5.2 + - - -
211B LEU* 3.9 23.7 - - - +
337B LYS* 2.8 21.0 + - - +
338B ALA* 3.5 11.0 - - - -
340B VAL* 1.3 74.4 - - - +
342B LEU* 1.3 57.7 + - - +
344B SER* 3.3 6.7 + - - -
345B TYR* 2.8 31.9 + - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B VAL* 5.6 3.6 - - + -
207B LEU* 4.3 29.8 - - + +
210B ALA* 4.4 8.7 - - + -
211B LEU* 3.9 37.7 - - + +
214B PHE* 4.4 16.5 - - + -
269B VAL* 5.7 2.0 - - + -
270B PHE* 3.9 31.5 - - + -
338B ALA 3.0 19.2 + - - +
339B LEU* 3.5 19.5 - - + +
340B VAL 3.2 0.2 - - - -
341B SER* 1.3 77.8 - - - +
343B ARG* 1.3 52.4 + - - +
345B TYR* 3.7 0.9 - - - +
346B HIS* 2.7 37.8 + - - +
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Residues in contact with ARG 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B PHE* 3.4 31.4 - - + +
271B GLN* 5.3 1.4 - - - +
274B ASP* 2.8 37.0 + - - -
292B LEU* 5.6 1.2 - - - +
339B LEU* 3.2 24.7 + - - +
340B VAL* 3.1 7.9 + - - +
342B LEU* 1.3 76.7 - - - +
344B SER* 1.3 57.3 + - - +
346B HIS* 3.4 10.1 + - - +
347B LEU* 2.9 30.8 + - - +
388B LEU* 5.3 1.7 - - - +
391B VAL* 3.2 26.4 - - - +
392B ARG* 4.0 29.3 - - + +
395B THR* 3.0 20.5 + - - -
503B HEM 2.6 34.5 + - - +
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Residues in contact with SER 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 2.9 20.5 + - - +
341B SER* 3.6 7.6 - - - -
343B ARG* 1.3 74.3 - - - +
345B TYR* 1.3 65.2 + - - +
347B LEU* 3.1 13.5 + - - +
348B GLN* 3.2 20.7 + - - +
392B ARG* 3.0 38.6 + - - +
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Residues in contact with TYR 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.6 15.7 - - + -
214B PHE* 3.9 40.2 - + + -
215B HIS* 3.2 43.7 - + - -
218B HIS* 3.0 33.2 + - - -
341B SER 2.8 20.7 + - - +
342B LEU 3.8 1.3 - - - +
344B SER* 1.3 69.8 - - - +
346B HIS* 1.3 68.2 + - - +
348B GLN* 2.8 41.5 + - + +
349B ILE* 3.0 27.5 + - + -
218C HIS 5.4 0.5 + - - -
219C ASP* 5.0 2.8 + - - -
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Residues in contact with HIS 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 4.2 16.8 - + + -
270B PHE* 4.7 7.9 - + + -
342B LEU 2.7 23.8 + - - +
343B ARG* 3.6 11.7 + - - +
345B TYR* 1.3 73.0 - - - +
347B LEU* 1.3 61.1 + - - +
349B ILE* 3.3 6.2 + - + +
350B VAL* 3.1 25.6 + - + +
388B LEU* 3.7 24.9 - - + +
503B HEM 2.3 96.6 + + + -
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B ARG 2.9 14.0 + - - +
344B SER 3.3 10.1 - - - +
345B TYR 3.0 0.4 - - - -
346B HIS* 1.3 76.6 - - - +
348B GLN* 1.3 64.8 + - - +
350B VAL* 3.3 2.2 + - + +
351B THR* 3.0 25.6 + - - -
385B MET* 3.5 36.8 - - + +
388B LEU* 3.9 30.1 - - + +
389B LYS* 3.8 30.1 - - + -
392B ARG* 4.1 27.6 - - + +
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 6.5 0.4 - - + -
344B SER* 3.2 15.0 + - - +
345B TYR* 2.8 33.7 + - + +
347B LEU* 1.3 77.7 - - + +
349B ILE* 1.3 62.1 + - + +
351B THR* 3.2 9.0 + - - +
352B LYS* 2.9 29.1 + - - +
219C ASP* 5.2 5.4 - - - +
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Residues in contact with ILE 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B PHE* 4.1 14.4 - - + -
217B ILE* 3.8 16.4 - - + -
218B HIS* 3.6 35.7 - - + +
345B TYR* 3.0 29.5 + - + +
346B HIS* 3.6 9.9 - - - +
347B LEU 3.2 0.2 - - - -
348B GLN* 1.3 79.7 - - + +
350B VAL* 1.3 57.5 + - - +
352B LYS* 4.7 0.2 - - - -
353B TYR* 2.8 43.1 + - + +
503B HEM 3.4 38.4 - - + -
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Residues in contact with VAL 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B HIS* 3.1 29.0 + - + +
347B LEU* 3.8 5.8 - - + +
348B GLN 3.3 0.2 - - - -
349B ILE* 1.3 75.5 - - - +
351B THR* 1.3 58.7 + - - +
354B ILE* 2.8 36.9 + - + +
355B LEU* 3.0 16.5 + - + -
384B LEU* 3.9 29.4 - - + -
385B MET* 4.9 3.1 - - - -
388B LEU* 3.7 25.8 - - + -
503B HEM 3.9 23.1 - - + +
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Residues in contact with THR 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU 3.0 14.6 + - - -
348B GLN* 3.4 12.6 - - - +
350B VAL* 1.3 77.7 - - - +
352B LYS* 1.3 62.9 + - + +
355B LEU* 3.3 26.1 - - + +
356B ILE* 3.0 51.3 + - + +
385B MET* 4.4 8.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B HIS* 2.7 47.6 + - + +
221B VAL 5.4 0.2 + - - -
223B PRO* 3.9 25.7 - - + +
348B GLN 2.9 16.2 + - - +
349B ILE* 3.9 3.4 - - - +
351B THR* 1.3 79.9 - - + +
353B TYR* 1.3 82.9 + - + +
356B ILE* 4.3 10.1 - - + +
357B PRO* 3.1 20.6 - - - +
146C GLU* 4.5 10.0 + - - -
216C GLN* 6.1 0.6 - - - +
219C ASP* 4.2 13.7 + - - +
220C HIS* 4.5 7.1 + - - -
----------------------------------------------------------
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ILE* 3.3 21.3 + - + -
218B HIS* 3.7 10.5 - - - -
221B VAL* 2.7 54.1 + - + -
223B PRO* 3.8 23.0 - - + +
226B PHE* 3.6 19.6 - - + -
227B PHE* 3.7 6.1 - - - +
349B ILE* 2.8 51.3 + - + +
352B LYS* 1.3 104.1 + - + +
354B ILE* 1.3 68.2 + - - +
357B PRO* 3.7 12.1 - - - +
503B HEM 3.9 22.0 - - + -
----------------------------------------------------------
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 3.6 20.4 - - + -
227B PHE* 3.5 16.9 - - + -
231B ARG* 4.4 13.7 - - + -
350B VAL* 2.8 26.1 + - + +
352B LYS 3.5 0.2 - - - -
353B TYR* 1.3 81.9 - - - +
355B LEU* 1.3 61.7 + - + +
356B ILE 3.4 1.3 - - - -
357B PRO* 3.3 1.9 - - - +
358B ALA* 2.9 32.7 + - - +
379B THR* 4.0 27.6 - - + +
380B GLY* 4.6 0.7 - - - -
384B LEU* 4.2 18.6 - - + -
503B HEM 3.6 28.5 - - + -
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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