Contacts of the helix formed by residues 315 - 342 (chain B) in PDB entry 3AFF
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 315 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LEU* 3.7 17.7 - - + -
313B GLU 3.3 10.1 - - - +
314B ILE* 1.4 89.8 - - + +
316B PHE* 1.3 64.7 + - - +
317B GLU* 4.2 25.4 - - + +
318B LEU* 3.0 19.2 + - + +
319B ARG* 3.3 9.6 + - - +
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Residues in contact with PHE 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE 3.6 2.6 + - - -
315B PRO* 1.3 69.7 - - - +
317B GLU* 1.3 54.3 + - - +
319B ARG* 3.0 32.3 + - - +
320B ALA* 2.8 45.4 + - + -
391B ASP* 3.2 52.9 - - + -
394B VAL* 3.9 22.4 - - + -
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Residues in contact with GLU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PRO* 3.2 18.0 - - + +
316B PHE* 1.3 79.8 - - - +
318B LEU* 1.3 63.6 + - - +
320B ALA* 3.5 7.5 + - - +
321B ARG* 3.1 55.4 + - + +
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Residues in contact with LEU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ASN* 4.3 7.4 - - - +
303B ASP* 4.2 11.9 - - + -
304B GLU* 3.5 38.6 - - + +
307B LEU* 3.8 28.0 - - + -
314B ILE* 4.0 4.0 - - + -
315B PRO* 3.0 19.0 + - + +
317B GLU* 1.3 88.1 + - - +
319B ARG* 1.3 60.7 + - - +
321B ARG* 3.3 39.3 + - - +
322B ALA* 2.9 27.4 + - - +
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Residues in contact with ARG 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PRO* 3.7 28.5 - - + +
234B GLY 5.6 0.2 - - - +
235B THR* 4.5 2.3 + - - +
304B GLU* 3.8 8.7 - - - +
314B ILE* 3.7 32.6 + - + -
315B PRO 3.3 6.0 + - - -
316B PHE* 3.0 30.6 + - - +
318B LEU* 1.3 80.2 - - - +
320B ALA* 1.3 56.0 + - - +
322B ALA* 3.4 3.4 + - - +
323B ARG* 3.1 30.5 + - - +
391B ASP 2.8 27.5 + - - -
392B THR* 3.4 17.6 + - - +
394B VAL* 3.3 35.8 + - + +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B PHE* 2.8 34.0 + - + +
317B GLU* 3.7 8.1 - - - +
319B ARG* 1.3 69.8 - - - +
321B ARG* 1.3 63.2 + - - +
323B ARG* 3.4 5.1 - - - +
324B ARG* 3.1 24.5 + - - +
394B VAL* 3.6 18.3 - - + +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLY 5.2 0.4 - - - -
300B ASN* 2.7 38.6 - - - +
303B ASP* 3.4 22.2 + - - -
317B GLU* 3.1 37.8 + - - +
318B LEU* 3.4 26.7 - - - +
320B ALA* 1.3 75.6 - - - +
322B ALA* 1.4 60.7 + - - +
324B ARG* 3.3 38.0 - - - +
325B ASP* 3.1 38.4 + - - -
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 5.9 0.2 - - - +
235B THR* 3.9 17.0 - - + +
297B LEU* 5.8 0.3 - - - +
300B ASN* 3.4 33.5 + - + +
304B GLU* 3.9 13.9 - - - +
318B LEU 2.9 17.3 + - - +
319B ARG 3.7 5.2 - - - +
321B ARG* 1.4 72.4 - - - +
323B ARG* 1.3 65.0 + - - +
325B ASP* 3.3 2.8 + - - +
326B GLN* 3.2 29.9 + - - +
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Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY* 3.5 22.2 + - - +
238B PRO* 3.6 24.3 - - - +
319B ARG 3.1 16.8 + - - +
320B ALA* 3.4 10.3 - - - +
322B ALA* 1.3 75.4 - - - +
324B ARG* 1.3 63.3 + - - +
326B GLN* 3.2 23.8 + - - +
327B VAL* 4.2 6.2 + - - +
372B ASP* 4.7 7.7 + - - -
374B GLU* 3.2 35.1 + - - +
375B ARG* 5.5 2.8 - - - +
378B VAL* 4.5 10.5 - - - +
393B MET 2.6 24.5 + - - -
394B VAL* 3.6 28.8 - - + +
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Residues in contact with ARG 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 5.5 1.8 - - - +
320B ALA 3.1 14.0 + - - +
321B ARG* 3.3 39.5 + - - +
323B ARG* 1.3 79.9 - - - +
325B ASP* 1.3 79.3 + - - +
326B GLN 3.4 0.9 + - - -
327B VAL* 3.5 12.3 - - + +
328B ARG* 3.3 53.5 + - - +
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Residues in contact with ASP 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 3.6 32.1 + - + +
297B LEU* 4.8 4.8 - - + +
300B ASN* 3.0 28.2 + - - +
321B ARG* 3.1 28.1 + - - +
322B ALA 3.8 1.8 - - - +
323B ARG 3.1 0.8 - - - -
324B ARG* 1.3 102.7 + - - +
326B GLN* 1.3 66.3 + - - +
327B VAL 3.3 0.2 - - - -
328B ARG* 3.5 16.2 - - - -
329B ALA* 2.9 27.0 + - - +
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Residues in contact with GLN 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 5.0 0.2 - - - +
235B THR* 4.0 5.4 - - - +
238B PRO* 3.6 39.8 - - + +
239B THR* 3.0 19.0 + - - +
242B SER* 2.6 42.5 + - - +
297B LEU* 3.3 15.7 - - - +
322B ALA* 3.2 24.4 + - - +
323B ARG* 3.2 18.6 + - - +
325B ASP* 1.3 76.4 - - - +
327B VAL* 1.3 62.8 + - + +
329B ALA* 4.0 0.7 - - - +
330B THR* 3.1 35.5 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG 4.3 8.5 - - - +
324B ARG* 3.5 14.6 + - - +
326B GLN* 1.3 76.9 - - + +
328B ARG* 1.3 69.6 + - + +
330B THR* 3.7 7.1 + - - -
331B GLY* 2.8 31.2 + - - -
366B ARG* 4.5 22.7 - - - +
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLN* 3.8 21.8 - - - +
324B ARG* 3.3 55.0 + - - +
325B ASP* 3.5 17.0 - - - +
326B GLN 3.4 0.2 - - - -
327B VAL* 1.3 82.2 - - + +
329B ALA* 1.3 58.6 + - - +
331B GLY* 3.9 0.2 - - - -
332B ARG* 3.0 41.3 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B VAL* 4.5 5.2 - - + -
293B ALA* 3.5 31.6 - - + +
296B GLN* 3.7 10.8 - - - +
297B LEU* 4.2 17.7 - - + +
325B ASP 2.9 18.0 + - - +
326B GLN 4.1 1.3 - - - +
328B ARG* 1.3 75.7 - - - +
330B THR* 1.3 65.3 + - + +
332B ARG* 3.5 0.6 + - - -
333B SER* 2.8 29.4 + - - -
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER* 3.6 37.9 - - - +
245B ILE* 4.0 26.7 - - + -
246B VAL* 4.6 2.5 - - + -
326B GLN 3.1 19.3 + - - +
327B VAL* 3.7 6.8 + - - -
329B ALA* 1.3 76.5 - - + +
331B GLY* 1.3 58.2 + - - +
333B SER* 3.4 5.6 + - - -
334B ILE* 2.9 40.6 + - - +
366B ARG* 4.0 16.9 + - - -
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Residues in contact with GLY 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B VAL 2.8 18.8 + - - -
328B ARG* 5.1 0.2 - - - -
330B THR* 1.3 78.5 + - - +
332B ARG* 1.3 56.0 + - - +
334B ILE* 3.9 3.7 - - - +
335B ALA* 3.0 29.5 + - - +
366B ARG* 6.0 2.9 - - - -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 4.1 32.5 + - - +
292B ALA* 3.8 32.3 + - - +
293B ALA* 4.2 10.3 - - + +
296B GLN* 3.9 28.1 + - - +
328B ARG* 3.0 26.2 + - - +
329B ALA 4.0 2.7 - - - +
331B GLY* 1.3 74.8 - - - +
333B SER* 1.3 61.1 + - - +
335B ALA* 3.4 8.1 + - - +
336B SER* 3.2 25.3 + - - -
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Residues in contact with SER 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 4.7 3.6 - - - -
246B VAL* 3.5 26.9 - - - +
249B ALA* 3.7 21.2 - - - +
290B ILE* 4.9 4.3 - - - -
293B ALA* 3.5 11.1 - - - +
329B ALA 2.8 19.8 + - - -
330B THR* 3.6 6.7 - - - -
332B ARG* 1.3 74.6 - - - +
334B ILE* 1.3 62.0 + - - +
336B SER* 3.3 7.9 + - - -
337B ILE* 3.0 31.4 + - - +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.7 15.0 - - + -
330B THR* 2.9 22.6 + - - +
331B GLY* 4.1 3.6 - - - +
333B SER* 1.3 74.3 - - - +
335B ALA* 1.3 60.8 + - - +
337B ILE* 3.3 6.4 + - + +
338B ASP* 2.9 30.2 + - - +
362B ALA* 3.6 41.5 - - + +
363B HIS* 3.5 34.8 - - + +
366B ARG* 3.6 26.9 - - + -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLY 3.0 18.1 + - - +
332B ARG* 3.6 8.1 - - - +
334B ILE* 1.3 76.2 - - - +
336B SER* 1.3 62.1 + - - +
338B ASP* 3.3 5.4 + - - -
339B ARG* 3.1 41.9 + - - +
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 3.7 12.6 + - - +
289B ASP* 3.6 24.8 + - - +
290B ILE* 3.6 27.7 - - - +
332B ARG 3.2 14.3 + - - -
333B SER 3.4 9.6 - - - -
335B ALA* 1.3 72.3 - - - +
337B ILE* 1.3 65.6 + - - +
339B ARG* 3.4 7.2 + - - +
340B LEU* 3.0 29.2 + - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE 4.8 1.3 - - - +
248B MET 4.0 4.9 - - - +
249B ALA* 3.5 38.4 - - + +
252B ALA* 3.9 16.1 - - + +
333B SER 3.0 17.9 + - - +
334B ILE* 3.6 12.8 - - + +
336B SER* 1.3 76.9 - - - +
338B ASP* 1.3 57.0 + - - +
340B LEU* 3.3 8.7 + - + +
341B PHE* 2.9 27.9 + - + +
355B ILE* 5.4 0.9 - - + +
358B PHE 4.3 2.2 - - - +
359B TRP* 3.7 34.8 - - + -
362B ALA* 3.5 31.0 - - + -
363B HIS* 5.5 1.1 - - + -
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Residues in contact with ASP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B ILE* 2.9 23.6 + - - +
335B ALA* 3.3 6.6 + - - +
337B ILE* 1.3 75.9 - - - +
339B ARG* 1.3 79.5 + - - +
341B PHE* 3.4 7.6 + - - +
342B GLU* 3.2 31.8 + - - +
359B TRP* 2.7 33.3 + - - +
363B HIS* 2.8 23.5 + - - -
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Residues in contact with ARG 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLU* 5.7 4.7 - - - +
286B ALA* 5.8 4.7 - - + -
335B ALA* 3.1 32.5 + - - +
336B SER* 3.7 11.0 - - - +
337B ILE 3.3 0.2 - - - -
338B ASP* 1.3 86.9 + - - +
340B LEU* 1.3 65.5 + - + +
342B GLU* 3.2 39.2 + - - +
343B ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ALA* 4.2 2.2 - - + -
253B TYR* 3.7 47.8 - - + +
256B HIS* 3.7 33.7 - - + +
284B ALA 5.6 2.0 - - - +
286B ALA* 4.1 17.9 - - + -
290B ILE* 4.4 7.4 - - + -
336B SER 3.0 26.8 + - - +
337B ILE* 3.7 7.6 - - - +
339B ARG* 1.3 73.8 - - + +
341B PHE* 1.3 58.7 + - - +
343B ALA* 3.0 12.0 + - + +
344B SER* 2.7 26.8 + - - -
355B ILE* 4.3 14.8 - - + -
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ILE 2.9 17.8 + - - +
338B ASP* 3.5 7.4 - - - +
339B ARG 3.3 0.2 - - - -
340B LEU* 1.3 76.3 - - - +
342B GLU* 1.3 66.3 + - + +
343B ALA 3.3 0.7 + - - -
344B SER 4.0 1.9 + - - -
345B GLY 4.9 0.7 - - - +
348B ALA* 3.5 49.0 - - + +
349B LEU* 3.8 22.7 - - + -
355B ILE* 4.1 21.9 - - + +
356B GLN* 3.7 18.4 - - + -
359B TRP* 3.7 56.5 - + + -
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASP* 3.2 19.6 + - - +
339B ARG* 3.5 33.9 + - - +
340B LEU 3.2 0.2 - - - -
341B PHE* 1.3 87.6 - - + +
343B ALA* 1.3 58.5 + - - +
344B SER 3.6 1.7 + - - -
345B GLY 5.4 1.9 + - - -
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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