Contacts of the helix formed by residues 313 - 342 (chain B) in PDB entry 2AY6
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 313 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B LEU 5.4 0.2 - - - -
311B THR 3.3 11.9 - - - +
312B THR* 1.3 82.9 - - + +
314B GLU* 1.3 61.8 + - - +
316B ARG* 3.5 6.4 + - + +
317B ALA* 3.1 25.9 + - - +
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Residues in contact with GLU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.1 28.8 + - - -
312B THR* 2.9 9.4 + - + +
313B PRO* 1.3 79.8 - - - +
315B LEU* 1.3 65.5 + - + +
317B ALA* 3.5 5.3 + - - +
318B ASP* 3.3 20.6 + - - +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 3.5 30.3 - - + +
55B ALA* 4.1 9.0 - - + -
56B ALA* 4.4 4.9 - - + +
59B ARG* 3.4 53.6 - - - +
308B THR* 4.2 12.3 - - + +
309B VAL* 3.9 15.3 - - - +
312B THR* 2.7 28.4 + - + +
314B GLU* 1.3 83.0 - - + +
316B ARG* 1.3 63.0 + - - +
317B ALA 3.2 1.6 - - - -
318B ASP* 3.3 4.2 + - + +
319B TRP* 3.0 25.1 + - - +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 5.3 1.4 + - - -
85B GLU* 5.5 5.3 + - - +
86B LEU* 4.8 25.0 - - - +
233B LEU* 5.1 3.2 - - - +
234B GLU* 4.8 11.5 + - - -
309B VAL* 3.3 20.7 + - - +
310B LEU* 3.7 41.5 + - + +
312B THR 2.9 11.8 + - - +
313B PRO* 4.0 6.7 - - + +
315B LEU* 1.3 75.2 - - - +
317B ALA* 1.3 58.7 + - - +
319B TRP* 3.3 11.6 + - + +
320B MET* 2.8 65.2 + - + +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PRO 3.1 18.5 + - - +
314B GLU* 3.6 7.9 - - - +
316B ARG* 1.3 78.2 - - - +
318B ASP* 1.3 63.8 + - - +
320B MET* 3.9 15.6 - - + +
321B ALA* 3.1 23.0 + - - +
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Residues in contact with ASP 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 2.9 60.2 + - - +
52B ALA* 3.9 8.0 + - + -
314B GLU 3.3 10.6 + - - +
315B LEU* 4.0 8.3 - - + +
317B ALA* 1.3 78.7 - - - +
319B TRP* 1.3 58.8 + - - +
321B ALA* 3.4 5.6 + - - +
322B GLU* 3.0 27.1 + - - +
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Residues in contact with TRP 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 3.4 28.8 - - + +
52B ALA* 4.0 10.7 - - + +
53B VAL* 5.4 1.6 - - + -
86B LEU* 4.3 11.4 - - + -
233B LEU* 3.5 35.9 - - + -
259B ASN* 2.7 34.3 + - + -
260B PHE* 3.6 39.9 - + - -
309B VAL* 3.8 13.0 - - + -
310B LEU* 3.8 23.8 - - + -
315B LEU 3.0 17.4 + - - +
316B ARG* 3.5 9.4 - - + +
317B ALA 3.2 0.2 - - - -
318B ASP* 1.3 74.4 - - - +
320B MET* 1.3 83.7 + - + +
322B GLU* 3.2 6.2 + - - +
323B LEU* 3.0 36.1 + - + +
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Residues in contact with MET 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 3.9 17.9 - - + -
316B ARG* 2.8 59.4 + - + +
317B ALA* 3.9 13.9 - - + +
319B TRP* 1.3 88.1 - - + +
321B ALA* 1.3 57.4 + - - +
323B LEU* 3.3 5.0 + - - +
324B GLU* 2.9 30.2 + - - +
327B ARG* 4.3 2.3 + - - -
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 4.6 3.4 - - - +
317B ALA 3.1 16.8 + - - +
318B ASP* 3.6 12.1 - - - +
320B MET* 1.3 77.8 - - - +
322B GLU* 1.3 55.9 + - - +
324B GLU* 3.3 8.5 + - - +
325B ALA* 3.0 27.8 + - - +
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 5.3 7.3 - - - +
49B ILE 4.5 2.1 - - - +
50B MET* 3.4 36.9 - - + +
51B ARG* 3.0 67.2 + - - +
52B ALA 4.5 1.0 + - - -
318B ASP* 3.0 13.4 + - - +
319B TRP* 3.7 5.0 - - - +
321B ALA* 1.3 72.3 - - - +
323B LEU* 1.3 65.2 + - - +
325B ALA* 3.2 9.5 + - + +
326B VAL* 3.0 31.3 + - + +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 3.7 12.7 - - + +
226B GLN 4.4 2.5 - - - +
227B GLY* 4.0 11.9 - - - +
228B PHE* 3.8 36.1 - - + -
233B LEU* 3.6 30.7 - - + -
258B LYS 5.1 0.2 - - - +
259B ASN* 4.0 12.3 - - - +
319B TRP* 3.0 35.3 + - + +
320B MET 3.6 2.0 - - - +
322B GLU* 1.3 76.2 - - - +
324B GLU* 1.3 57.9 + - - +
326B VAL* 3.1 8.1 + - + +
327B ARG* 2.8 52.9 + - - +
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Residues in contact with GLU 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B MET 2.9 17.9 + - - +
321B ALA* 3.5 9.0 - - - +
322B GLU 3.3 0.2 - - - -
323B LEU* 1.3 76.4 - - - +
325B ALA* 1.3 52.8 + - - +
327B ARG* 2.5 47.4 + - - +
328B SER* 2.6 50.3 + - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B ALA 3.0 12.9 + - - +
322B GLU* 3.3 13.2 - - + +
324B GLU* 1.3 74.7 - - - +
326B VAL* 1.3 65.0 + - + +
328B SER* 2.9 18.0 + - - -
329B GLY* 2.9 13.2 + - - -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.6 47.8 - - + +
50B MET* 5.3 4.5 - - + -
228B PHE* 3.3 35.7 - - + -
322B GLU* 3.0 29.3 + - + +
323B LEU* 3.2 12.6 - - + +
325B ALA* 1.3 76.7 - - + +
327B ARG* 1.3 63.9 + - - +
329B GLY* 3.8 0.9 - - - -
330B MET* 3.1 26.1 + - - +
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Residues in contact with ARG 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLY* 2.5 27.1 + - - +
228B PHE* 4.2 11.0 - - + +
229B GLY 3.9 15.3 - - - +
230B ASP 4.1 4.4 + - - -
231B GLY* 3.1 36.2 - - - +
233B LEU* 3.9 9.3 - - - +
320B MET* 4.3 2.8 + - - +
323B LEU* 2.8 44.9 + - - +
324B GLU* 2.5 50.6 + - - +
326B VAL* 1.3 78.1 - - - +
328B SER* 1.3 62.3 + - - +
330B MET* 3.3 8.0 + - - +
331B LEU* 2.9 32.1 + - + +
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Residues in contact with SER 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLU* 2.6 36.7 + - - +
325B ALA* 2.9 16.5 + - - -
327B ARG* 1.3 73.4 - - - +
329B GLY* 1.3 54.9 + - - +
331B LEU* 3.2 11.4 + - - +
332B ARG* 2.9 29.3 + - - +
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Residues in contact with GLY 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ALA 2.9 16.3 + - - -
326B VAL* 3.8 1.3 - - - -
328B SER* 1.3 75.9 - - - +
330B MET* 1.3 62.5 + - - +
332B ARG* 3.1 23.2 + - - +
333B LEU* 2.9 27.8 + - - +
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Residues in contact with MET 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 4.2 16.6 - - + -
228B PHE* 3.9 33.2 - - + +
326B VAL 3.1 17.6 + - - +
327B ARG* 3.6 9.2 - - - +
329B GLY* 1.3 74.7 - - - +
331B LEU* 1.3 65.1 + - + +
333B LEU* 3.0 7.2 + - + -
334B ARG* 3.0 27.1 + - + +
358B GLY 3.3 28.3 - - - +
359B MET* 3.4 28.0 - - + +
389B ILE* 3.4 26.1 - - + +
390B ALA* 4.3 13.0 - - + -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PHE 4.9 3.8 - - - +
229B GLY 4.0 18.8 - - - +
230B ASP* 6.4 0.2 - - - -
327B ARG* 2.9 37.1 + - + +
328B SER* 3.2 11.0 + - - +
330B MET* 1.3 78.0 - - + +
332B ARG* 1.3 62.8 + - - +
334B ARG* 3.3 17.3 + - - +
335B GLU* 3.1 27.6 + - - +
357B ARG* 3.2 33.4 - - - +
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B SER 2.9 14.2 + - - +
329B GLY* 3.1 24.2 + - - +
331B LEU* 1.3 77.0 - - - +
333B LEU* 1.3 66.4 + - - +
335B GLU* 3.3 13.5 - - + +
336B GLN* 3.2 54.1 + - + +
394B ASP* 4.7 5.5 + - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B GLY 2.9 18.9 + - - +
330B MET* 3.0 9.8 + - + +
332B ARG* 1.3 81.8 - - - +
334B ARG* 1.3 66.6 + - - +
335B GLU 3.1 1.6 - - - -
336B GLN* 2.8 36.0 + - - +
337B LEU* 3.0 14.1 + - - +
389B ILE* 3.8 26.7 - - + +
390B ALA* 4.6 7.0 - - - +
392B LEU* 3.3 20.0 - - + +
393B ASN* 3.7 24.2 - - + -
394B ASP* 4.6 2.7 - - - +
397B ILE* 3.8 8.5 - - + +
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Residues in contact with ARG 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B MET* 3.0 18.4 + - - +
331B LEU* 3.6 18.4 - - - +
333B LEU* 1.3 75.2 - - - +
335B GLU* 1.3 57.5 + - - +
337B LEU* 3.4 4.4 + - - +
338B ALA* 3.0 30.5 + - - +
353B VAL* 3.0 37.9 + - + +
354B ALA* 4.5 6.3 - - - +
356B HIS* 3.0 45.8 + - - +
357B ARG* 5.6 1.6 - - - +
358B GLY 2.7 37.8 + - - +
359B MET 4.1 0.2 - - - -
360B PHE 3.1 18.0 + - - -
361B SER* 3.4 13.3 + - - -
389B ILE* 3.7 33.9 - - + +
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 3.1 13.6 + - - +
332B ARG* 3.3 15.4 - - - +
334B ARG* 1.3 79.1 - - - +
336B GLN* 1.3 56.1 + - + +
338B ALA* 3.4 6.2 + - - +
339B GLY* 3.0 24.6 + - - -
354B ALA* 4.8 11.8 - - + +
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ARG* 3.2 33.0 + - + +
333B LEU* 2.8 23.4 + - - +
335B GLU* 1.3 73.6 - - + +
337B LEU* 1.3 55.7 + - - +
339B GLY* 2.9 3.9 + - - -
340B GLU* 2.7 35.1 + - - +
394B ASP* 3.0 25.4 + - - +
397B ILE* 3.2 28.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B LEU 3.0 8.4 + - - +
334B ARG* 3.8 7.6 - - - +
336B GLN* 1.3 76.7 - - - +
338B ALA* 1.3 64.0 + - - +
340B GLU* 3.6 0.5 - - - +
341B LEU* 3.0 44.8 + - + +
353B VAL* 3.8 26.2 - - + -
363B LEU* 6.2 3.1 - - + -
387B ILE* 4.3 17.0 - - + -
389B ILE* 5.6 2.9 - - + -
392B LEU* 5.5 3.8 - - + -
397B ILE* 3.9 34.4 - - + +
400B LEU* 3.6 33.0 - - + -
401B ALA* 4.8 4.0 - - + +
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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
----------------------------------------------------------
334B ARG 3.0 18.3 + - - +
335B GLU* 3.6 5.6 - - + +
337B LEU* 1.3 77.7 - - - +
339B GLY* 1.3 58.1 + - - +
341B LEU* 3.5 4.0 + - - +
342B ARG* 3.0 28.9 + - - +
350B PHE* 4.2 21.1 - - - +
351B GLY* 5.1 4.0 - - - +
353B VAL* 4.4 4.6 - - + +
354B ALA* 4.2 23.1 - - + +
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Residues in contact with GLY 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B GLU 3.0 11.3 + - - -
336B GLN* 2.9 7.3 + - - -
338B ALA* 1.3 73.7 - - - +
340B GLU* 1.3 65.4 + - - +
342B ARG* 3.3 7.8 + - - +
343B ASP* 3.0 34.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN 2.7 18.2 + - - +
337B LEU 3.6 4.5 - - - +
339B GLY* 1.3 71.6 - - - +
341B LEU* 1.3 59.1 + - - +
343B ASP* 3.3 4.9 + - - +
344B LEU* 2.8 38.6 + - + +
397B ILE* 4.1 13.7 - - + +
398B PRO* 3.7 30.5 - - + +
401B ALA* 3.6 24.5 - - + -
----------------------------------------------------------
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.0 36.2 + - + +
338B ALA 3.8 3.6 - - - +
340B GLU* 1.3 79.2 - - - +
342B ARG* 1.3 60.7 + - - +
344B LEU* 2.9 16.9 + - + -
345B SER* 2.8 23.6 + - - -
350B PHE* 3.6 44.4 - - + +
353B VAL* 5.0 4.5 - - + -
363B LEU* 5.4 3.6 - - + -
401B ALA* 3.6 27.8 - - + +
404B ILE* 3.3 32.8 - - + -
405B ILE* 5.1 2.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ALA 3.0 17.9 + - - +
339B GLY* 3.5 8.3 - - - +
340B GLU 3.3 0.2 - - - -
341B LEU* 1.3 75.5 - - - +
343B ASP* 1.3 69.9 + - - +
344B LEU 3.0 1.0 + - - -
346B GLY* 2.9 33.1 + - - -
347B SER 3.5 22.2 - - - +
348B ASP* 3.0 32.9 + - - +
350B PHE* 5.7 0.6 - - - +
----------------------------------------------------------
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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