Contacts of the helix formed by residues 321 - 345 (chain B) in PDB entry 1EJI
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 THR 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MSE 3.7 15.9 - - - -
317B LYS* 3.8 12.3 - - + +
318B GLN* 2.8 27.8 + - + +
319B ALA 4.0 1.4 - - - +
320B MSE 1.3 83.1 - - - +
322B THR* 1.3 60.7 + - - +
323B GLU* 3.5 14.0 + - - +
324B PHE* 3.0 17.8 + - - +
325B LYS* 3.2 21.5 + - - +
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Residues in contact with THR 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.5 28.0 - - + -
321B THR* 1.3 71.7 - - - +
323B GLU* 1.3 69.8 + - - +
324B PHE 2.9 1.8 - - - -
325B LYS* 3.1 13.7 + - + +
326B ILE* 2.8 29.8 + - + +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.2 12.3 - - + +
17A SER* 3.2 37.8 + - - -
18A HIS* 3.5 25.8 - - + +
21A MSE 4.2 12.4 - - + +
321B THR* 3.6 14.5 - - - +
322B THR* 1.3 89.7 + - - +
324B PHE* 1.3 56.8 + - - +
326B ILE* 2.8 24.7 - - - +
327B TYR* 3.1 14.0 + - - +
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MSE 4.7 2.5 - - + -
234B GLY* 3.8 15.7 - - - -
237B ALA* 4.6 1.3 - - + -
238B ALA* 4.2 11.2 - - + -
258B THR 3.9 12.6 - - - -
259B LEU* 4.1 17.9 - - + -
260B ARG* 3.6 27.6 - - + -
315B ALA 5.9 0.2 - - - -
318B GLN* 3.2 21.8 - - + +
319B ALA* 2.8 44.6 - - + -
321B THR* 3.0 11.8 + - - +
323B GLU* 1.3 75.3 - - - +
325B LYS* 1.3 67.3 + - - +
326B ILE 3.0 1.6 - - - -
327B TYR* 2.8 22.0 + + - +
328B GLN* 2.9 40.2 + - - +
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Residues in contact with LYS 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B ALA* 3.0 43.2 + - + +
239B GLY* 4.5 6.5 - - - -
240B VAL* 4.3 2.5 - - + +
319B ALA 5.0 0.2 + - - -
321B THR 3.2 10.0 + - - +
322B THR* 3.1 17.6 + - + +
324B PHE* 1.3 78.6 - - - +
326B ILE* 1.3 56.5 + - - +
328B GLN* 3.8 2.6 + - - +
329B LEU* 3.2 39.7 + - + +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.9 29.8 - - + +
14A LEU* 3.7 35.9 - - + -
15A TRP* 3.9 21.3 - - + +
18A HIS* 5.2 4.0 - - + -
322B THR* 2.8 17.1 + - + +
323B GLU* 2.8 34.3 - - - +
325B LYS* 1.3 76.3 - - - +
327B TYR* 1.3 64.3 + - - +
329B LEU* 3.1 12.2 + - + +
330B GLN* 3.0 21.6 + - + +
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 4.9 6.1 - + - -
18A HIS* 3.4 36.1 - + + +
55B ASN* 3.1 14.3 + - - -
258B THR 4.8 2.7 - - - -
260B ARG* 3.4 23.3 - - - -
323B GLU 3.1 6.4 + - - +
324B PHE* 2.8 16.5 + + - +
326B ILE* 1.3 76.3 - - - +
328B GLN* 1.3 96.3 + - - +
330B GLN* 3.0 9.6 + - - +
331B VAL* 2.9 39.6 + - + +
406B PRO* 2.9 28.1 + - - +
409B THR* 3.6 10.1 - - + -
410B SER* 3.0 34.3 + - - -
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Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 3.9 6.3 - - - -
235B LEU* 3.0 49.2 - - + +
238B ALA* 3.5 23.8 - - + -
240B VAL* 4.0 4.9 - - + -
258B THR* 3.3 17.6 + - - +
324B PHE* 2.9 38.7 + - - +
325B LYS 4.0 1.8 - - - +
327B TYR* 1.3 91.7 + - - +
329B LEU* 1.3 61.9 + - - +
331B VAL* 3.2 20.9 - - - +
332B LEU* 3.1 24.4 + - - +
406B PRO* 5.2 0.2 - - - +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B VAL* 3.8 22.0 - - + -
325B LYS* 3.2 27.5 + - + +
326B ILE* 3.1 16.9 + - + +
328B GLN* 1.3 77.1 - - - +
330B GLN* 1.3 64.9 + - - +
332B LEU* 3.3 11.2 + - + +
333B ALA* 3.0 22.7 + - - +
336B ARG* 4.8 6.3 + - - +
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Residues in contact with GLN 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 5.3 3.1 + - - -
11A ASP* 5.8 0.2 - - - +
15A TRP* 3.6 31.4 + - + +
326B ILE* 3.0 10.2 + - + +
327B TYR 3.0 9.3 + - - +
329B LEU* 1.3 76.0 - - - +
331B VAL* 1.3 55.2 + - - +
333B ALA* 3.2 5.1 + - - +
334B ASN* 2.6 78.5 + - - +
409B THR* 3.7 6.3 - - + -
414B LEU* 3.4 19.7 - - + +
415B GLU* 3.1 29.0 + - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 4.5 2.5 - - + -
327B TYR* 2.9 56.7 + - + +
328B GLN* 3.2 23.6 - - - +
329B LEU 3.1 0.2 - - - -
330B GLN* 1.3 76.3 - - - +
332B LEU* 1.3 62.6 + - - +
334B ASN* 3.5 0.9 + - - +
335B CYS* 3.2 11.8 + - - +
357B HIS* 4.0 11.6 - - + -
405B THR* 2.8 32.2 + - - +
406B PRO* 3.9 24.0 - - + -
409B THR* 3.7 12.3 - - + -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LEU* 4.4 12.6 - - + -
240B VAL* 3.5 44.4 - - + +
241B VAL* 4.4 3.4 - - + -
328B GLN 3.1 10.0 + - - +
329B LEU* 3.5 12.6 - - + +
331B VAL* 1.3 77.0 - - - +
333B ALA* 1.3 65.7 + - - +
335B CYS* 2.9 19.4 + - - +
336B ARG* 3.3 24.0 + - - +
355B ASP 3.8 8.1 - - - +
356B ASN* 3.2 42.0 - - - +
357B HIS* 4.1 1.1 - - - +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU 3.0 13.4 + - - +
330B GLN* 3.5 14.1 - - - +
332B LEU* 1.3 75.6 - - - +
334B ASN* 1.3 64.0 + - - +
336B ARG* 3.1 39.6 + - - +
337B ALA* 3.1 13.0 + - - +
415B GLU* 3.9 22.4 - - + +
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Residues in contact with ASN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B GLN* 2.6 42.5 + - - +
331B VAL 3.7 5.2 - - - +
333B ALA* 1.3 73.2 - - - +
335B CYS* 1.3 61.6 + - - +
337B ALA* 3.4 8.0 + - - +
338B LEU* 3.1 23.6 + - - +
405B THR* 4.1 2.7 - - - -
409B THR* 2.7 31.0 + - - +
413B LEU 3.0 19.2 + - - -
414B LEU 3.2 1.2 - - - -
415B GLU 3.2 18.0 + - - -
418B PHE* 3.2 29.1 - - + -
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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
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331B VAL 3.2 7.8 + - - +
332B LEU 2.9 12.3 + - - +
334B ASN* 1.3 75.1 - - - +
336B ARG* 1.3 67.5 + - + +
338B LEU* 3.1 6.0 + - - +
339B SER* 2.8 22.9 + - - -
354B SER* 3.4 35.7 - - - -
356B ASN 3.4 14.6 - - - +
357B HIS* 3.8 9.6 - - - -
358B LEU 3.8 4.0 - - - -
359B ILE* 3.6 16.1 - - - +
405B THR* 3.7 17.4 - - + +
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Residues in contact with ARG 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 4.8 6.3 + - - +
332B LEU* 4.0 19.4 + - - +
333B ALA* 3.1 37.7 + - - +
335B CYS* 1.3 77.6 - - + +
337B ALA* 1.3 65.6 + - - +
339B SER* 2.9 7.4 + - - -
340B ASP* 2.5 39.2 + - - +
354B SER* 5.3 9.9 - - - +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ALA 3.1 9.1 + - - +
334B ASN 3.4 10.1 - - - +
336B ARG* 1.3 79.7 - - - +
338B LEU* 1.3 56.2 + - - +
340B ASP* 3.7 5.9 - - - +
341B ALA* 3.0 31.9 + - - +
415B GLU* 3.8 40.4 - - + +
418B PHE* 4.6 2.5 - - + -
419B GLN* 4.8 8.6 - - + +
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 4.6 9.0 - - + -
334B ASN 3.1 10.6 + - - +
335B CYS* 3.6 7.9 - - - +
337B ALA* 1.3 79.3 - - - +
339B SER* 1.3 57.7 + - - +
341B ALA* 4.1 1.7 - - - -
342B LEU* 3.0 50.5 + - + +
359B ILE* 4.3 7.4 - - + -
403B LEU* 4.4 24.0 - - + -
404B GLY 5.4 0.2 - - - +
405B THR* 4.6 9.4 - - + -
418B PHE* 3.9 38.6 - - + +
421B VAL* 4.9 1.1 - - + -
422B ALA* 3.8 25.4 - - + +
425B ILE* 4.6 7.0 - - + -
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B CYS* 2.8 16.6 + - - -
336B ARG* 3.5 7.2 - - - -
338B LEU* 1.3 74.4 - - - +
340B ASP* 1.3 61.1 + - - +
342B LEU* 3.8 2.2 - - - +
343B THR* 2.7 37.6 + - - -
349B ILE* 3.7 25.4 - - - +
352B GLY 4.2 1.9 + - - -
353B GLY* 3.9 13.7 - - - -
354B SER 5.3 1.8 - - - -
359B ILE* 4.0 24.2 - - - +
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Residues in contact with ASP 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B ARG* 2.5 44.8 + - - +
337B ALA* 3.7 5.4 - - - +
339B SER* 1.3 73.2 - - - +
341B ALA* 1.3 56.6 + - - +
342B LEU 3.0 1.1 - - - -
343B THR* 3.0 6.4 + - - -
344B GLU* 2.6 38.4 + - - +
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B ALA 3.0 18.4 + - - +
338B LEU 4.1 0.7 - - - +
340B ASP* 1.3 76.1 - - - +
342B LEU* 1.3 59.4 + - - +
344B GLU* 3.5 16.2 - - - +
345B LEU* 3.0 32.4 + - + +
419B GLN* 4.4 22.7 - - + +
422B ALA* 3.7 22.4 - - + -
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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
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338B LEU* 3.0 31.1 + - + +
339B SER* 3.8 4.3 - - - +
340B ASP 3.0 0.6 - - - -
341B ALA* 1.3 76.5 - - - +
343B THR* 1.3 65.0 + - - +
345B LEU* 3.3 13.6 + - + +
346B GLY 3.4 0.7 + - - -
347B TYR* 3.1 36.1 + - + -
349B ILE* 4.6 6.7 - - + -
359B ILE* 3.9 11.7 - - + -
361B MSE 4.1 19.7 - - + -
403B LEU* 3.9 23.1 - - + -
422B ALA* 3.5 41.5 - - + +
425B ILE* 4.9 8.3 - - + -
426B HIS 5.4 0.2 - - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B SER* 2.7 25.1 + - - -
340B ASP* 3.6 5.8 - - - -
342B LEU* 1.3 75.0 - - - +
344B GLU* 1.3 56.5 + - - +
346B GLY* 2.6 28.4 + - - -
347B TYR 3.7 15.9 + - - +
349B ILE* 3.7 16.3 - - + +
352B GLY 4.3 6.8 + - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP 2.6 20.9 + - - +
341B ALA* 3.5 16.5 - - - +
343B THR* 1.3 72.9 - - - +
345B LEU* 1.3 59.9 + - + +
346B GLY* 3.0 5.2 + - - -
419B GLN* 5.6 1.2 - - - +
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ALA 3.0 21.6 + - - +
342B LEU* 3.6 11.7 - - + +
343B THR 3.1 0.6 - - - -
344B GLU* 1.3 77.8 - - + +
346B GLY* 1.3 58.4 + - - +
347B TYR* 4.0 15.6 - - + -
366B LYS* 5.3 1.4 + - - -
422B ALA* 4.1 16.6 - - + +
423B HIS* 4.5 11.7 - - + +
426B HIS* 3.3 55.9 + - + +
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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