Contacts of the helix formed by residues 321 - 345 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LYS* 3.8 12.6 - - + +
318A GLN* 2.9 24.4 + - - +
319A ALA 4.0 1.2 - - - +
320A MSE 1.3 84.2 - - - +
322A THR* 1.3 60.8 + - - +
323A GLU* 3.4 14.6 + - - +
324A PHE* 2.9 21.1 + - - +
325A LYS* 3.2 22.3 + - - +
21B MSE 3.7 17.5 - - - -
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Residues in contact with THR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A THR* 1.3 71.5 - - - +
323A GLU* 1.3 73.4 + - - +
324A PHE 2.9 2.0 - - - -
325A LYS* 3.7 12.4 - - + +
326A ILE* 2.9 26.7 + - + +
14B LEU* 3.4 24.0 - - + -
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Residues in contact with GLU 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A THR* 3.3 14.2 - - - +
322A THR* 1.3 90.5 + - - +
324A PHE* 1.3 55.5 + - - +
326A ILE* 2.7 24.5 - - - +
327A TYR 3.1 7.1 + - - -
14B LEU* 3.6 14.9 - - + +
17B SER* 3.2 37.6 + - - -
18B HIS* 3.2 34.9 - - + +
21B MSE 4.1 12.2 - - + +
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Residues in contact with PHE 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLY* 3.9 15.0 - - - -
237A ALA* 4.6 0.9 - - + -
238A ALA* 4.2 12.1 - - + -
258A THR 3.8 13.7 - - - -
259A LEU* 4.1 17.7 - - + -
260A ARG* 3.6 28.7 - - - -
315A ALA 5.9 0.2 - - - -
318A GLN* 3.2 21.3 - - + +
319A ALA* 2.7 44.6 - - + +
321A THR* 2.9 12.2 + - - +
323A GLU* 1.3 74.6 - - - +
325A LYS* 1.3 68.2 + - - +
326A ILE 3.0 1.3 - - - -
327A TYR* 2.8 22.3 + + - +
328A GLN* 2.9 37.4 + - - +
21B MSE 4.5 3.1 - - + +
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Residues in contact with LYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ALA* 2.9 43.8 + - + +
239A GLY* 4.5 6.6 - - - -
240A VAL* 4.3 1.6 - - + +
321A THR 3.2 10.9 + - - +
322A THR* 3.1 16.9 + - + +
324A PHE* 1.3 79.5 - - - +
326A ILE* 1.3 56.2 + - - +
328A GLN* 3.8 3.2 + - - +
329A LEU* 3.3 37.8 + - + +
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Residues in contact with ILE 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A THR* 2.9 16.7 + - + +
323A GLU* 2.7 35.0 - - - +
325A LYS* 1.3 76.9 - - - +
327A TYR* 1.3 64.6 + - - +
329A LEU* 3.1 12.5 + - + +
330A GLN* 2.9 21.7 + - + +
11B ASP* 4.1 14.8 - - - +
14B LEU* 3.3 29.8 - - + -
15B TRP* 3.5 37.9 - - + +
18B HIS* 5.0 4.0 - - + -
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 3.2 15.2 + - - -
258A THR 4.7 2.9 - - - -
260A ARG* 3.5 20.0 - - - -
323A GLU 3.1 5.3 + - - -
324A PHE* 2.8 16.3 + + - +
326A ILE* 1.3 78.0 - - - +
328A GLN* 1.3 97.8 + - - +
330A GLN* 2.9 10.2 + - - +
331A VAL* 2.9 38.0 + - + +
406A PRO* 2.9 28.8 + - - +
409A THR* 3.6 9.4 - - + -
410A SER* 3.0 34.7 + - - -
15B TRP* 4.7 5.6 - + - -
18B HIS* 3.3 39.9 - + + +
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A GLY 3.9 6.1 - - - -
235A LEU* 3.0 50.2 - - + +
238A ALA* 3.5 22.9 - - + -
240A VAL* 4.0 6.3 - - + -
258A THR* 3.4 16.5 + - - +
324A PHE* 2.9 37.4 + - - +
325A LYS 4.0 2.0 - - - +
327A TYR* 1.3 93.1 + - - +
329A LEU* 1.3 61.1 + - - +
331A VAL* 3.2 21.1 - - - +
332A LEU* 3.1 24.8 + - - +
406A PRO* 5.3 0.2 - - - +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A VAL* 3.8 22.9 - - + -
325A LYS* 3.3 27.4 + - + +
326A ILE* 3.1 14.7 + - + +
327A TYR 3.1 0.6 - - - -
328A GLN* 1.3 75.9 - - - +
330A GLN* 1.3 65.4 + - - +
332A LEU* 3.2 11.8 + - + +
333A ALA* 3.0 22.7 + - - +
336A ARG* 4.8 5.7 + - - +
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ILE* 2.9 12.3 + - + +
327A TYR 3.4 7.6 - - - +
329A LEU* 1.3 75.4 - - - +
331A VAL* 1.3 55.1 + - - +
333A ALA* 3.2 5.0 + - - +
334A ASN* 2.6 76.9 + - - +
409A THR* 3.7 4.9 - - + -
413A LEU 4.3 0.2 - - - +
414A LEU* 3.2 28.8 - - + +
415A GLU* 3.1 27.7 + - - +
15B TRP* 3.6 24.9 + - + +
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 4.5 2.2 - - + -
327A TYR* 2.9 56.6 + - + +
328A GLN* 3.2 23.6 - - - +
330A GLN* 1.3 76.7 - - - +
332A LEU* 1.3 63.3 + - - +
334A ASN* 3.5 0.7 + - - +
335A CYS* 3.2 11.8 + - - +
357A HIS* 4.0 11.6 - - + -
405A THR* 2.8 33.7 + - - +
406A PRO* 3.9 25.4 - - + -
409A THR* 3.6 11.9 - - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LEU* 4.3 11.9 - - + -
240A VAL* 3.4 45.8 - - + +
241A VAL* 4.3 3.1 - - + -
328A GLN 3.1 9.7 + - - +
329A LEU* 3.6 12.1 - - + +
331A VAL* 1.3 77.2 - - - +
333A ALA* 1.3 67.7 + - - +
335A CYS* 2.8 19.9 + - - +
336A ARG* 3.2 23.4 + - - +
355A ASP 3.7 8.3 - - - +
356A ASN* 3.1 42.5 - - - +
357A HIS* 4.1 1.1 - - - +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU 3.0 15.0 + - - +
330A GLN* 3.5 13.7 - - - +
332A LEU* 1.3 76.4 - - - +
334A ASN* 1.3 63.5 + - - +
336A ARG* 3.1 32.3 + - - +
337A ALA* 3.1 20.8 + - - +
415A GLU* 3.9 22.9 - - - +
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLN* 2.6 43.9 + - - +
331A VAL 3.7 5.2 - - - +
333A ALA* 1.3 72.5 - - - +
335A CYS* 1.3 63.8 + - - +
337A ALA* 3.4 7.7 - - - +
338A LEU* 3.0 23.6 + - - +
405A THR* 4.1 3.1 - - - -
409A THR* 2.8 29.9 + - - +
413A LEU 3.0 20.4 + - - -
414A LEU 3.3 16.1 - - - -
415A GLU* 3.3 1.8 + - - +
418A PHE* 3.2 28.9 - - + -
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Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A VAL 3.2 8.4 + - - +
332A LEU 2.8 12.8 + - - +
334A ASN* 1.3 75.6 - - - +
336A ARG* 1.3 67.8 + - + +
338A LEU* 3.0 6.4 + - - +
339A SER* 2.8 23.0 + - - -
354A SER* 3.6 13.2 - - - -
356A ASN 3.5 22.9 - - - +
357A HIS 3.8 9.9 - - - -
358A LEU* 3.8 4.7 - - - -
359A ILE* 3.5 31.5 - - - +
405A THR* 3.8 15.9 - - + +
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Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A LEU* 4.8 7.1 + - - +
332A LEU* 3.2 19.7 + - - +
333A ALA* 3.1 37.3 + - - +
335A CYS* 1.3 76.8 - - + +
337A ALA* 1.3 65.5 + - - +
339A SER* 2.9 7.0 + - - -
340A ASP* 2.6 38.3 + - - +
354A SER* 5.3 8.5 - - - +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A ALA 3.1 9.7 + - - +
334A ASN* 3.4 10.1 - - - +
336A ARG* 1.3 78.8 - - - +
338A LEU* 1.3 56.3 + - - +
340A ASP* 3.3 5.5 + - - +
341A ALA* 3.0 32.2 + - - +
415A GLU* 3.9 40.2 - - + +
418A PHE* 4.5 2.9 - - + -
419A GLN* 4.8 9.2 - - + +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.6 9.4 - - + -
334A ASN 3.0 12.9 + - - +
335A CYS* 3.5 7.9 - - - +
337A ALA* 1.3 73.2 - - - +
339A SER* 1.3 61.5 + - - +
341A ALA* 4.2 1.5 - - - +
342A LEU* 3.0 51.0 + - + +
359A ILE* 4.2 6.5 - - + -
403A LEU* 4.3 24.7 - - + -
405A THR* 4.5 9.4 - - + -
418A PHE* 3.9 36.9 - - + +
421A VAL* 4.8 1.6 - - + -
422A ALA* 3.8 25.6 - - + +
425A ILE* 4.4 7.2 - - + -
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A CYS* 2.8 20.1 + - - -
336A ARG* 3.5 7.2 - - - -
338A LEU* 1.3 73.8 - - - +
340A ASP* 1.3 59.6 + - - +
342A LEU* 3.8 2.4 - - - +
343A THR* 2.7 37.8 + - - -
349A ILE* 3.7 24.4 - - - +
352A GLY 4.2 2.6 + - - -
353A GLY* 3.8 13.9 - - - -
354A SER* 5.2 1.8 - - - -
359A ILE* 4.0 24.7 - - - +
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Residues in contact with ASP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A ARG* 2.6 44.1 + - - +
337A ALA* 3.7 5.4 - - - +
339A SER* 1.3 73.3 + - - +
341A ALA* 1.3 56.6 + - - +
342A LEU 3.0 1.6 - - - -
343A THR* 3.0 5.4 + - - -
344A GLU* 2.6 38.4 + - - +
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ALA 3.0 16.9 + - - +
338A LEU 4.2 0.4 - - - +
340A ASP* 1.3 76.6 - - - +
342A LEU* 1.3 58.4 + - - +
344A GLU* 3.5 16.0 - - - +
345A LEU* 3.0 33.4 + - + +
419A GLN* 4.4 23.6 - - + +
422A ALA* 3.7 22.9 - - + -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LEU* 3.0 30.9 + - + +
339A SER* 3.8 4.7 - - - +
340A ASP 3.0 0.6 - - - -
341A ALA* 1.3 75.8 - - - +
343A THR* 1.3 63.4 + - - +
344A GLU 3.2 0.2 - - - -
345A LEU* 3.3 12.8 + - + -
346A GLY 3.4 0.3 + - - -
347A TYR* 3.1 37.9 + - + +
349A ILE* 4.6 6.5 - - + -
359A ILE* 3.9 11.7 - - + -
361A MSE 4.1 20.2 - - + -
403A LEU* 3.9 22.7 - - + -
422A ALA* 3.5 40.8 - - + +
425A ILE* 4.9 8.7 - - + -
426A HIS 5.4 0.4 - - - +
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A SER* 2.7 25.7 + - - -
340A ASP* 3.6 5.6 - - - -
342A LEU* 1.3 72.7 - - - +
344A GLU* 1.3 57.5 + - - +
346A GLY* 2.6 28.8 + - - -
347A TYR 3.6 14.9 + - - +
349A ILE* 3.6 17.7 - - + +
352A GLY 4.3 7.4 + - - +
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Residues in contact with GLU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A ASP 2.6 21.5 + - - +
341A ALA* 3.5 16.0 - - - +
343A THR* 1.3 73.4 - - - +
345A LEU* 1.3 60.8 + - + +
346A GLY* 3.0 5.7 + - - -
419A GLN* 5.7 0.7 - - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ALA 3.0 22.0 + - - +
342A LEU* 3.6 12.8 - - + +
343A THR 3.1 0.6 - - - -
344A GLU* 1.3 78.5 - - + +
346A GLY* 1.3 58.8 + - - +
347A TYR* 3.7 15.4 - - + -
366A LYS* 5.3 1.2 + - - -
422A ALA* 4.1 17.3 - - + +
423A HIS* 4.5 10.5 - - + +
426A HIS* 3.3 56.4 + - + +
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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