Contacts of the helix formed by residues 317 - 344 (chain A) in PDB entry 1JQI
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 PHE 317 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LYS* 5.8 6.1 - - - -
242A GLN 5.1 1.3 - - - -
245A ASP* 3.6 39.3 - - + -
246A MET* 4.0 13.0 - - + -
249A ILE* 4.0 22.7 - - + -
307A ALA* 4.1 4.7 - - - +
310A LEU* 3.9 20.0 - - + -
311A LYS* 3.6 33.2 - - + -
315A LYS 3.3 14.4 - - - -
316A PRO* 1.3 76.1 - - + +
318A THR* 1.3 63.0 + - - +
319A LYS 3.4 2.2 - - - -
320A GLU* 3.3 12.1 + - + +
321A SER* 2.8 34.8 + - - -
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 3.0 41.1 + - - +
248A ARG* 5.3 2.2 + - - +
316A PRO* 3.9 1.6 - - - +
317A PHE* 1.3 80.1 + - - +
319A LYS* 1.3 62.8 + - - +
320A GLU* 4.0 0.2 + - - -
321A SER* 3.6 2.8 - - - -
322A ALA* 3.1 22.2 + - - +
377A VAL* 4.0 13.5 - - + -
381A HIS* 3.9 31.3 + - + -
400A CAA 3.5 17.1 + - - +
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Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ARG* 5.1 5.3 - - - +
317A PHE 3.4 0.4 - - - -
318A THR* 1.3 79.2 - - - +
320A GLU* 1.3 84.1 + - - +
322A ALA* 3.2 8.0 + - - +
323A MET* 2.9 61.3 + - + +
377A VAL* 5.0 3.1 - - - -
378A ILE* 4.3 13.8 - - + +
381A HIS* 3.9 36.3 - - + -
382A LEU* 4.3 23.6 - - - +
385A SER* 6.2 0.2 - - - -
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Residues in contact with GLU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 4.4 1.9 - - - +
306A ARG* 3.7 34.2 + - - +
307A ALA* 3.8 16.0 - - + +
310A LEU* 3.4 33.1 - - + +
316A PRO 3.8 4.4 - - - +
317A PHE* 3.3 22.4 - - - +
318A THR 3.4 0.2 - - - -
319A LYS* 1.3 100.1 + - - +
321A SER* 1.3 62.5 + - - +
323A MET* 3.4 2.8 + - - +
324A ALA* 3.1 24.6 + - - +
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Residues in contact with SER 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 2.6 32.9 + - - -
248A ARG* 3.3 16.9 - - - +
249A ILE* 3.5 9.4 - - - +
307A ALA* 4.0 9.8 - - - +
317A PHE* 2.8 26.3 + - - -
318A THR* 3.6 6.5 - - - -
320A GLU* 1.3 78.0 - - - +
322A ALA* 1.3 63.0 + - - +
324A ALA* 3.3 3.2 + - - +
325A LYS* 3.0 24.5 + - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ARG* 4.9 4.4 - - - +
318A THR 3.1 13.7 + - - +
319A LYS 3.2 7.8 + - - +
321A SER* 1.3 78.2 - - - +
323A MET* 1.3 55.9 + - - +
325A LYS* 3.8 2.1 - - - +
326A LEU* 3.0 32.4 + - - +
374A GLN* 3.2 29.7 - - - +
377A VAL* 4.0 16.8 - - + -
378A ILE* 3.9 17.7 - - + -
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Residues in contact with MET 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 4.2 14.0 - - + +
306A ARG* 3.5 26.2 - - - +
319A LYS* 2.9 49.5 + - - +
320A GLU* 3.7 5.4 - - - +
321A SER 3.3 0.2 - - - -
322A ALA* 1.3 76.6 - - - +
324A ALA* 1.3 57.6 + - - +
326A LEU* 3.8 2.4 - - - +
327A ALA* 3.0 32.7 + - - +
378A ILE* 3.7 35.9 - - + -
382A LEU* 6.2 1.3 - - + -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ILE* 5.7 2.5 - - - -
252A ALA* 3.7 7.9 - - + -
300A ALA 5.0 0.3 - - - +
303A LEU* 3.8 14.3 - - - +
304A THR* 3.5 38.7 + - - +
307A ALA* 4.6 4.5 - - + -
320A GLU 3.1 17.2 + - - +
321A SER 3.7 3.8 - - - +
323A MET* 1.3 73.4 - - - +
325A LYS* 1.3 61.1 + - - +
327A ALA* 4.1 0.2 - - - +
328A ALA* 2.8 36.0 + - - +
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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
----------------------------------------------------------
248A ARG* 3.7 34.1 - - + +
251A ILE* 4.0 16.8 - - + +
252A ALA* 3.7 11.1 - - - +
321A SER 3.0 17.3 + - - +
322A ALA* 3.8 5.8 - - - +
324A ALA* 1.3 77.1 - - - +
326A LEU* 1.3 61.6 + - - +
328A ALA* 4.1 0.3 - - - +
329A SER* 2.8 32.9 + - - +
364A THR 2.8 29.4 + - - +
365A GLU* 3.9 9.7 + - - +
367A TYR 3.2 20.5 + - - -
368A GLU* 4.4 3.6 - - - -
369A GLY 2.7 25.9 + - - -
370A THR 4.6 2.0 - - - -
371A SER* 4.7 0.8 + - - +
374A GLN* 4.0 16.5 - - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ALA 3.0 19.0 + - - +
323A MET* 3.8 3.8 - - - +
325A LYS* 1.3 80.0 - - - +
327A ALA* 1.3 62.6 + - - +
329A SER* 2.9 17.3 + - - -
330A GLU* 3.0 20.9 + - - +
371A SER* 3.4 44.0 - - - +
374A GLN* 4.2 6.3 - - + -
375A ARG* 3.7 46.0 - - + +
378A ILE* 4.1 16.4 - - + -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 4.2 9.7 - - + +
303A LEU* 3.6 24.2 - - + -
323A MET 3.0 19.3 + - - +
324A ALA 4.1 1.1 - - - +
326A LEU* 1.3 77.9 - - - +
328A ALA* 1.3 57.8 + - - +
330A GLU* 4.0 4.1 - - - +
331A ALA* 3.0 30.3 + - - +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 3.5 32.1 - - + +
255A ALA* 3.6 13.9 - - + +
256A LEU* 4.0 14.5 - - + +
300A ALA* 3.8 12.9 - - + +
304A THR* 4.5 1.1 - - - +
324A ALA 2.8 24.1 + - - +
327A ALA* 1.3 74.0 - - - +
329A SER* 1.3 58.2 + - - +
331A ALA* 3.2 3.8 + - - +
332A ALA* 2.9 23.7 + - - +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 5.8 0.7 - - - -
255A ALA* 3.8 5.7 - - - +
325A LYS* 2.8 24.6 + - - +
326A LEU* 2.9 14.7 + - - -
328A ALA* 1.3 75.6 - - - +
330A GLU* 1.3 64.7 + - - +
332A ALA* 3.1 12.3 + - - +
333A THR* 3.3 9.9 + - - -
364A THR* 3.1 50.3 + - - -
365A GLU* 3.9 15.6 - - - +
371A SER* 4.4 2.8 + - - -
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.0 26.0 + - + +
327A ALA* 4.2 4.0 - - - +
329A SER* 1.3 84.8 + - - +
331A ALA* 1.3 62.1 + - - +
333A THR* 3.6 2.3 + - - -
334A ALA* 3.2 23.4 + - - +
365A GLU* 3.9 20.6 - - - +
371A SER* 4.0 7.5 - - - +
375A ARG* 3.2 42.2 + - - -
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 6.3 0.4 - - + -
259A ALA* 4.8 2.2 - - + -
296A ALA* 4.2 32.5 - - + +
297A LEU* 4.9 1.6 - - + +
300A ALA* 4.6 2.2 - - + -
327A ALA 3.0 20.4 + - - +
328A ALA* 3.5 7.4 - - - +
330A GLU* 1.3 75.0 - - - +
332A ALA* 1.3 60.8 + - - +
334A ALA* 3.9 4.4 - - - +
335A ILE* 2.8 43.8 + - + +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ALA* 3.8 25.6 - - + +
258A ILE* 4.7 2.4 - - + +
259A ALA* 4.1 16.2 - - + +
328A ALA 2.9 12.6 + - - +
329A SER 3.1 10.9 + - - +
331A ALA* 1.3 77.6 - - - +
333A THR* 1.3 51.1 + - - +
336A SER* 2.6 40.5 + - - -
361A ALA* 3.8 17.6 - - + +
364A THR* 4.4 3.6 - - - +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER 3.3 4.1 + - - -
330A GLU 4.1 6.1 - - - +
332A ALA* 1.3 78.1 - - - +
334A ALA* 1.3 58.7 + - - +
336A SER* 3.1 6.5 + - - -
337A HIS* 2.8 33.2 + - + +
358A TYR* 4.2 6.1 + - + -
361A ALA* 3.9 19.2 + - - -
362A ARG* 4.0 3.8 + - - -
365A GLU* 2.7 31.4 + - - +
737B HIS* 3.9 10.8 - - + +
758B TYR* 3.7 22.9 - - - +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ALA* 6.3 0.9 - - + -
330A GLU 3.2 16.0 + - - +
331A ALA* 3.9 5.6 - - - +
333A THR* 1.3 81.3 - - - +
335A ILE* 1.3 59.2 + - + +
337A HIS* 3.2 7.7 + - - +
338A GLN* 3.0 34.1 + - + +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA* 3.6 39.3 - - + +
262A SER* 3.9 5.4 - - - -
263A LEU* 4.2 4.7 - - + +
293A MET* 3.3 64.6 - - + +
296A ALA* 4.2 6.7 - - + -
297A LEU* 3.9 17.7 - - + +
331A ALA* 2.8 29.0 + - + +
332A ALA 4.2 1.3 - - - +
334A ALA* 1.3 72.8 - - + +
336A SER* 1.3 64.3 + - - +
338A GLN 3.2 1.4 + - - -
339A ALA* 3.1 19.9 + - - +
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ILE* 5.0 0.9 - - - -
262A SER* 3.4 26.2 + - - -
332A ALA 2.6 29.2 + - - -
333A THR* 3.1 12.5 + - - -
335A ILE* 1.3 73.9 - - - +
337A HIS* 1.3 60.8 + - - +
339A ALA* 3.3 3.7 + - - +
340A ILE* 3.3 25.8 + - - +
354A ALA 4.6 1.6 - - - +
357A TYR* 3.9 6.1 - - - -
358A TYR* 3.6 34.4 - - - -
361A ALA* 3.7 3.3 - - - +
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 2.8 21.7 + - + +
334A ALA* 3.3 7.6 - - - +
335A ILE 3.1 0.2 - - - -
336A SER* 1.3 79.5 + - - +
338A GLN* 1.3 78.5 + - - +
340A ILE* 3.4 2.5 + - - +
341A GLN* 3.2 6.6 + - - -
358A TYR* 3.5 30.3 - + + -
733B THR* 4.1 9.9 - - + +
762B ARG* 2.8 57.9 + - - +
765B GLU* 3.1 35.7 + - - -
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 2.5 54.8 + - + +
293A MET* 3.8 30.1 - - + -
334A ALA* 3.0 18.4 + - + +
335A ILE 3.2 1.8 + - - +
337A HIS* 1.3 96.9 + - - +
339A ALA* 1.3 60.4 + - - +
341A GLN* 3.5 10.6 - - - +
342A ILE* 2.8 34.4 + - + +
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 3.6 31.9 - - - +
265A CYS* 5.5 2.2 - - + -
266A ALA* 4.2 15.5 - - + +
293A MET* 4.3 1.5 - - + +
335A ILE 3.1 12.4 + - - +
336A SER 3.5 10.3 - - - +
337A HIS 3.2 0.2 - - - -
338A GLN* 1.3 75.3 - - - +
340A ILE* 1.3 65.8 + - - +
342A ILE* 3.4 1.4 + - - +
343A LEU* 3.1 31.1 + - + +
354A ALA* 4.7 13.0 - - + -
357A TYR* 5.6 0.4 - - + -
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Residues in contact with ILE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A SER 3.3 10.4 + - - +
337A HIS 3.6 7.0 - - - +
339A ALA* 1.3 79.2 - - - +
341A GLN* 1.3 62.5 + - - +
343A LEU* 3.2 3.8 + - - +
344A GLY* 3.1 21.3 + - - +
347A GLY* 3.5 33.2 - - - +
348A TYR* 4.8 1.8 - - + -
354A ALA* 3.8 14.1 - - + +
355A GLU* 4.0 11.7 - - + -
358A TYR* 3.6 41.1 - - + -
607B LEU* 4.7 2.9 - - + -
762B ARG* 3.7 27.4 - - + +
766B ILE* 3.8 14.7 - - + +
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 4.5 3.8 - - - +
337A HIS* 3.2 9.3 + - - +
338A GLN* 3.5 24.9 - - - +
339A ALA 3.2 0.2 - - - -
340A ILE* 1.3 80.5 - - - +
342A ILE* 1.3 61.9 + - + +
344A GLY* 3.0 12.5 + - - -
762B ARG* 2.8 34.7 + - - +
765B GLU* 3.2 25.6 + - - +
766B ILE* 3.8 8.1 - - - +
770B THR* 3.9 7.7 - - - +
771B SER* 3.8 9.8 + - - +
772B GLU* 3.0 38.5 + - - +
799B FAD 2.8 18.4 + - - +
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Residues in contact with ILE 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ALA* 4.0 29.4 - - + +
269A TYR* 4.0 1.4 - - + -
270A ALA* 4.2 16.2 - - + +
280A LEU* 3.8 12.3 - - + +
286A ILE* 4.6 14.4 - - + +
289A LYS* 4.2 26.2 - - + -
290A LEU* 4.0 29.2 - - + -
293A MET* 4.2 11.0 - - - -
338A GLN 2.8 24.2 + - - +
339A ALA 3.9 3.6 - - - +
341A GLN* 1.3 72.1 - - - +
343A LEU* 1.3 60.8 + - + +
799B FAD 3.2 28.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A CYS* 4.1 16.6 - - - +
266A ALA* 4.3 9.0 - - - -
269A TYR* 3.6 52.7 + - + -
339A ALA 3.1 20.2 + - - +
340A ILE 3.2 0.4 + - - -
342A ILE* 1.3 77.0 - - + +
344A GLY* 1.3 63.3 + - - +
345A GLY 3.5 0.5 + - - -
346A MET* 3.3 16.4 + - + +
347A GLY* 3.5 20.4 - - - +
352A MET* 3.7 31.9 - - + -
354A ALA* 3.8 24.9 - - + -
799B FAD 4.4 5.4 + - - +
----------------------------------------------------------
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Residues in contact with GLY 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ILE 3.1 6.2 + - - +
341A GLN 3.0 15.8 + - - -
342A ILE 3.2 0.8 - - - -
343A LEU* 1.3 73.8 - - - +
345A GLY* 1.3 61.5 + - - +
347A GLY* 2.8 22.5 + - - -
766B ILE* 3.6 24.5 - - - +
770B THR* 5.3 0.9 - - - -
799B FAD 4.0 20.0 - - - -
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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