Contacts of the helix formed by residues 388 - 411 (chain E) in PDB entry 5I4V
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 GLU 388 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E LEU* 5.8 2.0 - - + +
296E GLY* 4.7 10.7 + - - -
299E ASP* 3.0 14.6 + - - +
386E VAL* 4.1 2.9 - - - -
387E GLN* 1.3 84.9 - - + +
389E PRO* 1.3 65.0 - - - +
390E GLY 3.3 2.5 - - - -
391E ARG* 2.9 63.8 + - + +
392E VAL* 3.5 14.6 + - - +
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Residues in contact with PRO 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E ALA* 3.4 31.5 - - + +
386E VAL* 3.9 19.2 - - + +
387E GLN 3.3 9.6 - - - +
388E GLU* 1.3 90.2 - - - +
390E GLY* 1.3 62.4 + - - +
392E VAL* 3.2 10.2 + - + -
393E GLU* 3.2 17.8 + - - +
422F THR* 5.7 8.7 - - + -
423F GLU* 5.3 5.2 - - - +
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Residues in contact with GLY 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E GLU 3.3 1.0 - - - -
389E PRO* 1.3 83.6 - - - +
391E ARG* 1.3 60.8 + - - +
393E GLU* 3.7 9.8 + - - +
394E ALA* 3.3 21.8 + - - +
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Residues in contact with ARG 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLN* 2.4 41.6 + - - +
295E LEU* 3.6 22.0 - - + +
296E GLY 5.2 1.0 - - - +
388E GLU* 2.9 55.8 + - + +
389E PRO 3.2 0.4 - - - -
390E GLY* 1.3 77.6 - - - +
392E VAL* 1.3 60.5 + - - +
394E ALA* 3.4 6.7 + - - +
395E LEU* 3.2 28.9 + - + +
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Residues in contact with VAL 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E LEU* 4.6 13.0 - - + -
299E ASP* 4.9 3.6 - - + +
303E LEU* 4.3 19.3 - - + -
379E PHE* 3.4 37.4 - - + +
380E SER 3.8 4.0 - - - +
381E ALA* 3.8 15.3 - - + +
386E VAL* 4.1 17.5 - - + -
388E GLU 3.5 15.0 - - - +
389E PRO 3.2 6.2 + - - +
391E ARG* 1.3 75.0 - - - +
393E GLU* 1.3 59.8 + - - +
395E LEU* 3.3 9.6 + - - +
396E GLN* 2.9 26.2 + - - +
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Residues in contact with GLU 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379E PHE 5.1 0.9 - - - -
381E ALA* 3.3 28.0 - - + +
389E PRO* 3.2 14.4 + - - +
390E GLY* 4.1 8.4 - - - +
392E VAL* 1.3 76.7 - - - +
394E ALA* 1.3 61.8 + - - +
396E GLN* 3.3 13.4 + - - +
397E GLN* 3.2 23.9 + - - +
423F GLU* 4.8 2.3 - - - +
427F LYS* 3.1 38.5 + - - +
492F ARG* 4.7 10.4 + - - +
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Residues in contact with ALA 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E GLY 3.3 15.6 + - - +
391E ARG* 3.7 7.2 - - - +
392E VAL 3.2 0.6 - - - -
393E GLU* 1.3 75.7 - - - +
395E LEU* 1.3 61.7 + - + +
397E GLN* 3.9 6.3 - - - +
398E PRO* 2.9 26.3 - - - +
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Residues in contact with LEU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B ILE* 3.7 37.5 - - + -
290E PRO 4.5 2.7 - - - +
291E GLY* 3.9 23.1 - - - +
294E GLN* 5.2 2.5 - - + +
295E LEU* 3.6 30.3 - - + -
379E PHE* 3.9 29.8 - - + -
391E ARG* 3.2 15.8 + - + +
392E VAL* 3.5 7.4 - - - +
394E ALA* 1.3 76.7 - - + +
396E GLN* 1.3 64.2 + - - +
397E GLN 3.3 0.5 + - - -
398E PRO* 3.4 9.1 - - - +
399E TYR* 3.0 24.2 - - + -
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Residues in contact with GLN 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376E ILE* 3.0 41.0 - - + +
379E PHE* 2.9 38.6 - - + +
380E SER* 4.0 7.6 + - - -
381E ALA 5.8 0.2 - - - -
392E VAL 2.9 10.7 + - - +
393E GLU* 3.3 11.9 + - - +
395E LEU* 1.3 76.9 - - - +
397E GLN* 1.3 63.7 + - - +
399E TYR* 3.0 8.1 + - - +
400E VAL* 3.0 21.4 + - + +
425E LEU* 5.4 1.2 - - - +
491F LEU* 3.7 32.2 - - - +
492F ARG* 6.2 0.2 - - - +
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Residues in contact with GLN 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E GLU 3.2 14.0 + - - +
394E ALA* 3.9 5.4 - - - +
396E GLN* 1.3 79.9 - - - +
398E PRO* 1.3 67.3 - - + +
400E VAL* 3.1 10.4 + - + +
401E GLU* 2.8 61.2 + - - +
488F LYS* 4.9 15.6 + - - -
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Residues in contact with PRO 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B LEU* 3.6 42.2 - - + +
513B ILE* 4.9 5.2 - - + -
224E GLN* 5.0 1.2 + - - +
227E MET* 5.0 9.6 - - + +
394E ALA 2.9 28.3 - - - +
395E LEU* 3.4 12.3 - - - +
397E GLN* 1.3 87.1 - - + +
399E TYR* 1.3 56.0 + - + +
401E GLU* 3.3 12.1 + - + +
402E ALA* 2.8 36.5 + - - +
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Residues in contact with TYR 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ILE* 5.1 3.1 - - + -
227E MET* 3.3 37.9 - - + +
231E LEU* 4.0 12.6 - - + -
289E VAL* 3.9 7.0 - - + -
290E PRO* 2.6 45.6 + - - +
372E LEU* 3.7 18.4 - - + +
375E ALA* 4.0 17.7 - - + -
376E ILE* 3.6 22.3 - - + +
379E PHE* 3.6 24.7 - + - -
395E LEU* 3.0 27.8 - - + -
396E GLN 3.0 7.0 + - - +
398E PRO* 1.3 79.0 - - + +
400E VAL* 1.3 60.7 + - - +
402E ALA* 4.4 3.1 - - - -
403E LEU* 3.2 23.2 + - - +
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Residues in contact with VAL 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E ILE* 4.0 24.7 - - + -
396E GLN* 3.0 23.9 + - + +
397E GLN* 3.4 10.5 - - + +
399E TYR* 1.3 74.4 - - - +
401E GLU* 1.3 66.4 + - + +
403E LEU* 3.2 4.3 + - - +
404E LEU* 3.0 21.6 + - + +
418E PHE* 4.1 12.7 - - + -
422E LEU* 5.0 3.8 - - + -
487F ALA* 3.9 28.3 - - + -
491F LEU* 3.9 24.2 - - + -
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Residues in contact with GLU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E GLN* 4.0 10.8 - - - +
397E GLN* 2.8 56.0 + - - +
398E PRO* 3.6 8.2 - - + +
400E VAL* 1.3 75.3 - - + +
402E ALA* 1.3 62.7 + - - +
404E LEU* 3.4 14.1 + - + +
405E SER* 3.1 25.3 + - - -
483F GLN 6.5 0.2 - - - -
484F GLY* 4.8 16.3 + - - -
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Residues in contact with ALA 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E LEU* 4.3 2.4 - - - +
224E GLN* 3.7 27.5 - - + +
227E MET* 5.3 7.6 - - - -
228E ILE* 4.3 11.6 - - + +
372E LEU* 4.2 16.8 - - + +
398E PRO 2.8 20.6 + - - +
399E TYR* 3.9 6.3 - - - +
401E GLU* 1.3 72.7 - - - +
403E LEU* 1.3 58.1 + - - +
405E SER* 3.5 1.6 + - - -
406E TYR* 2.8 31.2 + - - +
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Residues in contact with LEU 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E GLU* 4.2 13.7 - - + -
372E LEU* 3.7 27.5 - - + +
373E LEU* 4.4 11.0 - - + -
376E ILE* 3.7 22.4 - - + -
399E TYR 3.2 14.1 + - - +
400E VAL 3.2 5.9 + - - +
402E ALA* 1.3 78.0 - - - +
404E LEU* 1.3 65.0 + - - +
406E TYR* 4.4 1.6 - - + -
407E THR* 2.9 31.6 + - - +
418E PHE* 4.2 18.4 - - + -
421E MET* 3.5 40.4 - - + -
422E LEU* 4.6 5.6 - - + -
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Residues in contact with LEU 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E VAL* 3.0 12.7 + - + +
401E GLU* 3.5 17.9 - - + +
403E LEU* 1.3 76.0 - - - +
405E SER* 1.3 63.7 + - - +
407E THR* 3.2 3.0 - - - +
408E ARG* 3.0 66.5 + - - +
418E PHE* 3.6 40.4 - - + -
472F GLU* 5.1 1.8 - - - +
483F GLN* 4.4 17.5 - - + +
484F GLY* 5.6 3.6 - - - -
487F ALA* 5.9 2.5 - - + -
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Residues in contact with SER 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL 5.6 3.9 + - - +
219E GLN 3.6 19.7 + - - -
220E LEU* 3.5 21.5 - - - -
224E GLN* 3.9 12.2 + - - -
401E GLU 3.1 14.5 + - - -
402E ALA 3.8 1.8 - - - -
404E LEU* 1.3 78.0 - - - +
406E TYR* 1.3 65.4 + - - +
408E ARG* 3.2 5.4 + - - +
409E ILE* 3.1 27.8 + - - +
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Residues in contact with TYR 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A PHE* 3.8 26.1 + + - -
443A ARG* 4.3 4.5 + - - -
444A LEU* 3.6 38.2 + - + +
220E LEU* 3.6 11.8 - - + +
228E ILE* 3.6 24.9 - - + -
366E ASP* 2.4 32.7 + - - -
368E ALA* 3.6 18.8 - - + +
369E GLU* 3.7 28.3 - - + -
372E LEU* 4.4 3.6 - - + -
402E ALA 2.8 22.9 + - - +
403E LEU* 3.4 6.3 + - + +
405E SER* 1.3 72.6 - - - +
407E THR* 1.3 60.2 + - - +
409E ILE* 3.4 4.5 + - - +
410E LYS* 2.9 29.2 + - + +
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Residues in contact with THR 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E GLU* 3.4 9.2 + - - -
403E LEU* 2.9 32.2 + - - +
404E LEU 3.2 7.0 - - - +
406E TYR* 1.3 81.6 - - - +
408E ARG* 1.3 65.8 + - + +
410E LYS* 3.8 5.1 - - - +
411E ARG* 3.1 29.6 + - - +
414E ASP 5.3 0.5 - - - +
417E ARG* 3.1 35.8 - - + +
418E PHE* 3.7 31.4 - - + +
421E MET* 4.3 4.3 - - - -
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Residues in contact with ARG 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E VAL* 6.5 0.7 - - - -
404E LEU* 3.0 48.9 + - - +
405E SER* 3.8 4.3 - - - +
407E THR* 1.3 77.8 - - - +
409E ILE* 1.3 62.6 - - + +
411E ARG 4.7 2.5 - - - -
412E PRO* 3.4 28.1 - - + +
414E ASP 5.4 0.6 + - - -
415E GLN* 2.5 66.0 + - - +
418E PHE* 4.4 8.0 - - - +
419E PRO* 4.3 8.5 - - - +
472F GLU* 3.1 38.9 + - - -
476F LYS* 4.2 7.5 - - - +
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Residues in contact with ILE 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444A LEU* 3.8 24.6 - - + +
218E VAL 4.0 13.9 - - - +
219E GLN* 3.9 8.5 - - + -
220E LEU* 3.5 45.3 - - + +
405E SER* 3.1 16.8 + - - +
406E TYR* 3.8 4.0 - - - +
408E ARG* 1.3 79.3 - - + +
410E LYS* 1.3 65.8 + - - +
411E ARG 3.3 0.7 + - - -
412E PRO* 3.5 13.4 - - - +
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Residues in contact with LYS 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A ARG 3.4 4.2 + - - -
444A LEU* 3.3 40.3 + - + +
446A ASP* 2.8 30.6 + - - -
364E GLY 4.7 1.3 - - - -
366E ASP* 2.9 28.8 + - - +
369E GLU* 3.5 32.8 - - - +
406E TYR* 2.9 15.8 + - + +
407E THR* 3.7 5.8 + - - +
409E ILE* 1.3 79.0 - - - +
411E ARG* 1.3 85.5 + - + +
412E PRO* 3.8 2.9 - - - +
413E GLN* 5.0 0.3 - - - +
417E ARG* 3.8 13.9 - - - +
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Residues in contact with ARG 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A LEU 4.6 0.8 + - - -
446A ASP* 2.5 35.7 + - - -
364E GLY* 4.5 11.1 + - - -
407E THR 3.1 15.1 + - - +
408E ARG* 3.9 1.8 - - - +
410E LYS* 1.3 106.0 + - + +
412E PRO* 1.3 66.6 - - - +
413E GLN* 3.2 26.5 - - - +
414E ASP* 3.1 26.0 + - + +
415E GLN* 4.8 0.5 - - - +
417E ARG* 4.0 32.2 - - - +
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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
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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