Contacts of the helix formed by residues 373 - 409 (chain B) in PDB entry 1S0V
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 ALA 373 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLU* 1.3 72.9 - - - +
374B LEU* 1.3 70.8 + - + +
375B THR* 3.1 1.9 - - - +
376B ALA* 2.8 19.9 + - - +
377B TRP* 2.7 42.0 + - + +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA* 1.3 88.2 - - + +
375B THR* 1.3 64.2 + - + +
376B ALA 3.3 1.5 + - - -
377B TRP* 4.3 6.1 - - + -
378B LYS* 3.3 35.5 + - + +
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Residues in contact with THR 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLU* 3.1 37.1 + - + +
373B ALA 3.0 2.4 + - - +
374B LEU* 1.3 83.5 - - + +
376B ALA* 1.3 56.9 + - - +
379B ARG* 3.6 28.1 + - - +
660B ASP* 4.9 0.2 - - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLU* 3.8 20.2 - - + +
373B ALA 2.8 9.4 + - - +
375B THR* 1.3 78.9 - - - +
377B TRP* 1.3 82.0 + - + +
379B ARG* 3.8 8.4 - - - +
380B ALA* 4.1 7.6 + - - +
659B ILE* 6.0 4.7 - - + -
660B ASP* 3.4 25.1 - - - +
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Residues in contact with TRP 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLU 5.3 2.5 - - - -
373B ALA* 2.7 46.5 + - + +
374B LEU* 3.9 4.3 - - + +
376B ALA* 1.3 88.6 - - + +
378B LYS* 1.3 73.5 + - + +
379B ARG 3.1 1.1 - - - -
380B ALA* 3.1 15.9 + - - +
381B ALA* 3.2 9.9 + - - +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 3.3 25.3 + - + +
377B TRP* 1.3 83.4 - - + +
379B ARG* 1.3 66.0 + - - +
381B ALA* 2.9 27.9 + - + +
382B ALA* 3.0 17.7 + - - +
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Residues in contact with ARG 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU 4.5 0.4 + - - -
375B THR* 3.6 27.4 + - - +
376B ALA* 3.8 8.4 - - - +
377B TRP 3.9 0.2 - - - +
378B LYS* 1.3 79.8 - - - +
380B ALA* 1.3 60.8 + - - +
381B ALA 3.4 0.2 + - - -
382B ALA* 3.9 4.0 + - - +
383B ALA* 3.7 15.4 + - - +
656B GLN* 2.7 51.3 + - - +
660B ASP* 3.7 32.3 - - - +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA 4.1 7.8 + - - +
377B TRP* 3.1 10.4 + - - +
379B ARG* 1.3 79.6 - - + +
381B ALA* 1.3 68.1 + - - +
383B ALA* 3.3 9.0 + - + +
384B VAL* 3.2 25.0 + - + +
660B ASP* 5.8 3.6 - - + +
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TRP 3.2 5.8 + - - +
378B LYS* 2.9 34.5 + - + +
380B ALA* 1.3 74.7 - - - +
382B ALA* 1.3 52.3 + - - +
383B ALA 2.5 16.1 + - - -
384B VAL* 2.7 18.9 + - - +
385B TYR* 3.0 10.3 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ARG* 6.0 3.8 - - - +
378B LYS 3.0 11.0 + - - +
379B ARG* 4.3 4.3 - - - +
381B ALA* 1.3 76.4 - - - +
383B ALA* 1.3 57.8 + - - +
385B TYR* 4.0 15.2 - - + +
386B ARG* 3.6 35.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B ARG 3.7 11.4 + - - +
380B ALA* 3.5 14.5 - - - +
381B ALA 2.5 7.1 + - - -
382B ALA* 1.3 75.8 - - - +
384B VAL* 1.3 59.9 + - + +
385B TYR 3.2 1.3 - - - -
386B ARG* 4.3 10.1 - - - +
387B LYS* 2.9 27.6 + - - +
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Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA* 3.2 16.6 - - + +
381B ALA* 2.7 8.8 + - - +
383B ALA* 1.3 79.5 - - + +
385B TYR* 1.3 65.8 + - - +
387B LYS* 3.5 13.2 - - + +
388B ASP* 3.2 19.6 + - + +
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Residues in contact with TYR 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 6.1 1.0 - - - -
381B ALA 3.0 12.2 + - - +
382B ALA* 4.2 11.4 - - + -
384B VAL* 1.3 74.0 - - - +
386B ARG* 1.3 72.3 + - + +
388B ASP* 3.0 11.7 + - + +
389B LYS* 3.0 40.9 + - + +
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LYS* 4.6 16.2 - - - +
382B ALA* 3.6 32.9 + - - +
383B ALA* 4.3 8.9 - - - +
384B VAL 3.5 0.2 - - - -
385B TYR* 1.3 80.5 - - + +
387B LYS* 1.3 67.5 + - - +
389B LYS* 3.0 20.4 + - - +
390B ALA* 2.9 18.7 + - - +
4I G 3.6 42.3 + - - +
5I C 4.1 17.7 - - - +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLU* 4.8 12.1 + - - -
383B ALA 2.9 20.5 + - - +
384B VAL* 3.5 15.9 - - + +
385B TYR 3.0 0.4 + - - -
386B ARG* 1.3 78.7 - - - +
388B ASP* 1.3 64.4 + - - +
390B ALA* 3.0 13.4 + - + +
391B ARG* 3.0 21.8 + - + +
394B ARG* 5.5 6.6 - - - +
5I C 6.0 0.2 - - - -
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Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 3.2 8.6 + - + +
385B TYR* 3.0 13.8 + - + +
387B LYS* 1.3 78.1 - - - +
389B LYS* 1.3 78.4 + - - +
390B ALA 2.8 0.7 + - - -
391B ARG* 3.7 27.0 + - - +
392B LYS* 3.1 34.6 + - - +
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Residues in contact with LYS 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LYS* 5.5 5.9 + - - +
174B VAL* 5.8 3.6 - - - +
385B TYR* 3.0 32.6 + - + +
386B ARG* 3.2 26.0 - - - +
388B ASP* 1.3 85.1 + - - +
390B ALA* 1.3 56.1 - - - +
392B LYS* 2.9 25.5 - - - +
393B SER* 3.0 10.0 + - - -
3I G 3.0 27.6 + - - +
4I G 3.7 34.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ARG 2.9 10.2 + - - +
387B LYS* 3.1 11.4 - - - +
388B ASP 2.8 0.8 + - - -
389B LYS* 1.3 71.7 - - - +
391B ARG* 1.3 52.4 - - - +
392B LYS 2.3 10.5 + - - -
393B SER 2.2 28.9 + - - +
394B ARG* 2.6 26.9 + - - +
4I G 4.5 6.5 + - - +
5I C 3.4 38.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B HIS* 4.1 49.5 + - + +
347B CYS* 5.4 7.9 - - + -
350B GLU* 5.7 11.4 - - - +
387B LYS* 3.0 20.1 + - + +
388B ASP* 3.7 28.7 + - - +
390B ALA* 1.3 73.1 - - - +
392B LYS* 1.3 57.0 + - - +
394B ARG* 3.2 26.1 - - - +
395B ARG* 4.2 13.5 + - - +
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Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B HIS* 6.3 0.2 - - - -
388B ASP* 3.1 24.3 + - - +
389B LYS* 2.9 16.6 - - + +
390B ALA 2.3 18.7 + - - -
391B ARG* 1.3 69.6 - - - +
393B SER* 1.3 62.3 + - - +
394B ARG 3.3 1.1 + - - -
395B ARG* 3.7 7.4 + - - +
396B ILE* 3.1 28.0 + - + +
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Residues in contact with SER 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B LYS* 3.0 11.1 + - - -
390B ALA 2.2 19.1 + - - -
392B LYS* 1.3 72.8 - - - +
394B ARG* 1.3 62.2 + - - +
395B ARG 3.4 0.2 + - - -
396B ILE* 3.8 8.0 + - - +
397B SER* 3.6 17.0 + - - -
16H C 4.4 18.4 + - - -
3I G 5.6 0.5 + - - -
4I G 4.1 29.2 + - - -
5I C 4.4 10.4 + - - -
----------------------------------------------------------
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B CYS* 5.4 16.8 - - + +
350B GLU* 4.1 21.7 + - - +
387B LYS* 4.5 6.7 + - - +
390B ALA* 2.6 26.5 + - - +
391B ARG* 3.2 39.2 - - - +
393B SER* 1.3 69.6 - - - +
395B ARG* 1.3 70.4 + - - +
397B SER* 3.4 9.5 + - - +
398B LEU* 3.1 16.6 + - - +
437B ASN* 5.5 6.7 - - - +
5I C 3.2 34.1 + - - +
6I G 3.4 25.4 + - - -
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Residues in contact with ARG 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B THR* 2.7 42.7 + - - -
343B LYS* 4.5 4.2 - - - +
345B LYS 4.5 2.2 + - - -
346B HIS* 3.7 47.3 + - + +
391B ARG 4.2 12.2 + - - +
392B LYS* 3.7 11.9 + - - +
393B SER 3.3 0.4 - - - -
394B ARG* 1.3 74.8 - - - +
396B ILE* 1.3 61.8 + - + +
398B LEU* 2.2 55.0 + - - +
399B GLU* 3.1 41.0 + - + +
402B LEU* 6.0 0.6 - - - +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LYS* 3.1 29.4 - - + +
393B SER* 4.0 9.2 - - - +
395B ARG* 1.3 84.8 - - + +
397B SER* 1.3 66.6 + - - +
399B GLU* 3.6 9.1 + - + +
400B PHE* 3.5 17.5 + - - +
16H C 4.8 23.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B SER 3.6 8.4 + - - -
394B ARG* 3.4 11.7 + - - +
395B ARG 2.7 4.4 + - - -
396B ILE* 1.3 76.6 - - - +
398B LEU* 1.3 66.4 + - - +
400B PHE* 3.0 8.3 + - - +
401B MET* 2.9 33.5 + - - +
437B ASN* 4.3 12.8 + - - -
16H C 6.5 0.7 - - - -
5I C 6.0 1.3 - - - -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B THR* 3.8 26.7 - - + -
346B HIS 4.1 5.2 - - - +
347B CYS* 5.0 5.4 - - - -
348B PRO* 4.0 18.6 - - + -
394B ARG 3.1 8.2 + - - +
395B ARG* 2.2 43.3 + - - +
397B SER* 1.3 74.1 + - - +
399B GLU* 1.3 52.9 + - - +
401B MET* 3.1 5.0 + - - +
402B LEU* 2.5 43.3 + - + -
437B ASN* 5.9 2.2 - - - +
439B MET* 3.0 33.2 - - + -
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ARG* 3.1 53.5 + - + +
396B ILE* 4.0 9.2 - - + +
397B SER 3.4 0.2 - - - -
398B LEU* 1.3 77.6 - - - +
400B PHE* 1.3 54.1 + - - +
402B LEU* 3.0 8.7 - - - +
403B GLU* 2.7 34.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 6.1 1.1 - - - -
267B MET* 3.3 33.4 - - + -
268B PHE 5.7 1.6 - - - -
269B GLN* 6.0 1.8 - - + -
396B ILE 3.5 8.9 + - - +
397B SER* 3.0 10.2 + - - +
399B GLU* 1.3 75.2 - - - +
401B MET* 1.3 88.7 + - + +
402B LEU 2.9 1.4 + - - -
403B GLU* 3.1 10.3 + - - +
404B GLN* 2.9 45.0 + - - +
431B MET* 3.8 38.4 - - + -
432B PHE* 4.4 4.7 - - + -
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Residues in contact with MET 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B SER* 2.9 28.3 + - - +
398B LEU* 3.8 4.9 - - + +
400B PHE* 1.3 87.4 - - + +
402B LEU* 1.3 66.6 + - - +
405B ALA* 3.2 14.4 + - - +
431B MET* 4.0 9.0 - - - +
432B PHE* 3.3 47.0 - - + -
433B ASN* 4.2 2.5 - - - +
436B GLY* 5.0 7.9 - - - -
437B ASN* 5.4 1.8 - - - +
439B MET* 5.9 2.7 - - + -
440B THR* 3.1 52.0 - - + +
443B LEU* 4.5 2.9 - - + +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.6 28.9 - - + -
338B ALA* 4.7 5.2 - - + -
339B ASN* 4.1 17.5 - - - +
342B THR* 3.7 26.7 - - + +
395B ARG* 6.0 0.4 - - - +
398B LEU* 2.5 29.3 + - + +
399B GLU* 3.0 14.1 - - - +
400B PHE 2.9 0.8 - - - -
401B MET* 1.3 71.6 - - - +
403B GLU* 1.3 67.5 + - - +
405B ALA* 2.9 10.2 + - - +
406B ASN* 3.1 13.8 + - - +
439B MET* 4.5 4.7 - - + +
443B LEU* 3.9 13.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 403 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 6.0 1.4 - - - +
269B GLN* 5.7 0.5 + - - -
399B GLU 2.7 19.3 + - - +
400B PHE* 3.5 12.7 - - - +
402B LEU* 1.3 70.9 - - - +
404B GLN* 1.3 102.9 + - - +
405B ALA 2.5 14.9 + - - -
406B ASN* 2.6 24.1 + - - +
407B LYS* 2.7 29.3 + - + +
----------------------------------------------------------
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 6.3 0.6 - - - -
269B GLN* 2.9 41.7 + - - +
270B PRO* 3.9 6.6 - - + +
400B PHE* 2.9 31.6 + - + +
403B GLU* 1.3 109.3 + - - +
405B ALA* 1.3 61.4 + - - +
407B LYS* 3.6 3.8 - - - -
408B PHE* 3.2 34.5 + - + +
432B PHE* 3.3 41.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.1 29.6 - - + +
335B LEU* 3.9 8.7 - - + -
401B MET 3.2 4.8 + - - +
402B LEU 2.9 11.8 + - - +
403B GLU 2.5 4.9 + - - -
404B GLN* 1.3 73.2 - - - +
406B ASN* 1.3 56.3 + - - +
408B PHE 3.0 2.1 + - - -
409B ALA* 2.4 38.5 + - - -
432B PHE* 3.8 5.4 - - + -
443B LEU* 3.5 26.7 - - + -
----------------------------------------------------------
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Residues in contact with ASN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 2.9 19.4 - - - +
339B ASN* 2.6 45.5 + - - -
402B LEU* 3.1 26.4 + - - +
403B GLU* 2.6 15.2 + - - +
405B ALA* 1.3 75.4 - - - +
407B LYS* 1.3 65.4 + - - +
409B ALA* 3.1 13.0 - - - +
----------------------------------------------------------
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 17.6 - - - +
42B GLU* 3.3 18.3 + - - +
269B GLN* 2.4 41.0 - - - +
403B GLU* 2.7 31.5 + - + +
404B GLN* 3.5 8.7 + - - +
406B ASN* 1.3 77.4 - - - +
408B PHE* 1.3 93.6 + - + +
409B ALA 3.4 0.2 + - - -
410B ASN 4.6 1.4 + - - -
411B HIS* 3.8 13.7 + - + -
----------------------------------------------------------
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.7 15.5 - - + -
269B GLN* 4.5 3.1 - - + -
270B PRO* 3.6 36.8 - - + -
271B CYS 5.1 0.7 - - - -
272B VAL* 5.4 1.1 - - + -
330B ILE* 3.9 11.6 + - + +
404B GLN* 3.2 21.7 + - + +
405B ALA 3.0 5.4 + - - +
407B LYS* 1.3 117.9 - - + +
409B ALA* 1.3 67.6 + - - +
410B ASN 2.8 5.8 + - - -
411B HIS* 3.3 28.6 + + - +
414B ILE* 3.2 51.2 - - + +
----------------------------------------------------------
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ILE* 3.8 15.4 - - + +
332B LYS* 2.8 34.5 + - + +
335B LEU* 3.8 14.8 - - + -
405B ALA 2.4 21.7 + - - +
406B ASN* 3.1 20.9 - - - +
407B LYS 3.1 1.6 - - - -
408B PHE* 1.3 74.1 - - - +
410B ASN* 1.4 61.0 + - - +
----------------------------------------------------------
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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