Contacts of the helix formed by residues 417 - 449 (chain B) in PDB entry 1JB0
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 HIS 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706A TRP* 6.2 2.2 - - + -
413B ARG 2.8 28.6 + - - -
414B VAL* 3.1 21.2 + - - -
416B GLN* 1.3 77.7 - - - +
418B LYS* 1.3 64.8 + - - +
419B GLU* 3.3 4.7 - - - -
420B ALA* 3.0 23.2 + - + -
421B ILE* 3.2 26.9 + - + +
1227B CLA 2.4 91.4 + + + -
1228B CLA 5.9 1.6 - - - -
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A SER* 5.6 1.8 - - - -
414B VAL 3.2 8.2 + - - +
415B LEU* 3.2 18.2 + - + +
417B HIS* 1.3 76.1 - - - +
419B GLU* 1.3 81.2 + - - +
421B ILE* 3.3 4.8 + - - +
422B ILE* 2.9 35.4 + - + +
545B LEU* 3.4 44.4 + - + +
546B ASP* 2.9 21.9 + - - +
549B GLY 2.9 20.6 + - - -
550B SER* 4.5 0.8 - - - +
139F SER* 2.6 30.1 + - - -
140F PRO 4.1 4.8 + - - -
141F ARG* 3.9 11.4 - - + +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A GLU 5.4 0.2 - - - -
703A SER* 3.4 32.2 - - - +
706A TRP* 3.5 40.8 - - + +
416B GLN 4.1 0.2 - - - +
417B HIS* 4.0 2.2 - - - -
418B LYS* 1.3 92.4 + - - +
420B ALA* 1.3 63.3 + - - +
423B SER* 2.9 30.8 + - - -
138F VAL* 3.8 12.3 - - - +
139F SER* 4.1 4.2 + - - -
141F ARG* 2.6 42.2 + - - -
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Residues in contact with ALA 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TRP* 3.5 25.2 - - + -
417B HIS* 3.0 25.6 + - + +
419B GLU* 1.3 78.1 - - - +
421B ILE* 1.3 63.1 + - - +
423B SER* 2.8 16.0 + - - -
424B HIS* 2.8 19.3 + - - -
1227B CLA 4.4 9.0 - - + -
1228B CLA 3.6 24.5 - - - +
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B VAL* 3.7 33.7 - - + +
417B HIS* 3.2 36.5 + - + +
418B LYS* 3.5 9.6 - - - +
420B ALA* 1.3 78.1 - - - +
422B ILE* 1.3 63.0 + - - +
424B HIS* 3.4 0.5 + - - +
425B LEU* 3.2 19.5 + - + +
541B VAL* 4.4 20.9 - - + -
545B LEU* 4.5 3.8 - - + -
1227B CLA 3.9 32.8 - - + +
1236B CLA 3.6 22.7 - - + +
4009B BCR 4.6 8.7 - - + -
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LEU* 4.0 14.8 - - + -
703A SER* 3.5 31.6 - - - +
704A ILE* 6.2 0.2 - - + -
418B LYS* 2.9 24.2 + - + +
421B ILE* 1.3 69.8 - - - +
423B SER* 1.3 61.3 + - - +
425B LEU* 3.2 8.1 + - - +
426B SER* 2.9 27.2 + - - -
538B LEU* 3.8 4.5 - - + +
541B VAL* 4.7 2.9 - - + -
542B LYS* 3.9 48.9 - - + +
545B LEU* 4.1 20.0 - - + -
546B ASP* 3.9 20.0 - - - +
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Residues in contact with SER 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A SER* 3.5 22.2 - - - -
704A ILE* 4.8 2.0 - - - -
706A TRP* 4.4 0.9 - - - -
707A ALA* 3.9 8.5 - - - +
1138A CLA 3.3 31.6 - - - +
419B GLU 2.9 16.5 + - - -
420B ALA* 2.8 24.1 + - - -
422B ILE* 1.3 77.9 - - - +
424B HIS* 1.3 64.2 + - - +
426B SER* 3.2 9.7 - - - -
427B TRP 3.0 20.6 + - - -
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Residues in contact with HIS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706A TRP* 5.6 0.7 - + - -
1138A CLA 4.2 8.7 - - - -
420B ALA* 2.8 22.3 + - - +
421B ILE 3.8 0.2 - - - +
422B ILE 3.2 0.2 - - - -
423B SER* 1.3 85.7 + - - +
425B LEU* 1.3 58.9 + - - +
426B SER 3.0 1.8 - - - -
427B TRP* 2.8 23.8 + + + +
428B VAL* 2.9 20.7 + - - +
1227B CLA 3.2 48.2 - - + +
1228B CLA 2.4 82.0 + + + -
1236B CLA 4.7 7.4 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ILE* 3.2 11.7 + - + +
422B ILE* 3.2 8.0 + - - +
424B HIS* 1.3 75.0 - - - +
426B SER* 1.3 63.3 + - - +
428B VAL* 3.6 3.7 + - - +
429B SER* 2.9 29.2 + - - -
534B HIS* 4.1 24.7 - - + +
537B THR* 3.9 15.9 - - + -
538B LEU* 3.7 32.1 - - + -
541B VAL* 4.0 22.2 - - + -
1236B CLA 3.1 53.8 - - + +
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A LEU* 4.8 4.0 - - - +
704A ILE* 3.5 15.7 - - - +
1013A CLA 3.1 20.5 - - - +
1138A CLA 2.8 19.4 + - - -
422B ILE 2.9 13.0 + - - -
423B SER* 3.2 15.5 - - - -
424B HIS 3.0 0.2 - - - -
425B LEU* 1.3 78.1 - - - +
427B TRP* 1.3 61.8 + - - +
429B SER* 3.7 1.9 - - - -
430B LEU* 3.0 25.5 + - - +
538B LEU* 3.9 16.6 - - - +
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Residues in contact with TRP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A CLA 3.0 58.3 - - + +
423B SER 3.0 6.7 + - - +
424B HIS* 2.8 16.3 + + + +
426B SER* 1.3 72.8 - - - +
428B VAL* 1.3 83.6 + - + +
430B LEU* 3.2 5.9 + - - +
431B PHE* 2.7 68.7 + + + +
1228B CLA 3.2 59.5 - + + +
1229B CLA 2.8 46.6 + - + -
1235B CLA 4.7 6.1 - - + -
1236B CLA 4.1 11.7 - - + -
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Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B HIS 2.9 15.1 + - - +
425B LEU* 4.0 4.0 - - - +
427B TRP* 1.3 91.5 - - + +
429B SER* 1.3 54.2 + - - +
431B PHE* 3.4 4.3 - - - +
432B LEU* 2.7 45.2 + - + +
534B HIS* 3.6 29.4 - - + +
1235B CLA 4.2 18.6 - - + -
1236B CLA 3.5 39.3 - - + -
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A CLA 2.8 28.0 - - - +
425B LEU 2.9 17.7 + - - -
426B SER 3.7 3.8 - - - -
428B VAL* 1.3 74.8 - - - +
430B LEU* 1.3 56.9 + - - +
432B LEU* 4.5 0.9 - - - -
433B GLY 2.8 30.8 + - - -
531B LEU* 3.3 7.9 - - - +
534B HIS* 3.6 10.1 + - - +
535B THR* 3.5 37.6 + - - -
538B LEU* 4.2 2.2 - - - +
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Residues in contact with LEU 430 (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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1013A CLA 3.6 34.4 - - + +
1138A CLA 3.2 51.1 - - + +
426B SER* 3.0 16.2 + - - +
427B TRP* 3.4 0.4 - - - +
429B SER* 1.3 78.7 - - - +
431B PHE* 1.3 63.0 + - - +
434B PHE* 2.9 51.1 + - + -
1229B CLA 3.4 15.9 - - - -
4014B BCR 3.5 27.8 - - + -
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B TRP* 2.7 43.5 + + + +
428B VAL* 3.4 5.4 - - - +
430B LEU* 1.3 75.5 - - - +
432B LEU* 1.3 62.2 + - - +
435B HIS* 2.9 60.7 + + - +
1229B CLA 3.2 51.1 - + + +
1235B CLA 3.1 60.6 - - + -
4015J BCR 3.4 22.2 - - + -
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Residues in contact with LEU 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B VAL* 2.7 27.3 + - + +
429B SER 3.7 3.1 - - - +
431B PHE* 1.3 72.4 - - - +
433B GLY* 1.3 59.2 + - - +
435B HIS* 4.3 0.5 - - - +
436B THR* 2.8 35.7 + - - -
527B HIS* 4.1 17.0 - - + +
530B ALA* 3.6 32.5 - - + +
531B LEU* 3.6 13.7 - - + +
534B HIS* 3.7 16.4 - - + +
1235B CLA 3.7 41.1 - - + -
4015J BCR 3.9 19.7 - - + -
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Residues in contact with GLY 433 (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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1013A CLA 3.2 30.0 + - - -
429B SER 2.8 14.6 + - - -
432B LEU* 1.3 71.1 - - - +
434B PHE* 1.3 65.6 + - - +
436B THR* 4.9 0.2 - - - -
437B LEU* 2.9 29.9 + - - +
531B LEU* 3.6 15.4 - - - +
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Residues in contact with PHE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A CLA 3.7 41.7 - - + -
1138A CLA 3.9 17.0 - - + -
4011A BCR 4.6 17.2 - - + +
430B LEU* 2.9 51.7 + - + +
431B PHE 4.1 2.2 - - - +
433B GLY* 1.3 71.0 - - - -
435B HIS* 1.3 66.3 + - + +
437B LEU* 4.4 2.2 - - - +
438B GLY* 3.0 22.5 + - - -
1229B CLA 4.0 31.9 - - + -
1230B CLA 4.0 3.8 - - - +
4014B BCR 3.4 52.9 - - + -
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Residues in contact with HIS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4011A BCR 6.5 0.4 - - + -
431B PHE* 2.9 54.7 + + - +
433B GLY 3.2 0.4 - - - -
434B PHE* 1.3 82.5 - - + +
436B THR* 1.3 61.2 + - - +
438B GLY* 3.0 0.3 + - - -
439B LEU* 2.8 34.9 + - + +
1229B CLA 2.4 66.8 + + + -
1230B CLA 3.8 12.2 - - + +
4015J BCR 3.5 42.8 - - + +
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Residues in contact with THR 436 (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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432B LEU* 2.8 25.1 + - - -
433B GLY* 4.9 0.4 - - - -
435B HIS* 1.3 73.8 - - - +
437B LEU* 1.3 68.6 + - - +
438B GLY 3.2 0.2 + - - -
439B LEU* 3.3 3.8 + - - +
440B TYR* 3.2 39.1 + - + -
524B LEU* 3.9 19.7 - - + +
527B HIS* 3.6 22.8 + - + +
528B ALA* 4.1 8.3 - - - +
531B LEU* 5.6 0.7 - - - -
1021B CLA 3.9 21.1 - - + -
4015J BCR 3.8 12.5 - - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A PHE* 3.9 27.6 - - + -
1013A CLA 3.6 42.6 - - + -
4011A BCR 4.0 9.6 - - + -
433B GLY 2.9 20.3 + - - +
434B PHE* 4.4 1.6 - - - +
436B THR* 1.3 79.4 - - - +
438B GLY* 1.3 62.7 + - - +
440B TYR* 3.3 1.2 + - - +
441B VAL* 3.0 44.1 + - + +
622B LEU* 4.7 6.7 - - + -
1012B CLA 4.0 17.0 - - + +
1021B CLA 3.8 25.5 - - + +
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Residues in contact with GLY 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4011A BCR 4.1 15.5 - - - -
434B PHE 3.0 14.5 + - - -
435B HIS 3.0 0.4 + - - -
437B LEU* 1.3 78.4 - - - +
439B LEU* 1.3 57.0 + - - +
441B VAL* 3.4 1.4 + - - +
442B HIS* 2.9 28.6 + - - +
1230B CLA 3.2 33.9 - - - +
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Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B HIS 2.8 24.0 + - - +
436B THR 3.3 0.9 + - - +
438B GLY* 1.3 69.0 - - - +
440B TYR* 1.3 65.8 + - - +
442B HIS* 3.2 4.3 + - - +
443B ASN* 2.9 33.3 + - - +
456B ILE* 3.8 29.6 - - + +
458B ILE* 4.6 4.5 - - + -
523B PHE* 4.8 2.7 - - + -
524B LEU* 3.8 25.8 - - + -
1230B CLA 3.8 33.0 - - + -
4015J BCR 3.7 48.0 - - + -
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B THR* 3.2 38.0 + - + -
437B LEU 3.7 6.1 - - - +
439B LEU* 1.3 76.4 - - - +
441B VAL* 1.3 58.9 + - - +
443B ASN* 3.3 3.3 + - - +
444B ASP* 2.8 33.6 + - - +
521B GLY 4.7 0.2 + - - -
524B LEU* 3.3 26.6 - - + +
525B VAL* 3.2 35.5 + - - +
619B SER 3.5 24.4 + - - -
620B THR 3.6 18.4 - - - -
621B TYR* 4.3 0.5 - - - -
622B LEU* 3.6 42.2 - - + -
625B TRP* 4.3 2.4 + - - -
1021B CLA 3.7 30.2 - - + +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4011A BCR 4.0 16.4 - - + -
437B LEU* 3.0 37.0 + - + +
438B GLY 3.9 3.8 - - - +
440B TYR* 1.3 73.2 - - - +
442B HIS* 1.3 67.3 + - - +
444B ASP* 3.7 7.2 - - - +
445B VAL* 3.0 30.2 + - + +
1012B CLA 3.9 45.3 - - + -
1230B CLA 3.6 31.0 - - + -
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Residues in contact with HIS 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B GLY 2.9 15.3 + - - +
439B LEU* 3.2 10.7 + - - +
441B VAL* 1.3 77.6 - - - +
443B ASN* 1.3 85.3 + - - +
445B VAL* 3.3 2.3 + - - +
446B VAL* 3.0 32.5 + - + +
454B LYS 2.8 21.7 + - - -
455B GLN* 4.1 1.1 - - - -
456B ILE* 3.3 25.7 - - + +
1230B CLA 2.4 92.5 + + + +
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Residues in contact with ASN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU 2.9 16.0 + - - +
440B TYR 3.7 0.9 - - - +
442B HIS* 1.3 83.6 - - - +
444B ASP* 1.3 63.4 + - - +
446B VAL* 4.4 0.9 - - - -
447B VAL* 2.8 28.6 + - - +
455B GLN* 3.4 25.9 + - - +
456B ILE* 3.0 40.9 + - - +
457B LEU* 3.8 6.3 - - - +
524B LEU* 3.8 10.1 - - - +
620B THR 2.9 29.6 + - - +
621B TYR* 3.9 3.1 - - + -
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TYR* 2.6 27.1 + - - +
674A LEU* 4.0 7.9 - - + -
677A LEU* 4.3 0.2 - - - -
440B TYR 2.8 24.1 + - - +
441B VAL* 3.7 7.0 - - - +
442B HIS 3.3 0.2 - - - -
443B ASN* 1.3 72.4 - - - +
445B VAL* 1.3 54.1 + - - +
448B ALA* 2.8 36.2 + - - +
621B TYR* 3.4 9.5 - - - +
622B LEU* 2.6 32.9 + - - +
623B MET* 2.9 23.2 + - - +
1012B CLA 3.6 16.9 - - + +
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A LEU* 4.0 16.4 - - + -
1107A CLA 3.7 28.7 - - + -
441B VAL* 3.0 22.6 + - + +
442B HIS 3.6 3.8 - - - +
444B ASP* 1.3 75.3 - - + +
446B VAL* 1.3 58.6 + - - +
448B ALA* 3.1 3.9 + - - +
449B PHE* 2.9 44.3 + - + -
1012B CLA 4.8 5.2 - - + -
1230B CLA 3.7 45.1 - - + -
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Residues in contact with VAL 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL 5.7 0.9 - - - +
442B HIS* 3.0 24.5 + - + +
443B ASN 3.9 1.1 - - - +
445B VAL* 1.3 78.9 - - - +
447B VAL* 1.3 61.7 + - - +
449B PHE* 3.4 8.3 + - - -
451B THR* 2.9 48.2 + - - +
454B LYS* 3.5 37.7 - - + +
455B GLN* 3.5 36.8 - - + +
1230B CLA 4.7 12.8 - - + -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665A TYR* 3.9 19.7 - - + +
666A GLY* 4.3 4.7 + - - -
443B ASN 2.8 24.7 + - - +
444B ASP 3.8 2.5 - - - +
446B VAL* 1.3 70.3 - - - +
448B ALA* 1.3 65.9 + - - +
450B GLY* 3.1 13.7 + - - -
452B PRO* 4.1 19.2 - - + +
455B GLN* 3.3 40.4 - - + +
621B TYR* 3.9 28.9 - - + +
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 4.4 0.5 - - - +
665A TYR* 3.6 36.1 - - + -
666A GLY* 2.7 24.1 + - - -
670A SER* 3.4 14.3 + - - +
674A LEU* 3.9 19.7 - - + -
444B ASP 2.8 19.8 + - - +
445B VAL 3.1 5.4 + - - +
447B VAL* 1.3 77.5 - - - +
449B PHE* 1.3 58.6 + - + +
450B GLY 3.3 0.9 + - - -
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Residues in contact with PHE 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 3.9 12.6 - - + +
122A GLY* 3.7 26.9 - - - +
123A GLN* 3.7 24.5 - - + -
125A ILE* 3.6 33.4 - - + +
126A LEU* 4.3 10.3 - - + -
670A SER* 3.8 13.5 - - - -
674A LEU* 4.2 10.5 - - + -
1107A CLA 3.7 37.7 - + + -
445B VAL* 2.9 33.7 + - + +
446B VAL* 3.9 5.8 - - - +
447B VAL 3.2 0.6 - - - -
448B ALA* 1.3 81.9 - - + +
450B GLY* 1.3 59.0 + - - +
451B THR* 3.3 14.4 + - + +
1230B CLA 5.0 2.0 - - + -
22F VAL* 4.3 8.1 - - - +
----------------------------------------------------------
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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