Contacts of the helix formed by residues 411 - 442 (chain B) in PDB entry 3ODX
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 PRO 411 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LYS* 1.3 54.9 - - - +
413B SER* 2.8 14.0 + - - +
414B GLN* 2.5 51.3 + - + +
415B VAL* 3.1 13.1 + - - -
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Residues in contact with LYS 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO* 1.3 68.9 - - - +
413B SER* 1.3 60.1 + - - +
415B VAL* 3.3 25.8 + - + +
416B LYS* 3.0 60.3 + - - +
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO* 2.8 18.2 + - - +
412B LYS* 1.3 75.0 - - - +
414B GLN* 1.3 63.0 + - - -
417B ARG* 3.1 25.1 + - - +
578B ASN* 3.2 42.5 - - - +
580B GLU* 5.7 4.1 - - - +
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Residues in contact with GLN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO* 2.5 40.0 + - + +
413B SER* 1.3 78.4 + - - +
415B VAL* 1.3 58.1 + - + +
416B LYS 3.3 0.2 - - - -
417B ARG* 3.8 25.3 - - - +
418B GLN* 2.6 38.0 + - + +
489B ILE* 5.9 1.2 - - - +
490B GLU* 6.3 0.4 - - - +
578B ASN 4.0 6.8 - - - +
580B GLU* 3.2 33.8 + - - +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B PRO 3.1 6.5 + - - +
412B LYS* 3.3 37.0 + - + +
414B GLN* 1.3 75.7 - - - +
416B LYS* 1.3 73.8 + - - +
418B GLN* 3.7 5.1 - - - +
419B GLU* 2.9 53.5 + - + +
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LYS* 3.0 43.0 + - - +
415B VAL* 1.3 86.1 - - - +
417B ARG* 1.3 60.5 + - - +
419B GLU* 3.0 23.6 + - + +
420B VAL* 2.6 47.5 + - + +
574B SER* 5.4 0.7 - - - +
578B ASN* 3.4 24.0 - - - +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B SER 3.1 20.8 + - - +
414B GLN* 3.0 27.4 + - - +
416B LYS* 1.3 75.4 - - - +
418B GLN* 1.3 57.9 + - - +
420B VAL* 4.4 2.6 - - - +
421B ILE* 3.0 42.6 + - + +
489B ILE* 3.5 29.4 - - - +
490B GLU* 3.6 13.3 - - - +
491B GLU 3.6 10.9 - - - +
492B ILE* 4.0 12.1 - - - +
575B ILE* 4.2 15.7 - - + +
578B ASN* 3.3 27.0 - - + +
579B THR* 2.8 23.4 + - - +
580B GLU* 3.8 12.3 + - - -
584B GLU* 3.5 28.3 + - - +
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Residues in contact with GLN 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLN* 2.6 20.4 + - + +
415B VAL* 3.7 4.9 - - - +
417B ARG* 1.3 75.1 - - - +
419B GLU* 1.3 57.4 + - + +
421B ILE* 3.7 5.0 - - - +
422B SER* 2.8 36.5 + - - +
482B ARG* 3.6 32.1 - - - +
489B ILE* 3.1 42.1 + - - +
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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
----------------------------------------------------------
415B VAL* 2.9 40.8 + - - +
416B LYS* 3.0 25.5 + - + +
418B GLN* 1.3 77.4 - - + +
420B VAL* 1.3 52.9 + - + +
422B SER* 3.1 8.7 + - - -
423B GLU* 2.7 35.4 + - - +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LYS* 2.6 35.4 + - + +
419B GLU* 1.3 69.4 - - + +
421B ILE* 1.3 67.9 + - - +
423B GLU* 2.9 11.7 + - - +
424B LEU* 2.9 23.4 + - - +
571B LEU* 3.4 45.8 - - + +
574B SER* 3.5 26.2 - - - +
575B ILE* 3.5 16.8 - - + +
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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
----------------------------------------------------------
417B ARG* 3.0 31.4 + - - +
418B GLN* 3.9 6.7 - - - +
420B VAL* 1.3 77.3 - - - +
422B SER* 1.3 63.8 + - - +
424B LEU* 3.5 7.3 + - + +
425B LEU* 3.3 17.6 + - + +
478B LEU* 6.2 1.1 - - + -
482B ARG* 6.2 2.5 - - - -
489B ILE* 4.0 41.7 - - + -
492B ILE* 3.9 44.6 - - + -
575B ILE* 3.6 29.8 - - + -
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A GLU* 2.9 45.1 + - - +
418B GLN* 2.8 26.3 + - - +
419B GLU* 3.3 11.7 - - - -
420B VAL 3.1 0.2 - - - -
421B ILE* 1.3 69.7 - - - +
423B GLU* 1.3 68.1 + - - +
425B LEU* 2.9 9.0 + - - +
426B VAL* 2.9 25.5 + - - +
482B ARG* 5.4 5.4 + - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU 2.7 17.1 + - - +
420B VAL* 2.9 16.6 + - - +
422B SER* 1.3 70.0 - - - +
424B LEU* 1.3 63.4 + - - +
426B VAL* 3.4 4.8 + - - +
427B THR* 3.0 43.5 + - + +
571B LEU* 3.5 26.0 - - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B VAL 2.9 11.2 + - - +
421B ILE* 3.7 11.7 - - + +
423B GLU* 1.3 75.5 - - - +
425B LEU* 1.3 64.7 + - - +
427B THR* 3.2 5.9 + - - -
428B GLU* 2.9 24.6 + - - +
474B PHE* 4.3 20.2 - - + -
478B LEU* 4.1 19.1 - - + -
492B ILE* 5.8 2.2 - - + -
496B LEU* 4.5 9.2 - - + -
564B ARG* 3.4 13.5 + - - +
568B TYR* 4.1 18.2 - - + -
571B LEU* 3.9 26.1 - - + +
572B LEU* 4.4 19.1 - - + -
575B ILE* 4.5 14.6 - - + -
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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
----------------------------------------------------------
728A LEU* 3.8 20.0 - - + -
735A ALA* 3.2 33.9 - - + -
737A ILE* 4.7 1.1 - - + -
421B ILE* 3.3 9.7 + - + +
422B SER* 2.9 11.7 + - - +
424B LEU* 1.3 74.6 - - - +
426B VAL* 1.3 69.6 + - - +
428B GLU* 2.9 14.2 + - - +
429B ALA* 3.1 9.7 + - - +
475B LEU* 3.8 5.2 - - + +
478B LEU* 3.6 52.5 - - + +
479B MET* 3.9 15.7 - - + -
482B ARG* 4.2 15.9 - - + -
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Residues in contact with VAL 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A LEU* 4.9 1.3 - - + -
729A PHE 4.6 0.4 - - - +
730A THR* 2.9 42.0 - - - +
734A GLU* 4.4 19.7 - - - +
735A ALA* 4.4 12.8 - - + +
422B SER 2.9 18.4 + - - +
423B GLU* 3.8 3.6 - - - +
425B LEU* 1.3 85.7 - - + +
427B THR* 1.3 67.7 + - + +
429B ALA* 3.3 9.2 + - - +
430B ALA* 3.2 24.0 + - + +
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU* 3.0 34.8 + - + +
424B LEU* 3.2 3.5 + - - -
426B VAL* 1.3 83.6 - - + +
428B GLU* 1.3 65.6 + - - +
429B ALA 3.3 0.2 - - - -
430B ALA* 3.8 9.0 - - + +
431B HIS* 3.0 23.2 + - - +
564B ARG* 2.7 35.4 + - - -
571B LEU* 4.3 2.6 - - + +
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Residues in contact with GLU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU 2.9 14.7 + - - +
425B LEU* 2.9 11.6 + - - +
427B THR* 1.3 78.7 - - - +
429B ALA* 1.3 56.3 + - - +
431B HIS* 3.3 5.0 + - - +
432B VAL* 2.9 28.1 + - - +
471B HIS* 2.8 43.0 + - - +
474B PHE* 3.5 21.5 - - + -
475B LEU* 3.9 24.0 - - + -
478B LEU* 4.5 4.3 - - + -
564B ARG* 2.5 29.6 + - - +
568B TYR* 2.5 20.2 + - - -
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 3.5 27.3 - - - +
728A LEU* 4.4 12.6 - - + -
730A THR* 3.8 11.7 - - + -
425B LEU 3.1 7.6 + - - +
426B VAL 3.5 8.7 - - - +
428B GLU* 1.3 72.5 - - - +
430B ALA* 1.3 55.2 + - - +
432B VAL* 3.0 3.7 + - - +
433B ARG* 2.5 37.1 + - - +
475B LEU* 3.4 22.7 - - + +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A THR* 4.3 5.2 - - - +
426B VAL* 3.2 11.0 + - + +
427B THR* 3.8 12.6 - - + +
429B ALA* 1.3 76.0 - - - +
431B HIS* 1.3 63.2 + - - +
433B ARG* 3.0 38.0 + - - +
434B MET* 3.2 16.9 + - - +
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Residues in contact with HIS 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR 3.0 18.4 + - - +
428B GLU* 3.4 7.6 - - - +
429B ALA 3.1 0.2 - - - -
430B ALA* 1.3 76.8 - - - +
432B VAL* 1.3 60.9 + - - +
434B MET* 3.5 4.9 + - - +
435B LEU* 3.0 35.8 + - + +
471B HIS* 3.6 33.8 + + + -
560B THR* 3.7 29.0 - - + +
561B GLU* 2.7 32.5 + - - -
564B ARG* 3.6 35.1 - - + +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A MET* 5.4 3.6 - - - -
716A ARG* 4.6 11.2 - - - +
428B GLU 2.9 20.8 + - - +
429B ALA* 3.6 7.6 - - - +
431B HIS* 1.3 73.7 - - - +
433B ARG* 1.3 67.3 + - - +
435B LEU* 3.8 6.5 - - + +
436B ARG* 3.1 37.8 + - + +
468B ILE* 4.8 2.9 - - + +
471B HIS* 3.7 40.6 - - + +
472B SER* 3.8 18.8 - - - +
475B LEU* 4.4 13.0 - - + -
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Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A SER 3.8 6.3 + - - -
713A ALA 4.2 6.5 + - - -
714A MET* 3.5 20.5 - - + +
730A THR* 3.3 37.8 + - - +
429B ALA 2.5 17.0 + - - +
430B ALA* 3.0 29.8 + - - +
432B VAL* 1.3 74.6 - - - +
434B MET* 1.3 58.5 + - - +
436B ARG* 3.1 11.6 + - - +
437B VAL* 3.1 28.6 + - + +
548B ARG* 4.4 3.7 + - - +
550B ARG* 3.7 48.5 - - - +
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Residues in contact with MET 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ALA 3.2 9.0 + - - +
431B HIS* 3.7 8.7 - - - +
433B ARG* 1.3 77.4 - - + +
435B LEU* 1.3 71.5 + - + +
436B ARG 2.8 4.0 - - - -
437B VAL* 2.6 26.4 + - + +
438B LEU* 2.6 22.1 + - + +
552B LEU* 4.3 17.7 - - - -
557B MET* 3.5 41.3 - - + +
560B THR* 3.6 37.7 - - + +
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Residues in contact with LEU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B HIS* 3.0 42.6 + - + +
432B VAL* 3.8 6.5 - - - +
434B MET* 1.3 87.1 - - + +
436B ARG* 1.3 60.5 + - + +
438B LEU* 3.7 15.0 - - + +
439B HIS 3.2 10.6 + - - -
464B LEU* 4.1 19.5 - - + +
467B LEU* 3.9 27.4 - - + +
468B ILE* 3.2 33.5 - - + +
471B HIS* 3.9 10.5 - - + -
515B PHE* 5.3 2.0 - - + -
557B MET 6.0 0.7 - - - +
560B THR* 5.3 1.3 - - + -
561B GLU* 3.9 20.4 - - + +
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Residues in contact with ARG 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A ARG* 4.8 12.8 - - - +
432B VAL* 3.1 29.5 + - - +
433B ARG* 3.3 10.5 - - - +
434B MET 2.7 7.7 + - - -
435B LEU* 1.3 74.3 - - - +
437B VAL* 1.3 54.2 + - - +
439B HIS* 3.2 4.2 - - + +
440B ASP* 2.7 54.4 + - - +
468B ILE* 4.1 26.7 - - + +
469B GLU* 5.6 2.2 + - - -
472B SER* 5.5 0.4 + - - -
548B ARG* 4.1 9.3 - - - +
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Residues in contact with VAL 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B ARG* 3.1 19.9 + - + +
434B MET* 2.6 20.0 + - + +
436B ARG* 1.3 68.2 - - - +
438B LEU* 1.3 65.7 + - - +
440B ASP* 4.3 0.4 - - - +
441B LEU* 2.8 46.1 + - + +
442B PHE* 3.8 1.2 - - + -
548B ARG* 3.3 60.8 - - + +
549B CYS* 4.4 1.1 - - - -
557B MET* 4.3 22.2 - - + -
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B MET* 2.6 21.0 + - + +
435B LEU* 3.7 17.7 - - + +
437B VAL* 1.3 74.0 - - - +
439B HIS* 1.3 63.7 + - - +
442B PHE* 3.2 15.9 - - + +
443B PHE 3.1 18.9 + - - -
461B PHE* 4.0 17.5 - - + -
464B LEU* 4.0 16.6 - - + -
515B PHE* 4.5 17.3 - - + -
554B LEU* 3.5 31.6 - - + -
557B MET* 4.2 35.2 - - + +
558B ILE* 4.6 3.6 - - + -
----------------------------------------------------------
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Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU 3.2 12.4 + - - +
436B ARG* 3.2 9.8 + - + +
437B VAL 3.1 0.2 - - - -
438B LEU* 1.3 81.9 - - - +
440B ASP* 1.3 80.9 + - - +
443B PHE* 3.3 19.9 + + - -
444B GLN* 2.8 64.2 + - + +
464B LEU* 3.7 11.5 - - + +
465B ASP* 3.1 28.9 + - - -
468B ILE* 3.6 17.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ARG* 2.7 37.1 + - - +
439B HIS* 1.3 106.6 + - - +
441B LEU* 1.3 62.6 + - + +
442B PHE 3.5 0.2 - - - -
444B GLN* 4.1 7.5 - - - +
445B PRO* 3.2 19.1 - - - +
548B ARG* 3.3 33.4 + - - +
----------------------------------------------------------
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B VAL* 2.8 33.5 + - + +
440B ASP* 1.3 80.6 - - + +
442B PHE* 1.3 73.2 + - + +
445B PRO* 3.5 14.0 - - - +
539B PHE* 4.3 4.3 - - - -
543B ALA* 3.7 20.3 - - + +
546B ARG* 4.2 26.0 - - + -
548B ARG* 3.6 46.4 - - + +
549B CYS* 4.0 15.0 - - - -
----------------------------------------------------------
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Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B VAL* 3.8 8.7 - - + -
438B LEU* 3.2 23.1 + - + +
440B ASP 3.5 1.0 - - - -
441B LEU* 1.3 98.8 - - + +
443B PHE* 1.3 69.9 + - - +
445B PRO* 3.1 2.5 - - - +
446B MET* 2.9 44.4 + - + +
461B PHE* 4.6 2.7 - - + -
539B PHE* 5.0 2.7 - + - -
540B VAL* 4.4 7.4 - - + -
543B ALA* 4.0 20.6 - - + -
544B GLU* 3.9 24.5 - - + -
549B CYS* 4.1 18.6 - - - -
554B LEU* 3.7 40.8 - - + -
557B MET* 4.2 14.8 - - + -
----------------------------------------------------------
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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).
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