Contacts of the helix formed by residues 438 - 466 (chain B) in PDB entry 3QMK
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 ASP 438 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 2.7 25.3 + - + +
437B VAL* 1.3 82.7 - - + +
439B PRO* 1.3 64.0 - - - +
440B GLU* 3.8 7.4 + - - +
441B LYS* 3.1 35.7 + - + +
442B ALA 3.1 6.2 + - - -
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Residues in contact with PRO 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A GLN* 5.9 0.2 + - - -
362A GLU* 4.2 11.8 - - + +
363A GLU* 5.9 4.9 - - + -
366A SER* 2.9 39.5 - - - +
434B VAL 3.7 0.4 - - - -
435B ALA* 3.5 7.9 - - - +
437B VAL 3.7 4.7 - - - +
438B ASP* 1.3 89.5 - - - +
440B GLU* 1.3 61.7 + - - +
442B ALA* 3.3 8.5 + - + +
443B GLN* 3.1 21.1 + - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ASP* 3.2 8.1 + - - +
439B PRO* 1.3 78.9 - - - +
441B LYS* 1.3 62.5 + - - +
443B GLN* 3.3 12.2 + - - +
444B GLN* 3.2 26.9 + - - +
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Residues in contact with LYS 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 3.8 12.1 - - + -
438B ASP* 3.1 29.4 + - - +
440B GLU* 1.3 75.6 - - - +
442B ALA* 1.3 65.6 + - - +
444B GLN* 3.1 30.2 + - - +
445B MET* 3.1 17.0 + - - +
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Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.8 12.5 - - + +
431B TYR* 3.6 11.9 - - + -
434B VAL* 3.6 8.2 - - + +
435B ALA* 3.6 41.7 - - + +
438B ASP 3.1 6.6 + - - +
439B PRO* 3.4 11.0 - - + +
441B LYS* 1.3 77.4 - - - +
443B GLN* 1.3 60.5 + - - +
445B MET* 3.4 9.9 - - - +
446B ARG* 3.1 19.9 + - - +
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 5.2 1.0 - - - +
359A GLN* 2.6 39.2 + - - +
362A GLU* 3.7 1.5 + - - +
439B PRO 3.1 12.4 + - - +
440B GLU* 3.4 13.6 + - - +
441B LYS 3.2 0.2 - - - -
442B ALA* 1.3 78.4 - - - +
444B GLN* 1.3 64.6 + - + +
445B MET 3.5 0.2 + - - -
446B ARG* 3.5 41.8 + - - +
447B PHE 5.0 0.2 + - - -
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU* 3.2 15.0 - - - +
441B LYS* 3.1 24.8 + - - +
443B GLN* 1.3 81.3 - - + +
445B MET* 1.3 58.5 + - + +
446B ARG 3.8 0.2 + - - -
447B PHE* 4.9 3.3 + - - +
448B GLN* 5.3 2.1 + - - +
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Residues in contact with MET 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B HIS* 3.4 36.1 - - + +
431B TYR* 3.8 29.8 - - + -
434B VAL* 3.7 33.2 - - + -
441B LYS 3.1 8.0 + - - +
442B ALA* 3.4 9.6 - - - +
444B GLN* 1.3 74.8 - - - +
446B ARG* 1.3 67.9 + - - +
447B PHE 3.4 1.8 - - - -
448B GLN* 2.9 29.1 + - + +
449B VAL* 2.9 24.9 + - + +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 3.9 2.6 - - - +
332A TRP* 4.6 2.5 - - + -
355A GLN* 3.1 52.3 + - - +
358A LEU* 3.7 34.6 - - + +
359A GLN* 3.6 17.4 + - - +
362A GLU* 2.7 41.0 + - - +
431B TYR* 3.7 11.4 - - + +
442B ALA 3.1 10.4 + - - +
443B GLN* 3.5 45.6 + - - +
444B GLN 3.5 0.8 - - - -
445B MET* 1.3 76.4 - - - +
447B PHE* 1.3 62.3 + - - +
449B VAL* 3.3 4.1 + - - +
450B HIS* 3.1 22.8 + - - +
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Residues in contact with PHE 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A TRP* 4.0 19.3 - + - -
351A ASN* 4.4 11.9 - - - -
355A GLN* 4.1 17.6 + - - +
443B GLN 5.0 0.4 + - - -
444B GLN 4.9 3.0 + - - +
445B MET 3.4 0.6 - - - -
446B ARG* 1.3 78.4 - - - +
448B GLN* 1.3 59.9 + - - +
450B HIS* 3.4 19.6 + + - +
451B THR* 2.9 49.6 + - + -
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Residues in contact with GLN 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR* 6.1 0.2 - - - +
444B GLN 5.3 1.7 + - - +
445B MET* 2.9 22.7 + - + +
447B PHE* 1.3 78.3 - - - +
449B VAL* 1.3 65.8 + - - +
451B THR* 3.7 6.8 - - - +
452B HIS* 2.8 51.6 + - - +
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Residues in contact with VAL 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 3.8 20.0 - - + -
427B THR* 4.0 22.7 - - + +
428B LEU* 5.3 2.9 - - + -
431B TYR* 3.9 34.1 - - + -
445B MET* 2.9 32.8 + - + +
446B ARG 3.6 7.2 - - - +
448B GLN* 1.3 80.6 - - - +
450B HIS* 1.3 61.3 + - - +
452B HIS* 3.0 6.3 + - - +
453B LEU* 2.8 39.4 + - + +
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Residues in contact with HIS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A MET* 3.7 21.6 + - - +
332A TRP* 3.5 69.8 + + + +
333A ALA* 3.9 8.1 - - - -
336A ASP* 3.1 25.2 + - - -
446B ARG 3.1 5.3 + - - +
447B PHE* 3.5 22.6 - + - +
449B VAL* 1.3 80.7 - - - +
451B THR* 1.3 62.3 + - - +
453B LEU* 3.4 5.2 + - - +
454B GLN* 3.2 48.3 + - + +
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Residues in contact with THR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B PHE* 2.9 44.3 + - + -
448B GLN* 3.7 8.5 - - - +
450B HIS* 1.3 74.3 - - - +
452B HIS* 1.3 65.8 + - - +
454B GLN* 3.2 15.9 + - + +
455B VAL* 3.0 31.7 + - + +
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Residues in contact with HIS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU* 2.7 29.1 + - + -
426B HIS* 6.1 1.6 - - - -
427B THR* 3.2 29.7 + - + +
448B GLN* 2.8 38.8 + - - +
449B VAL* 3.0 7.6 + - - +
451B THR* 1.3 74.0 - - - +
453B LEU* 1.3 62.0 + - - +
455B VAL* 3.1 23.7 + - + +
456B ILE* 3.1 21.5 + - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASN* 4.9 3.6 - - - +
329A MET* 3.6 38.8 - - + -
424B GLN* 3.9 32.5 - - + +
427B THR* 4.0 21.5 - - + -
428B LEU* 3.9 17.9 - - + -
449B VAL* 2.8 29.7 + - + +
450B HIS* 3.7 4.9 - - - +
451B THR 3.3 0.2 - - - -
452B HIS* 1.3 71.6 - - - +
454B GLN* 1.3 58.6 + - + +
456B ILE* 3.4 9.1 + - + +
457B GLU* 3.1 25.7 + - - +
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 4.0 22.3 + - + +
336A ASP* 3.4 25.7 + - - +
450B HIS* 3.2 40.0 + - + +
451B THR* 3.2 15.4 + - + +
453B LEU* 1.3 75.8 - - + +
455B VAL* 1.3 66.2 + - - +
457B GLU* 3.7 7.2 - - - +
458B GLU* 3.0 24.8 + - - +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B THR* 3.0 27.8 + - + +
452B HIS* 3.1 18.1 + - + +
454B GLN* 1.3 75.7 - - + +
456B ILE* 1.3 64.6 + - - +
458B GLU* 3.3 7.3 + - - +
459B ARG* 3.1 39.5 + - + +
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Residues in contact with ILE 456 (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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420B GLU* 3.8 32.3 - - + +
423B GLU* 3.7 18.4 - - + -
424B GLN* 4.0 20.4 - - + -
427B THR* 4.0 8.3 - - - +
452B HIS* 3.1 36.3 + - + +
453B LEU* 3.6 14.6 - - + +
455B VAL* 1.3 76.6 - - + +
457B GLU* 1.3 63.7 + - - +
459B ARG* 3.1 36.3 + - - +
460B VAL* 3.1 15.6 + - + +
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Residues in contact with GLU 457 (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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453B LEU 3.1 16.3 + - - +
454B GLN* 3.7 8.7 - - - +
455B VAL 3.3 0.2 - - - -
456B ILE* 1.3 77.9 - - - +
458B GLU* 1.3 63.4 + - - +
460B VAL* 3.4 8.6 + - - +
461B ASN* 3.1 35.6 + - - +
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Residues in contact with GLU 458 (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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454B GLN 3.0 17.4 + - - +
455B VAL* 3.6 7.0 - - - +
457B GLU* 1.3 74.0 - - - +
459B ARG* 1.3 65.4 + - - +
461B ASN* 3.3 15.8 + - - +
462B GLN* 3.0 47.9 + - + +
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Residues in contact with ARG 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 3.5 33.0 - - - +
416B TYR* 3.7 5.8 - - - +
420B GLU* 2.7 37.3 + - - +
423B GLU* 2.7 33.9 + - - -
455B VAL* 3.1 24.0 + - + +
456B ILE* 3.1 23.2 + - - +
458B GLU* 1.3 78.3 - - - +
460B VAL* 1.3 57.1 + - - +
462B GLN* 3.2 7.7 + - + +
463B SER* 2.8 33.7 + - - +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 4.1 7.2 - - - -
417B LEU* 3.7 26.0 - - + -
420B GLU* 3.6 32.3 - - + -
456B ILE* 3.1 16.9 + - + +
457B GLU* 3.6 10.5 - - - +
458B GLU 3.3 0.2 - - - -
459B ARG* 1.3 76.9 - - - +
461B ASN* 1.3 61.3 + - - +
463B SER* 3.3 1.7 + - - -
464B LEU* 2.8 47.0 + - + +
485B LEU* 4.2 9.0 - - + -
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Residues in contact with ASN 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLU* 3.1 36.5 + - - +
458B GLU* 3.8 17.0 + - - +
459B ARG 3.3 0.2 - - - -
460B VAL* 1.3 79.1 - - - +
462B GLN* 1.3 52.9 + - - +
464B LEU* 3.4 14.9 + - - +
465B GLY* 2.8 30.3 + - - -
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Residues in contact with GLN 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 3.0 42.1 + - + +
459B ARG* 3.5 7.2 - - - +
461B ASN* 1.3 74.6 - - - +
463B SER* 1.3 66.4 + - - +
465B GLY* 3.0 12.7 + - - -
466B LEU* 3.2 13.6 + - - +
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Residues in contact with SER 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.1 11.3 - - - +
395B PHE* 3.3 18.8 - - - -
413B LEU* 5.7 0.4 - - - -
416B TYR* 2.6 50.7 + - - -
459B ARG* 2.8 13.1 + - - +
460B VAL 3.7 1.1 - - - -
462B GLN* 1.3 75.8 - - - +
464B LEU* 1.3 63.2 + - - +
466B LEU* 3.0 29.3 + - - +
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Residues in contact with LEU 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 5.1 0.4 - - - -
413B LEU* 3.7 39.3 - - + -
417B LEU* 4.5 7.2 - - + -
460B VAL* 2.8 32.7 + - + +
461B ASN* 3.6 14.4 - - - +
463B SER* 1.3 76.2 - - - +
465B GLY* 1.3 55.4 + - - +
467B LEU* 2.7 36.8 + - + +
468B ASP* 3.5 7.5 + - - +
481B ILE* 4.3 13.0 - - + -
485B LEU* 3.7 35.0 - - + -
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Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B ASN 2.8 16.2 + - - -
462B GLN* 3.0 9.1 + - - -
464B LEU* 1.3 76.7 - - - +
466B LEU* 1.3 60.3 + - - +
468B ASP* 3.0 30.9 + - - +
469B GLN* 3.8 4.7 + - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 4.8 8.1 - - + -
395B PHE* 4.1 11.9 - - + -
396B LEU* 3.4 32.3 - - + -
399B LEU* 3.6 21.5 - - + +
462B GLN 3.2 12.0 + - - +
463B SER* 3.0 23.0 + - - +
464B LEU 2.9 0.8 + - - -
465B GLY* 1.3 76.4 - - - +
467B LEU* 1.3 59.1 + - - +
468B ASP 3.6 0.2 + - - -
469B GLN* 3.6 18.1 + - - +
470B ASN* 5.6 1.0 - - - +
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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