Contacts of the helix formed by residues 445 - 469 (chain A) 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 MET 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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427A THR 5.5 0.4 - - - +
430A HIS* 3.5 33.2 - - + +
431A TYR* 3.7 33.7 - - + -
434A VAL* 3.6 35.7 - - - -
441A LYS* 3.3 12.6 - - + +
442A ALA* 2.8 7.6 + - - +
444A GLN* 1.3 79.5 - - + +
446A ARG* 1.3 68.3 + - - +
447A PHE 3.4 1.3 - - - -
448A GLN* 3.0 16.5 + - + +
449A VAL* 2.9 29.6 + - + +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TYR* 3.6 14.8 - - - +
442A ALA 3.3 1.6 + - - +
443A GLN* 3.7 39.8 + - - +
444A GLN 3.5 0.6 - - - -
445A MET* 1.3 78.9 - - - +
447A PHE* 1.3 64.4 + - - +
449A VAL* 3.2 2.8 + - - +
450A HIS* 2.9 23.6 + - - +
329B MET* 4.0 6.5 - - - +
332B TRP* 4.5 4.3 - - + -
355B GLN* 3.0 52.8 + - - +
358B LEU* 3.8 23.4 - - + +
359B GLN* 3.3 33.6 - - - +
362B GLU* 2.7 43.4 + - - +
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Residues in contact with PHE 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN 5.1 2.3 + - - +
445A MET 3.4 0.6 - - - -
446A ARG* 1.3 78.1 - - - +
448A GLN* 1.3 65.8 + - + +
450A HIS* 3.1 15.3 + + - +
451A THR* 2.9 42.1 + - - -
332B TRP* 4.2 26.1 - + - -
336B ASP* 6.1 0.4 - - - -
351B ASN* 4.9 4.9 - - - -
355B GLN* 4.7 10.5 - - - +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLN 3.5 20.7 + - - +
445A MET* 3.0 16.7 + - + +
447A PHE* 1.3 78.3 - - + +
449A VAL* 1.3 59.5 + - + +
451A THR* 3.3 5.9 + - - -
452A HIS* 2.9 31.9 + - - +
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Residues in contact with VAL 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A THR* 4.1 23.6 - - + +
428A LEU* 5.0 2.7 - - + -
431A TYR* 3.8 41.1 - - + -
445A MET* 2.9 28.2 + - + +
446A ARG 3.5 6.5 - - - +
448A GLN* 1.3 75.4 - - + +
450A HIS* 1.3 64.2 + - - +
452A HIS* 3.2 1.9 + - - +
453A LEU* 2.9 45.9 + - + +
329B MET* 3.8 16.6 - - + -
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Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG 2.9 13.4 + - - +
447A PHE* 3.2 23.6 - + - +
449A VAL* 1.3 78.0 - - - +
451A THR* 1.3 61.6 + - - +
453A LEU* 3.6 3.6 + - - +
454A GLN* 3.3 36.7 + - - +
329B MET* 3.7 20.6 + - - +
332B TRP* 3.4 50.5 - + + -
333B ALA* 3.3 37.9 - - + +
336B ASP* 2.6 24.3 + - - -
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Residues in contact with THR 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PHE* 2.9 37.7 + - - -
448A GLN* 3.6 6.3 - - - -
450A HIS* 1.3 75.9 - - - +
452A HIS* 1.3 64.6 + - - +
454A GLN* 3.2 14.8 + - - +
455A VAL* 3.0 30.3 + - + +
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Residues in contact with HIS 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423A GLU* 2.5 33.6 + - + -
426A HIS* 6.3 1.3 - + - -
427A THR* 3.5 31.2 + - + +
448A GLN 2.9 20.6 + - - +
449A VAL* 3.9 2.9 - - - +
451A THR* 1.3 70.2 - - - +
453A LEU* 1.3 67.6 + - - +
455A VAL* 3.1 16.0 + - + +
456A ILE* 3.1 26.0 + - + +
459A ARG* 5.8 0.4 + - - -
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Residues in contact with LEU 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A GLN* 3.8 42.4 + - + +
427A THR* 4.1 13.7 - - + -
428A LEU* 3.7 17.3 - - + -
449A VAL* 2.9 32.9 + - + +
450A HIS 3.9 4.0 - - - +
452A HIS* 1.3 76.3 - - - +
454A GLN* 1.3 62.9 + - + +
456A ILE* 3.5 7.3 + - + +
457A GLU* 3.1 22.5 + - - +
326B ASN* 4.4 7.6 - - - +
329B MET* 3.6 37.2 - - + -
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Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A HIS* 3.3 33.1 + - + +
451A THR* 3.2 12.8 + - - +
452A HIS 3.2 0.6 - - - -
453A LEU* 1.3 77.0 - - + +
455A VAL* 1.3 65.4 + - + +
457A GLU* 3.1 7.7 + - - +
458A GLU* 2.9 25.1 + - - +
333B ALA* 3.4 40.6 + - + +
336B ASP* 4.5 8.0 + - - +
337B ASN* 5.0 5.5 - - - +
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Residues in contact with VAL 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A THR* 3.0 31.1 + - + +
452A HIS* 3.1 18.8 + - + +
454A GLN* 1.3 76.3 - - + +
456A ILE* 1.3 63.5 + - - +
458A GLU* 3.1 7.4 + - - +
459A ARG* 2.9 43.5 + - + +
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Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A GLU* 3.4 33.2 - - + +
423A GLU* 3.9 7.4 - - + +
424A GLN* 3.6 41.1 - - + +
427A THR* 4.1 3.4 - - - +
452A HIS* 3.1 37.2 + - + +
453A LEU* 3.7 12.1 - - + +
455A VAL* 1.3 74.9 - - - +
457A GLU* 1.3 64.9 + - - +
459A ARG* 3.3 23.6 + - - +
460A VAL* 3.0 31.3 + - + +
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Residues in contact with GLU 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A LEU 3.1 10.5 + - - +
454A GLN* 3.1 10.8 + - - +
456A ILE* 1.3 81.1 - - - +
458A GLU* 1.3 62.1 + - - +
460A VAL* 3.5 8.2 + - + +
461A ASN* 3.0 53.8 + - - +
330B ARG* 2.8 34.1 + - - +
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454A GLN 2.9 16.5 + - - +
455A VAL* 3.6 6.1 - - - +
457A GLU* 1.3 75.9 + - - +
459A ARG* 1.3 60.5 + - - +
461A ASN* 3.2 11.1 + - - +
462A GLN* 2.9 36.2 + - + +
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Residues in contact with ARG 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ARG* 3.5 28.6 - - - +
392A LEU* 6.5 1.1 - - - -
416A TYR* 3.8 4.9 - - - -
420A GLU* 2.6 37.0 + - - +
423A GLU* 2.8 36.2 + - - -
455A VAL* 2.9 30.0 + - + +
456A ILE* 3.5 20.8 - - - +
458A GLU* 1.3 77.2 - - - +
460A VAL* 1.3 57.5 + - - +
462A GLN* 3.2 8.5 + - - +
463A SER* 2.9 33.8 + - - +
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Residues in contact with VAL 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 3.8 7.8 + - + +
417A LEU* 3.8 26.7 - - + -
420A GLU* 3.8 31.2 - - + -
456A ILE* 3.0 20.7 + - + +
457A GLU* 3.6 12.3 - - + +
459A ARG* 1.3 76.5 - - - +
461A ASN* 1.3 64.4 + - - +
463A SER* 3.3 3.1 + - - -
464A LEU* 3.0 40.2 + - + +
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Residues in contact with ASN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A GLU* 3.0 39.9 + - - +
458A GLU* 3.2 9.9 + - - +
460A VAL* 1.3 78.8 - - - +
462A GLN* 1.3 68.7 + - - +
464A LEU* 3.1 18.0 + - - +
465A GLY* 3.1 18.2 + - - -
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Residues in contact with GLN 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A GLU* 2.9 23.2 + - + +
459A ARG* 3.6 6.7 - - - +
461A ASN* 1.3 80.5 - - - +
463A SER* 1.3 63.2 + - - +
465A GLY* 3.2 14.4 + - - -
466A LEU* 3.6 8.1 + - - +
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Residues in contact with SER 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.9 16.2 - - - +
395A PHE* 3.5 13.3 - - - -
416A TYR* 2.7 47.7 + - - -
459A ARG* 2.9 14.0 + - - +
460A VAL 3.6 1.6 - - - -
462A GLN* 1.3 75.1 - - - +
464A LEU* 1.3 65.1 + - - +
466A LEU* 3.0 30.2 + - - +
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 5.1 3.1 - - - -
413A LEU* 3.9 33.7 - - + -
416A TYR* 6.1 0.4 - - + -
417A LEU* 4.9 9.9 - - + -
460A VAL* 3.0 34.5 + - + +
461A ASN* 3.1 19.5 + - - +
463A SER* 1.3 75.7 - - - +
465A GLY* 1.3 57.8 + - - +
467A LEU* 2.9 36.8 + - + +
468A ASP* 4.1 3.0 + - - +
481A ILE* 5.9 3.6 - - + -
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Residues in contact with GLY 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ASN 3.1 12.4 + - - -
462A GLN* 3.2 8.0 + - - -
463A SER 3.1 1.2 - - - -
464A LEU* 1.3 72.8 - - - +
466A LEU* 1.3 61.0 + - - +
467A LEU 2.9 6.5 + - - -
468A ASP* 3.0 36.2 + - - +
469A GLN* 3.9 2.3 + - - +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 4.6 12.8 - - + -
395A PHE* 4.2 13.5 - - + -
396A LEU* 3.4 32.5 - - + -
399A LEU* 4.0 20.1 - - + +
462A GLN 3.6 7.5 + - - +
463A SER* 3.0 26.2 + - - +
465A GLY* 1.3 77.1 - - - +
467A LEU* 1.3 59.9 + - - +
469A GLN* 3.3 21.1 - - - +
470A ASN* 4.7 0.5 + - - +
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A PHE* 4.2 20.6 - - + -
399A LEU* 3.5 26.2 - - + -
409A VAL* 4.8 1.6 - - + -
413A LEU* 4.6 15.9 - - + -
464A LEU* 2.9 22.2 + - + +
466A LEU* 1.3 76.0 - - - +
468A ASP* 1.3 52.8 + - - +
469A GLN 2.7 15.5 + - - -
470A ASN* 2.7 28.7 + - + +
473A LEU* 5.0 4.9 - - + -
474A ALA* 4.0 22.5 - - + +
477A LEU* 4.5 23.1 - - + -
481A ILE* 5.2 9.0 - - + -
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Residues in contact with ASP 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A LEU 4.4 2.3 - - - +
465A GLY* 3.0 27.4 + - - +
467A LEU* 1.3 76.2 - - - +
469A GLN* 1.3 60.6 + - - +
470A ASN 3.1 1.6 + - - -
471A PRO* 3.9 12.5 - - - +
474A ALA* 5.0 7.3 - - - +
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Residues in contact with GLN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLY 3.9 2.3 + - - +
466A LEU* 3.3 19.0 + - - +
467A LEU 2.7 1.4 + - - -
468A ASP* 1.3 79.4 - - - +
470A ASN* 1.3 57.2 + - + +
471A PRO* 3.5 7.5 - - - +
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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) + - + + + + + -
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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