Contacts of the helix formed by residues 438 - 460 (chain A) in PDB entry 1KNU
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 LYS 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 3.7 11.4 - - + -
373A LYS* 4.6 16.3 + - + +
374A PHE* 3.4 38.8 - - + +
377A LEU* 3.6 37.2 - - - +
387A PHE* 5.2 2.9 - - + -
434A LYS* 3.5 29.6 + - - +
435A LEU 3.0 15.9 + - - +
437A GLN* 1.3 75.3 - - - +
439A MET* 1.3 63.6 + - - +
440A THR 3.1 0.7 - - - -
441A ASP* 3.0 36.7 + - - +
442A LEU* 3.3 9.5 + - + +
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Residues in contact with MET 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 4.8 6.7 - - - +
387A PHE* 3.9 27.4 - - + -
390A VAL* 4.9 9.0 - - + -
391A ILE* 3.5 37.7 - - + +
394A SER* 5.0 6.5 - - - +
436A LEU* 2.9 26.5 - - + +
437A GLN 3.1 0.6 - - - -
438A LYS* 1.3 77.0 - - - +
440A THR* 1.3 63.1 + - - +
442A LEU* 3.1 14.4 + - - +
443A ARG* 3.0 33.9 + - + +
437B GLN* 6.1 5.6 - - + +
440B THR* 4.1 14.8 - - + +
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Residues in contact with THR 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 3.3 13.2 + - - +
438A LYS 3.1 0.6 - - - -
439A MET* 1.3 80.5 - - - +
441A ASP* 1.3 67.2 + - - +
443A ARG* 3.6 4.5 + - - +
444A GLN* 3.4 19.5 + - + +
440B THR* 3.2 29.4 - - - +
443B ARG* 3.7 42.3 - - + +
444B GLN* 4.1 17.0 + - - +
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Residues in contact with ASP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A PHE* 3.4 28.2 - - + -
373A LYS* 4.7 17.5 - - - +
437A GLN 4.0 4.0 - - - +
438A LYS* 3.0 33.3 + - - +
440A THR* 1.3 79.5 - - - +
442A LEU* 1.3 62.3 + - - +
444A GLN* 3.3 6.5 + - - +
445A ILE* 3.1 28.0 + - + +
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Residues in contact with LEU 442 (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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324A GLU* 3.3 37.5 - - + +
327A TYR* 4.1 16.3 - - + -
328A THR* 3.5 20.0 - - - +
370A PHE* 3.7 27.4 - - + -
387A PHE* 4.4 5.8 - - + -
391A ILE* 4.1 8.7 - - + -
438A LYS* 3.3 10.3 + - + +
439A MET* 3.1 30.9 + - - +
441A ASP* 1.3 79.2 - - - +
443A ARG* 1.3 65.0 + - - +
445A ILE* 3.0 17.2 + - + +
446A VAL* 3.1 17.3 + - - +
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Residues in contact with ARG 443 (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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324A GLU* 3.1 31.4 + - - -
396A ASP* 3.5 29.5 + - - -
397A ARG* 3.9 10.6 - - - +
439A MET* 3.0 25.6 + - + +
440A THR* 3.9 5.8 - - - +
442A LEU* 1.3 74.1 - - - +
444A GLN* 1.3 61.2 + - - +
446A VAL* 3.2 10.9 + - - +
447A THR* 3.1 24.9 + - - -
440B THR* 5.1 11.3 + - - +
441B ASP* 5.4 2.6 + - - +
444B GLN* 4.1 39.4 + - - +
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Residues in contact with GLN 444 (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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440A THR* 3.4 9.2 + - + +
441A ASP* 3.3 10.0 + - - +
442A LEU 3.2 0.8 - - - -
443A ARG* 1.3 75.5 - - - +
445A ILE* 1.3 67.5 + - + +
447A THR* 3.3 17.9 + - - +
448A GLU* 3.0 52.1 + - - +
444B GLN* 5.1 10.6 + - - +
447B THR* 5.1 14.1 + - - +
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Residues in contact with ILE 445 (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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327A TYR* 3.5 29.4 - - + -
366A PRO* 3.4 41.9 - - + +
367A LYS* 3.5 27.6 + - + +
370A PHE* 4.3 16.6 - - + -
441A ASP* 3.1 19.6 + - + +
442A LEU* 3.0 12.4 + - + +
444A GLN* 1.3 78.0 - - + +
446A VAL* 1.3 64.9 + - - +
448A GLU* 3.9 8.9 - - - +
449A HIS* 3.0 22.0 + - - +
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Residues in contact with VAL 446 (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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320A TYR 6.1 0.2 - - - +
323A HIS* 4.0 29.2 - - + +
324A GLU* 4.3 18.8 - - + +
327A TYR* 4.0 12.6 - - + -
442A LEU 3.1 12.4 + - - +
443A ARG* 3.4 10.3 - - - +
445A ILE* 1.3 78.5 - - - +
447A THR* 1.3 63.5 + - - +
449A HIS* 3.3 3.5 + - - +
450A VAL* 3.0 34.8 + - + +
473A TYR* 5.1 6.7 - - + +
476A LEU* 5.5 12.3 - - + -
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Residues in contact with THR 447 (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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443A ARG 3.1 13.3 + - - -
444A GLN* 3.6 26.7 + - - +
445A ILE 3.2 0.4 - - - -
446A VAL* 1.3 75.2 - - - +
448A GLU* 1.3 68.5 + - - +
450A VAL* 3.0 27.7 - - + +
451A GLN* 3.2 21.7 + - + +
444B GLN* 5.6 2.3 + - - -
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Residues in contact with GLU 448 (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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366A PRO* 3.9 31.6 - - + +
367A LYS* 6.2 0.4 - - - +
444A GLN* 3.0 52.2 + - - +
445A ILE* 3.9 7.3 + - - +
447A THR* 1.3 75.5 - - + +
449A HIS* 1.3 63.1 + - - +
451A GLN* 3.4 15.3 + - - +
452A LEU* 3.1 23.6 + - - +
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Residues in contact with HIS 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.4 15.6 + - - +
363A PHE* 3.3 26.6 - + - -
367A LYS* 2.8 27.9 + - - +
445A ILE 3.0 13.7 + - - +
446A VAL* 3.4 10.3 - - - +
448A GLU* 1.3 76.9 - - - +
450A VAL* 1.3 57.5 + - - +
452A LEU* 3.1 10.1 + - - +
453A LEU* 2.9 41.3 + - + +
473A TYR* 3.3 21.5 - - - +
1001A YPA 2.9 42.9 + + + -
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Residues in contact with VAL 450 (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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446A VAL* 3.0 23.9 + - + +
447A THR* 3.0 23.1 - - + +
449A HIS* 1.3 74.2 - - - +
451A GLN* 1.3 72.6 + - + +
453A LEU* 3.1 13.5 + - + +
454A GLN* 2.9 32.4 + - - +
473A TYR* 3.7 33.2 - - + -
476A LEU* 5.9 6.5 - - + -
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Residues in contact with GLN 451 (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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447A THR* 3.2 24.0 + - + +
448A GLU* 3.5 16.5 - - - +
450A VAL* 1.3 86.4 - - + +
452A LEU* 1.3 64.9 + - - +
454A GLN* 2.9 29.4 + - + +
455A VAL* 3.1 11.8 + - - +
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Residues in contact with LEU 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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359A PRO* 4.1 19.7 - - + +
362A ASP* 3.8 18.4 - - + +
363A PHE* 3.4 58.3 - - + +
367A LYS* 6.1 0.2 - - - +
448A GLU 3.1 11.1 + - - +
449A HIS* 3.3 10.3 - - - +
451A GLN* 1.3 79.5 - - - +
453A LEU* 1.3 61.9 + - - +
455A VAL* 3.2 14.6 + - + +
456A ILE* 3.2 27.5 + - + +
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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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282A PHE* 4.3 14.1 - - + -
363A PHE* 3.4 35.4 - - + -
449A HIS* 2.9 24.9 + - + +
450A VAL* 3.1 13.0 + - + +
452A LEU* 1.3 75.3 - - - +
454A GLN* 1.3 66.1 + - - +
456A ILE* 3.3 7.0 + - - +
457A LYS* 3.0 25.1 + - - +
465A LEU* 4.7 19.7 - - + -
473A TYR* 3.4 42.4 - - + -
1001A YPA 4.1 4.3 - - - +
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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 VAL* 2.9 29.1 + - - +
451A GLN* 3.1 16.6 - - + +
453A LEU* 1.3 76.7 - - - +
455A VAL* 1.3 66.2 + - + +
457A LYS* 3.4 21.5 + - - +
458A LYS* 3.2 23.8 + - + +
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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
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359A PRO* 4.8 11.4 - - + -
451A GLN 3.1 12.7 + - - +
452A LEU* 3.4 18.2 - - + +
453A LEU 3.1 0.2 - - - -
454A GLN* 1.3 77.4 - - + +
456A ILE* 1.3 71.2 + - + +
458A LYS* 3.0 16.1 + - - +
459A THR* 3.0 30.4 + - + +
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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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282A PHE* 4.5 8.5 - - + -
359A PRO* 3.8 32.3 - - + -
360A PHE* 3.7 28.5 - - + -
363A PHE* 4.3 20.0 - - + -
452A LEU* 3.2 20.4 + - + +
453A LEU* 3.3 5.6 + - - +
455A VAL* 1.3 77.8 - - + +
457A LYS* 1.3 55.4 + - - +
459A THR* 3.4 6.1 - - - +
460A GLU* 2.7 61.3 + - + +
463A MET* 4.4 11.2 - - + -
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Residues in contact with LYS 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 3.0 16.9 + - - +
454A GLN* 3.5 20.2 - - - +
455A VAL 3.1 0.2 - - - -
456A ILE* 1.3 77.9 - - - +
458A LYS* 1.3 61.3 + - + +
460A GLU 4.3 11.7 + - - +
461A THR* 4.6 6.6 + - - +
465A LEU* 6.4 2.9 - - + -
470A GLN* 5.5 9.7 - - - +
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Residues in contact with LYS 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* 3.2 18.4 - - + +
455A VAL* 3.0 5.5 + - - +
457A LYS* 1.3 80.0 - - + +
459A THR* 1.3 66.5 + - + +
460A GLU 3.5 0.4 - - - -
461A THR* 4.2 13.4 - - - +
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Residues in contact with THR 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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357A ARG* 5.1 3.7 + - - -
359A PRO* 5.5 2.3 - - - +
455A VAL* 3.0 30.5 + - + +
456A ILE* 3.4 12.1 + - - +
458A LYS* 1.3 82.8 - - + +
460A GLU* 1.3 78.0 + - - +
461A THR* 3.8 3.0 + - - -
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Residues in contact with GLU 460 (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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279A ILE* 3.6 20.5 - - - +
357A ARG* 2.9 36.3 + - - +
360A PHE* 4.4 5.8 - - + -
456A ILE* 2.7 43.2 + - + +
457A LYS* 4.3 5.8 - - - +
459A THR* 1.3 90.8 + - - +
461A THR* 1.3 55.7 + - - +
462A ASP* 3.1 18.0 - - - +
463A MET* 3.0 40.2 + - + +
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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
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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