Contacts of the helix formed by residues 454 - 470 (chain A) in PDB entry 1KIX
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 ASN 454 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ASP* 4.0 20.5 + - + -
450A ASN 3.0 15.4 + - - +
451A LEU* 3.8 13.6 - - - +
453A LYS* 1.3 73.3 - - - +
455A ALA* 1.3 61.5 + - - +
456A ASP* 3.0 22.5 + - - +
457A ALA* 3.1 25.1 + - + +
458A ARG* 3.5 12.8 + - - +
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Residues in contact with ALA 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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451A LEU 5.3 0.9 - - - -
453A LYS 3.1 8.5 + - - +
454A ASN* 1.3 71.4 + - - +
456A ASP* 1.3 69.2 + - - +
458A ARG* 3.5 22.7 + - - +
459A LYS* 3.2 34.2 + - - +
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Residues in contact with ASP 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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454A ASN* 3.0 8.5 + - - +
455A ALA* 1.3 79.4 - - - +
457A ALA* 1.3 67.3 + - - +
459A LYS* 3.2 10.6 + - - +
460A LYS* 2.9 29.6 + - + +
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Residues in contact with ALA 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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446A VAL* 4.4 14.7 - - + +
449A ASP* 4.2 11.9 - - - +
451A LEU* 3.7 20.9 - - + -
454A ASN* 3.1 28.7 + - + +
456A ASP* 1.3 77.2 - - - +
458A ARG* 1.3 61.9 + - - +
460A LYS* 3.4 10.2 + - - +
461A LEU* 3.0 28.1 + - - +
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Residues in contact with ARG 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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383A VAL* 4.1 8.7 - - + +
384A LYS* 3.6 40.2 - - + +
451A LEU* 3.9 19.6 + - + +
454A ASN 3.5 12.4 + - - +
455A ALA* 3.6 22.4 + - - +
456A ASP 3.1 0.2 - - - -
457A ALA* 1.3 80.6 - - - +
459A LYS* 1.3 83.1 + - - +
461A LEU* 3.1 7.1 + - - +
462A GLU* 2.8 59.0 + - + +
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Residues in contact with LYS 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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455A ALA* 3.2 21.6 + - - +
456A ASP* 3.2 10.5 + - - +
458A ARG* 1.3 93.4 - - - +
460A LYS* 1.3 66.9 + - - +
462A GLU* 3.0 21.0 + - - +
463A ASP* 2.9 32.6 + - - +
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Residues in contact with LYS 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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445A ASN 4.8 4.6 + - - -
446A VAL* 3.9 29.1 - - + +
456A ASP* 2.9 19.6 + - + +
457A ALA* 3.4 9.9 - - - +
459A LYS* 1.3 77.3 - - - +
461A LEU* 1.3 60.8 + - - +
463A ASP* 3.4 13.0 + - - +
464A SER* 3.3 23.3 + - - -
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Residues in contact with LEU 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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383A VAL* 3.9 5.6 - - + -
386A TRP* 3.7 24.9 - - + -
411A PHE* 4.0 20.2 - - + -
444A PHE* 3.5 44.6 - - + -
446A VAL* 4.7 14.4 - - + -
451A LEU* 3.5 36.3 - - + -
457A ALA 3.0 17.7 + - - +
458A ARG 3.6 6.7 - - - +
460A LYS* 1.3 75.7 - - + +
462A GLU* 1.3 65.6 + - - +
464A SER* 3.1 7.1 + - - +
465A ALA 3.0 18.0 + - - -
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Residues in contact with GLU 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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383A VAL* 4.1 23.5 - - + +
458A ARG* 2.8 47.2 + - - +
459A LYS* 3.0 28.1 + - - +
461A LEU* 1.3 77.1 - - - +
463A ASP* 1.3 63.5 + - - +
465A ALA* 3.3 8.9 + - - +
466A GLU* 3.2 19.9 + - - +
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Residues in contact with ASP 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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459A LYS* 2.9 22.1 + - - +
460A LYS* 3.6 13.5 - - - +
462A GLU* 1.3 75.1 - - - +
464A SER* 1.3 61.0 + - - +
466A GLU* 3.1 13.6 + - - +
467A LEU* 2.8 29.8 + - - +
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Residues in contact with SER 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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444A PHE* 4.0 28.3 + - - -
460A LYS 3.3 11.4 + - - -
461A LEU* 3.1 11.9 + - - +
463A ASP* 1.3 80.2 - - - +
465A ALA* 1.3 56.1 + - - +
467A LEU* 3.2 11.2 + - - +
468A LEU* 2.8 36.7 + - - +
493A LEU* 3.8 18.6 - - - +
495A TYR* 5.0 3.3 + - - -
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Residues in contact with ALA 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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378A ILE* 3.6 19.1 - - + -
383A VAL* 4.9 5.2 - - + -
386A TRP* 3.7 24.7 - - + -
461A LEU 3.0 7.7 + - - +
462A GLU* 3.5 12.6 - - - +
463A ASP 3.2 0.2 - - - -
464A SER* 1.3 75.1 - - - +
466A GLU* 1.3 60.3 - - - +
468A LEU* 3.4 1.2 + - - +
469A THR* 2.8 32.6 + - - +
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Residues in contact with GLU 466 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A GLU 3.2 9.2 + - - +
463A ASP* 3.1 15.3 + - - +
465A ALA* 1.3 78.4 - - - +
467A LEU* 1.3 57.9 + - - +
469A THR* 3.0 5.4 + - - -
470A LYS* 2.8 65.9 + - + +
471A PHE* 3.6 27.5 - - + -
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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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330A LEU* 3.5 31.0 - - + -
335A LEU* 3.3 31.0 - - + +
463A ASP 2.8 16.3 + - - +
464A SER* 3.4 12.3 - - - +
466A GLU* 1.3 77.3 - - - +
468A LEU* 1.3 59.1 + - + +
469A THR 3.5 0.7 + - - -
470A LYS 4.4 0.9 + - - -
471A PHE* 3.8 23.5 + - + +
473A SER* 4.3 5.7 + - - -
493A LEU* 4.9 9.6 - - + -
495A TYR* 3.4 42.4 - - + +
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Residues in contact with LEU 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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335A LEU* 3.8 16.9 - - + +
375A VAL* 3.3 30.8 + - + +
378A ILE* 4.1 12.8 - - + -
415A PHE* 3.9 31.4 - - + -
443A PHE* 4.4 5.6 - - + -
444A PHE* 4.2 16.8 - - + -
464A SER 2.8 22.7 + - - +
465A ALA 3.8 4.3 - - - +
466A GLU 3.2 0.2 - - - -
467A LEU* 1.3 74.5 - - + +
469A THR* 1.3 59.6 + - + +
471A PHE 5.7 0.2 - - - -
473A SER 4.8 7.9 - - - +
475A VAL* 3.5 31.6 - - + -
493A LEU* 4.2 17.3 - - + -
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Residues in contact with THR 469 (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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375A VAL* 3.7 35.3 - - + +
376A THR 4.7 3.8 - - - +
377A LYS* 4.5 7.6 - - - +
378A ILE* 4.2 11.4 - - + +
465A ALA 2.8 22.5 + - - +
466A GLU* 3.0 5.2 + - - -
468A LEU* 1.3 84.9 - - - +
470A LYS* 1.3 74.4 + - - +
471A PHE 3.8 2.5 - - - -
472A ASN 5.5 1.0 + - - -
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Residues in contact with LYS 470 (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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466A GLU* 2.8 46.5 + - + +
469A THR* 1.3 88.6 - - - +
471A PHE* 1.3 79.9 + - + +
472A ASN 3.8 1.6 - - - -
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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
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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