Contacts of the helix formed by residues 470 - 481 (chain E) in PDB entry 3IKM
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 470 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467E HIS* 4.3 10.5 + - + +
469E SER* 1.3 75.2 - - - +
471E LEU* 1.3 52.4 + - - +
472E LYS 2.9 2.9 - - - -
473E ASP* 2.6 43.6 + - + -
474E PHE* 2.6 31.0 + - + +
477E LYS* 6.3 2.7 - - - -
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Residues in contact with LEU 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 6.3 0.4 - - + -
406E LEU* 4.9 14.6 - - + -
441E VAL* 5.6 15.5 - - + -
453E ILE* 5.3 8.5 - - + -
455E LEU* 5.9 0.7 - - + -
466E MET* 4.3 18.5 - - + +
467E HIS 4.3 6.4 + - - +
468E ILE* 3.7 27.8 - - + -
469E SER 3.9 13.0 - - - +
470E LYS* 1.3 75.8 - - - +
472E LYS* 1.3 66.5 + - - +
474E PHE* 3.0 39.6 + - + +
475E LEU* 3.2 22.9 + - + +
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Residues in contact with LYS 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E GLU* 4.7 21.7 + - + +
406E LEU* 5.1 10.5 - - + +
409E ASN* 3.4 35.5 + - + +
411E ILE* 5.6 2.3 - - - +
469E SER 3.5 13.5 + - - +
470E LYS 2.7 3.0 + - - -
471E LEU* 1.3 81.2 - - - +
473E ASP* 1.3 102.4 + - - +
474E PHE 3.2 0.3 + - - -
475E LEU* 3.8 6.9 + - - +
476E ILE* 3.5 19.1 + - + +
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Residues in contact with ASP 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E SER 4.5 3.1 - - - +
470E LYS* 2.6 24.7 + - + +
472E LYS* 1.3 114.6 + - - +
474E PHE* 1.3 63.8 + - - +
476E ILE* 3.5 22.1 - - - +
477E LYS* 3.7 13.5 + - - +
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Residues in contact with PHE 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439E PHE* 6.2 4.9 - + + -
455E LEU* 4.9 17.0 - - + -
466E MET* 4.7 18.4 - - + -
470E LYS* 2.6 26.6 + - + +
471E LEU* 3.0 34.2 + - + +
473E ASP* 1.3 69.4 - - - +
475E LEU* 1.3 103.9 + - + +
477E LYS* 2.7 20.1 + - + +
478E TYR* 3.1 42.6 + + + -
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Residues in contact with LEU 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E LYS* 5.9 2.7 - - - +
385E LEU* 6.3 2.9 - - + -
406E LEU* 3.6 31.2 - - + -
411E ILE* 4.2 17.0 - - + -
439E PHE* 5.4 17.5 - - + -
471E LEU* 3.2 19.0 + - + +
472E LYS 4.2 3.8 - - - +
474E PHE* 1.3 103.2 - - + +
476E ILE* 1.3 51.4 + - + +
478E TYR* 2.3 16.0 + - + -
479E ILE* 2.3 59.7 + - + -
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Residues in contact with ILE 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409E ASN* 5.6 5.2 - - + -
411E ILE* 4.6 15.5 - - + -
472E LYS* 3.5 19.7 - - + +
473E ASP* 3.5 16.6 - - - +
475E LEU* 1.3 76.1 - - + +
477E LYS* 1.3 60.3 + - + +
479E ILE* 3.8 15.2 - - + +
480E SER* 2.4 50.7 + - - -
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Residues in contact with LYS 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470E LYS* 6.3 2.7 - - - -
473E ASP 3.8 11.4 - - - +
474E PHE* 2.7 13.0 + - + +
476E ILE* 1.3 81.9 - - + +
478E TYR* 1.3 58.9 + - - +
479E ILE 3.2 0.7 - - - -
480E SER* 4.4 4.4 + - - +
481E SER* 3.1 33.3 + - - +
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Residues in contact with TYR 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373E LYS* 5.7 1.7 + - - -
375E HIS* 6.0 2.5 - + - -
439E PHE* 2.8 53.8 - + - -
457E SER* 5.6 0.7 + - - -
474E PHE* 3.1 42.0 + + + -
475E LEU* 2.3 28.0 + - + +
477E LYS* 1.3 70.7 - - - +
479E ILE* 1.3 57.9 + - + +
482E ALA* 2.9 22.6 - - + +
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Residues in contact with ILE 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377E CYS* 5.6 2.8 - - + +
380E PRO* 4.6 29.4 - - + -
381E ILE* 5.6 9.2 - - + -
410E GLY 5.8 0.4 - - - +
411E ILE* 4.2 20.6 - - + -
475E LEU* 2.3 61.0 + - + +
476E ILE* 3.8 12.8 - - + +
478E TYR* 1.3 75.4 - - + +
480E SER* 1.3 55.6 + - - +
482E ALA* 3.5 12.6 - - - +
483E LYS* 2.7 34.3 + - - +
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Residues in contact with SER 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E ILE* 2.4 39.9 + - - -
477E LYS* 4.5 6.2 + - - -
479E ILE* 1.3 72.9 - - - +
481E SER* 1.3 50.6 + - - +
482E ALA 3.0 4.5 - - - -
483E LYS* 3.2 22.5 + - - +
484E ASN* 2.6 21.9 + - - +
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Residues in contact with SER 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477E LYS* 3.1 24.9 + - - +
480E SER* 1.3 74.3 - - - +
482E ALA* 1.3 54.0 + - - +
483E LYS 2.8 5.6 - - - -
484E ASN* 2.8 48.5 + - - +
485E VAL* 3.6 13.3 + - - +
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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