Contacts of the strand formed by residues 487 - 491 (chain E) in PDB entry 1KXT
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 PHE 487 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322E LYS* 3.4 26.5 - - + -
323E ILE* 3.9 30.3 - - + -
326E GLY* 4.4 11.2 - - - -
390E GLU* 4.6 8.7 - - + -
394E MET* 4.9 1.8 - - + -
427E ILE* 3.8 12.3 - - + -
428E VAL 3.1 17.0 - - - +
429E PHE* 3.6 31.6 - + + -
451E ASP* 4.4 0.5 - - - +
453E ILE* 3.3 54.9 - - + +
479E ILE* 3.9 4.0 - - - +
485E ASP* 2.8 28.2 + - + +
486E PRO* 1.3 77.5 - - - +
488E ILE* 1.3 65.6 + - - +
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Residues in contact with ILE 488 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427E ILE* 3.2 4.2 - - - +
428E VAL* 2.8 42.8 + - + +
451E ASP* 3.4 29.2 - - + +
453E ILE* 4.1 0.9 - - - -
465E ILE* 4.5 19.7 - - + -
467E VAL* 4.0 13.7 - - + -
477E PHE* 3.9 30.7 - - + -
478E SER 4.7 8.5 - - - +
479E ILE* 4.0 22.7 - - + -
485E ASP 5.8 0.4 - - - +
487E PHE* 1.3 78.1 - - - +
489E ALA* 1.3 68.6 + - - +
490E ILE* 4.6 0.4 - - + -
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Residues in contact with ALA 489 (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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394E MET* 3.8 16.2 - - - -
397E PHE* 4.6 4.7 - - + -
426E PHE 3.6 6.1 - - - +
427E ILE* 3.7 18.8 - - + -
451E ASP* 3.0 8.0 + - - +
452E VAL* 2.9 45.7 + - + +
453E ILE* 3.6 6.9 - - + +
488E ILE* 1.3 76.9 - - - +
490E ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 490 (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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397E PHE* 3.6 2.4 - - - -
426E PHE* 2.8 44.0 + - + +
442E THR* 4.9 3.1 - - + -
444E LEU* 4.0 20.6 - - + +
449E TYR* 3.8 21.8 - - + -
450E CYS 3.2 17.5 - - - +
451E ASP* 3.9 1.1 - - - -
452E VAL* 5.1 0.2 - - - -
467E VAL* 3.7 48.0 - - + -
469E VAL* 4.2 7.6 - - + -
477E PHE* 4.5 12.8 - - + -
488E ILE* 4.6 0.9 - - + -
489E ALA* 1.3 81.6 - - - +
491E HIS* 1.3 66.6 + - - +
494E SER* 3.9 3.8 - - - -
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Residues in contact with HIS 491 (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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393E ASN 4.4 3.3 + - - -
396E TRP* 3.5 25.9 - + - -
397E PHE* 3.9 36.7 - + + -
400E VAL* 3.7 13.3 - - + +
401E VAL* 4.9 0.2 - - + -
424E ARG 3.3 15.9 - - - +
425E GLY* 4.0 2.2 - - - -
444E LEU* 4.4 2.2 - - - -
449E TYR* 3.5 13.9 - - - -
452E VAL* 3.9 23.6 - - + +
490E ILE* 1.3 77.6 - - - +
492E ALA* 1.3 64.4 + - - +
493E GLU* 2.9 36.3 + - + +
494E SER* 2.9 40.9 + - - -
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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