Contacts of the strand formed by residues 406 - 411 (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 406 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E LEU 5.5 0.2 - - - -
278E LYS* 3.7 18.4 - - + -
331E HIS* 4.2 18.6 - + - -
332E PRO* 3.9 30.6 - - + +
404E GLN 3.8 1.8 + - - -
405E PRO* 1.3 77.0 - - - +
407E ALA* 1.3 65.8 + - - +
409E TRP* 3.5 43.7 - + + -
419E PHE* 3.8 33.9 - + + -
420E GLY 3.4 7.2 - - - -
421E ARG* 4.3 5.3 - - - +
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Residues in contact with ALA 407 (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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405E PRO* 3.8 10.5 - - + +
406E PHE* 1.3 84.4 - - - +
408E ASN* 1.3 73.9 + - - +
409E TRP 3.2 4.0 + - - -
419E PHE* 3.5 2.4 - - - +
420E GLY* 2.6 40.9 + - - +
422E GLY* 4.7 9.6 - - - +
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Residues in contact with ASN 408 (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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407E ALA* 1.3 86.9 - - - +
409E TRP* 1.3 65.7 + - - +
410E TRP* 3.6 4.3 + - - +
418E ALA 3.7 5.4 - - - +
419E PHE* 3.7 3.8 - - - -
420E GLY* 4.5 2.0 - - - +
422E GLY 4.7 4.0 - - - +
426E PHE* 4.0 13.6 - - + -
441E GLN* 3.5 39.4 - - + +
442E THR 4.0 1.4 - - - +
443E GLY* 3.5 25.1 - - - -
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Residues in contact with TRP 409 (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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274E MET 4.2 3.6 - - - -
275E SER 3.7 10.5 - - - -
277E LEU* 3.6 11.7 - - + -
278E LYS* 3.4 64.2 - - + +
327E PHE* 4.9 3.8 - + - -
406E PHE* 3.5 35.4 - + + -
407E ALA 3.2 2.0 + - - -
408E ASN* 1.3 80.0 - - - +
410E TRP* 1.3 69.7 + - - +
411E ASP* 3.0 21.7 + - - -
417E VAL* 2.9 39.0 - - + -
418E ALA 3.3 8.1 - - - -
419E PHE* 3.8 26.0 - + + -
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Residues in contact with TRP 410 (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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408E ASN 4.4 3.8 - - - +
409E TRP* 1.3 82.1 - - - +
411E ASP* 1.3 78.9 + - - +
412E ASN* 4.1 15.7 - - + +
416E GLN* 3.6 43.5 - - + -
417E VAL* 3.3 9.8 - - - +
418E ALA* 2.8 49.7 + - + +
426E PHE* 5.9 0.7 - - + -
428E VAL* 5.1 0.7 - - + -
436E LEU* 4.7 9.9 - - + -
438E SER* 3.9 31.1 + - - -
439E THR 6.2 0.2 - - - -
440E LEU* 4.1 21.3 - - + +
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Residues in contact with ASP 411 (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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275E SER* 3.6 18.0 - - - +
278E LYS* 5.1 2.6 - - - +
409E TRP* 3.0 24.8 + - - +
410E TRP* 1.3 94.7 + - - +
412E ASN* 1.3 57.8 + - - +
413E GLY* 2.6 34.1 + - - -
416E GLN 3.0 15.3 - - - +
417E VAL* 3.7 13.7 - - + -
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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