Contacts of the helix formed by residues 406 - 416 (chain E) in PDB entry 1XFV
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 ASP 406 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341E SER* 4.8 12.8 + - - -
363E TYR* 5.2 1.1 + - - -
404E LYS 3.1 8.6 + - - +
405E LEU* 1.3 82.1 - - - +
407E HIS* 1.3 72.0 + - + +
408E LEU* 3.3 29.4 - - - +
409E ARG* 2.9 33.3 + - - +
410E ILE* 3.7 13.2 + - - +
451E ASN* 4.9 7.6 - - - +
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Residues in contact with HIS 407 (chain E).
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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406E ASP* 1.3 85.2 + - + +
408E LEU* 1.3 74.6 + - + +
410E ILE* 3.4 15.6 + - - +
411E GLU* 4.0 9.5 + - - +
451E ASN* 4.0 20.0 + - - +
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Residues in contact with LEU 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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406E ASP* 3.3 16.8 + - - +
407E HIS* 1.3 79.4 - - + +
409E ARG* 1.3 57.8 + - - +
410E ILE 2.7 15.9 + - - -
411E GLU* 2.9 23.3 + - - +
412E GLU* 3.4 8.0 + - - +
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Residues in contact with ARG 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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334E LEU* 3.4 28.5 + - - +
337E ASN* 4.3 6.7 - - - +
338E LEU* 3.5 31.8 - - + +
359E PRO 5.0 0.2 + - - -
361E ALA* 2.8 36.2 + - - +
363E TYR* 4.5 6.7 - - - +
405E LEU* 4.3 22.0 - - + +
406E ASP* 2.9 29.9 + - - +
408E LEU* 1.3 78.1 - - - +
410E ILE* 1.3 60.0 + - - +
412E GLU* 3.4 30.7 + - - +
413E LEU* 3.1 56.7 + - + +
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Residues in contact with ILE 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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405E LEU* 4.6 16.4 - - + +
406E ASP 3.7 11.4 + - - +
407E HIS* 3.4 12.4 + - - +
408E LEU 2.7 4.2 + - - -
409E ARG* 1.3 71.0 - - - +
411E GLU* 1.3 64.8 + - + +
412E GLU 2.6 16.7 + - - -
413E LEU* 2.9 17.2 + - - +
414E LYS* 3.1 19.0 + - + +
419E ILE* 3.3 29.2 - - + +
421E LYS* 4.3 31.4 - - + +
435E LEU* 4.1 22.2 - - + -
446E ILE* 5.3 7.4 - - + -
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Residues in contact with GLU 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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407E HIS 4.3 11.7 - - - +
408E LEU* 2.9 13.9 + - - +
410E ILE* 1.3 80.7 - - + +
412E GLU* 1.3 55.8 + - - +
414E LYS* 3.0 27.3 - - + +
415E GLU* 3.5 15.1 - - - +
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Residues in contact with GLU 412 (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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333E LYS 5.5 0.2 - - - +
334E LEU* 6.5 0.4 - - - -
337E ASN* 2.4 41.8 + - - +
408E LEU 3.4 4.6 + - - +
409E ARG* 3.4 29.8 + - - +
410E ILE 2.6 6.3 + - - -
411E GLU* 1.3 74.4 - - - +
413E LEU* 1.3 63.2 + - + +
414E LYS 2.6 10.0 + - - -
415E GLU* 3.8 9.7 - - - +
416E ASN* 2.9 51.3 + - - +
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Residues in contact with LEU 413 (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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358E GLY 4.4 3.1 - - - +
359E PRO* 4.0 20.0 - - + +
361E ALA* 5.2 0.9 - - + -
405E LEU* 3.9 27.8 - - + -
409E ARG* 3.1 59.9 - - + +
410E ILE* 2.9 5.1 + - - +
412E GLU* 1.3 78.9 - - + +
414E LYS* 1.3 59.3 + - - +
416E ASN* 4.3 3.6 - - + -
417E GLY 4.2 0.4 - - - -
418E ILE* 2.8 42.7 + - + -
419E ILE* 2.9 34.1 + - + -
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Residues in contact with LYS 414 (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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410E ILE* 3.1 23.7 + - + +
411E GLU* 3.0 25.6 - - + +
412E GLU 2.6 1.4 - - - -
413E LEU* 1.3 77.7 - - - +
415E GLU* 1.3 63.3 + - + +
417E GLY* 2.9 20.4 + - - -
419E ILE* 2.4 38.1 + - - +
420E LEU* 3.6 9.3 - - - +
421E LYS* 3.5 36.1 - - + +
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Residues in contact with GLU 415 (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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411E GLU 3.5 15.7 - - - +
412E GLU* 3.6 18.4 + - - +
414E LYS* 1.3 73.9 - - - +
416E ASN* 1.3 74.0 + - - +
417E GLY* 2.8 8.3 + - - -
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Residues in contact with ASN 416 (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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333E LYS* 6.0 2.3 - - - +
334E LEU* 5.7 8.5 - - - +
412E GLU* 2.9 46.7 + - + +
413E LEU* 4.3 5.8 - - + -
415E GLU* 1.3 88.3 + - - +
417E GLY* 1.3 60.3 + - - +
418E ILE* 4.6 12.8 - - + +
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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