Contacts of the helix formed by residues 456 - 466 (chain A) in PDB entry 2EBU
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 GLN 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A MET* 5.5 0.2 - - - -
454A SER 5.7 0.2 - - - -
455A GLY* 1.3 78.3 - - - -
457A SER* 1.3 69.4 + - - +
458A LYS 3.3 2.2 - - - -
459A SER* 2.7 28.7 + - - +
460A ASP* 3.3 8.0 + - - +
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Residues in contact with SER 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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455A GLY* 3.3 2.0 - - - -
456A GLN* 1.3 85.8 - - - +
458A LYS* 1.3 64.8 + - - +
459A SER 3.3 0.2 + - - -
460A ASP* 3.4 10.8 + - - +
461A LYS* 3.2 25.6 + - - +
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Residues in contact with LYS 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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413A VAL* 4.7 8.5 - - + -
415A THR* 3.9 27.1 - - + +
439A GLY 4.7 11.8 + - - -
440A ASN* 5.2 5.9 + - - +
441A VAL* 3.4 32.3 - - + +
448A LEU* 3.8 25.8 - - + -
450A MET* 4.3 4.3 - - + -
455A GLY* 4.1 14.2 + - - +
456A GLN 3.3 0.4 - - - -
457A SER* 1.3 79.9 - - - +
459A SER* 1.3 61.1 + - - +
461A LYS* 4.2 0.6 - - - +
462A ALA* 3.0 24.9 + - - +
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Residues in contact with SER 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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448A LEU* 4.2 0.2 - - - -
450A MET* 3.5 26.9 - - - +
456A GLN* 2.7 26.0 + - - +
458A LYS* 1.3 77.7 - - - +
460A ASP* 1.3 70.7 + - - +
462A ALA* 3.0 7.0 + - - +
463A ALA* 2.8 26.8 + - - +
469A ILE* 4.1 14.1 - - - +
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Residues in contact with ASP 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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456A GLN 3.3 8.6 + - - +
457A SER* 3.6 14.7 + - - +
459A SER* 1.3 84.7 + - - +
461A LYS* 1.3 67.0 + - - +
463A ALA* 3.3 4.8 + - - +
464A ALA* 3.0 22.5 + - - +
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Residues in contact with LYS 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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441A VAL* 3.7 26.9 - - + +
457A SER 3.2 12.6 + - - +
458A LYS* 4.2 3.1 - - - +
460A ASP* 1.3 83.0 - - - +
462A ALA* 1.3 64.8 + - - +
464A ALA* 3.1 11.7 + - + +
465A LEU* 3.0 42.0 + - + +
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Residues in contact with ALA 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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441A VAL* 4.3 12.1 - - + +
448A LEU* 3.7 21.1 - - + -
458A LYS 3.0 20.7 + - - +
459A SER* 3.0 5.9 + - - +
461A LYS* 1.3 77.3 - - - +
463A ALA* 1.3 57.8 + - - +
465A LEU* 3.2 1.4 + - - -
466A GLY 2.8 23.6 + - - -
467A THR* 2.9 32.1 + - + -
469A ILE* 4.4 7.4 - - + -
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Residues in contact with ALA 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 SER 2.8 18.8 + - - +
460A ASP* 3.6 5.6 - - - +
462A ALA* 1.3 72.9 - - - +
464A ALA* 1.3 65.4 + - - +
466A GLY* 2.8 15.8 + - - -
467A THR 4.4 8.9 + - - +
469A ILE* 4.9 8.4 - - + +
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Residues in contact with ALA 464 (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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460A ASP* 3.0 17.2 + - - +
461A LYS* 3.3 15.5 - - + +
463A ALA* 1.3 78.6 - - - +
465A LEU* 1.3 67.3 + - + +
466A GLY* 4.3 0.3 - - - -
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Residues in contact with LEU 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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441A VAL* 3.4 25.4 - - + +
442A SER* 3.3 30.5 - - - +
443A LYS* 4.3 33.7 - - + +
461A LYS* 3.0 26.8 + - + +
462A ALA* 3.8 4.7 - - - +
464A ALA* 1.3 78.6 - - + +
466A GLY* 1.3 60.1 + - - +
467A THR* 4.4 5.6 - - - +
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Residues in contact with GLY 466 (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 THR 4.9 2.9 - - - +
446A ASN 5.1 1.0 - - - +
462A ALA 2.8 3.6 + - - -
463A ALA* 2.8 17.2 + - - -
464A ALA 4.3 0.4 - - - -
465A LEU* 1.3 82.1 - - - +
467A THR* 1.3 58.9 + - - -
468A LYS* 4.2 0.9 + - - +
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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