Contacts of the helix formed by residues 426 - 434 (chain Z) in PDB entry 5GJQ
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 LEU 426 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424Z GLY 3.8 0.2 + - - -
425Z GLY* 1.3 71.6 - - - -
427Z THR* 1.3 58.2 + - - +
428Z GLN 3.6 1.1 - - - -
429Z ILE* 4.0 11.7 - - + -
430Z ASP* 2.3 64.6 + - + +
462Z ALA* 6.2 3.6 - - + -
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Residues in contact with THR 427 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424Z GLY 4.1 12.0 + - - -
425Z GLY 3.4 4.0 + - - -
426Z LEU* 1.3 79.5 - - - +
428Z GLN* 1.3 64.1 + - - +
430Z ASP* 4.2 0.2 - - - +
431Z LYS* 3.3 19.1 + - - +
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Residues in contact with GLN 428 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388Z ASP* 6.3 2.9 - - + -
391Z LEU* 6.0 2.7 - - + -
392Z THR* 5.9 8.5 - - - +
414Z LEU* 4.1 24.7 - - + -
427Z THR* 1.3 78.1 - - - +
429Z ILE* 1.3 67.2 + - - +
431Z LYS* 3.6 4.1 + - - +
432Z TYR* 3.1 25.9 + - - +
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Residues in contact with ILE 429 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411Z ALA* 6.0 0.9 - - - -
414Z LEU* 5.5 2.2 - - - +
415Z GLY* 6.1 2.9 - - - +
426Z LEU* 3.8 15.4 + - + -
427Z THR 3.5 0.2 - - - -
428Z GLN* 1.3 78.0 - - - +
430Z ASP* 1.3 53.0 + - - +
432Z TYR* 3.0 3.6 + - - -
433Z LEU* 2.3 39.4 + - - +
444Z ALA* 3.1 25.9 - - + +
447Z ALA* 5.1 7.4 - - + -
448Z CYS* 4.9 13.0 - - + +
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Residues in contact with ASP 430 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426Z LEU* 2.3 47.5 + - + +
427Z THR 4.2 0.4 - - - +
429Z ILE* 1.3 72.4 - - - +
431Z LYS* 1.3 63.3 + - - +
433Z LEU* 2.9 25.1 + - - +
434Z TYR 3.5 3.6 + - - +
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Residues in contact with LYS 431 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427Z THR 3.3 17.8 + - - +
428Z GLN* 3.8 5.2 - - - +
429Z ILE 3.3 0.4 - - - -
430Z ASP* 1.3 77.5 - - - +
432Z TYR* 1.3 54.0 + - - +
434Z TYR 2.8 26.5 - - - +
435Z SER* 4.2 4.7 + - - -
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Residues in contact with TYR 432 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399Z LEU* 6.5 1.6 - - + -
411Z ALA* 4.2 24.7 - - + -
428Z GLN 3.1 16.2 + - - +
429Z ILE* 3.0 4.1 + - - +
431Z LYS* 1.3 74.5 - - + +
433Z LEU* 1.3 65.7 + - - +
434Z TYR* 2.7 13.5 + - - -
435Z SER* 3.7 5.0 + - - +
440Z ILE* 2.9 24.5 - - + +
444Z ALA* 4.5 1.8 - - - +
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Residues in contact with LEU 433 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429Z ILE 2.3 30.4 + - - +
430Z ASP* 3.0 17.7 - - - +
432Z TYR* 1.3 66.1 - - - +
434Z TYR* 1.3 59.5 + - - +
441Z LYS* 3.0 27.2 - - - +
444Z ALA* 3.4 18.8 - - + +
469Z TYR* 5.9 6.7 - - + -
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Residues in contact with TYR 434 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430Z ASP 3.5 3.7 + - - +
431Z LYS 2.8 19.7 - - - +
432Z TYR 2.7 5.5 + - - -
433Z LEU* 1.3 79.4 - - - +
435Z SER* 1.3 59.6 + - - +
437Z GLU 5.3 0.7 - - - +
441Z LYS* 4.5 7.9 - - + +
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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