Contacts of the helix formed by residues 414 - 419 (chain G) in PDB entry 5DK3
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 LYS 414 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358G MET* 2.8 53.4 + - + +
359G THR* 4.4 6.3 + - - +
360G LYS 3.6 13.2 + - - +
361G ASN* 2.9 22.0 + - - +
362G GLN* 4.2 0.2 - - - +
363G VAL* 4.0 20.6 - - + -
412G VAL 3.4 2.8 + - - -
413G ASP* 1.3 70.6 - - - +
415G SER* 1.4 51.6 + - - +
417G TRP* 3.2 3.6 + - - +
418G GLN* 2.7 61.2 + - - +
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Residues in contact with SER 415 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413G ASP* 3.8 14.4 + - - +
414G LYS* 1.4 75.9 - - - +
416G ARG* 1.4 52.9 + - - +
418G GLN* 3.6 9.5 + - - +
419G GLN* 2.7 45.7 + - - +
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Residues in contact with ARG 416 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412G VAL* 4.8 3.6 - - + -
413G ASP* 3.0 19.5 + - + +
415G SER* 1.4 80.4 + - - +
417G TRP* 1.3 60.0 + - - +
419G GLN* 3.6 16.7 + - - +
421G ASN* 3.4 42.8 + - - +
423G PHE* 4.4 12.1 - - + -
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Residues in contact with TRP 417 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352G PRO* 3.7 16.2 - - + -
353G PRO* 3.6 30.3 - - + +
358G MET* 4.0 27.9 - - + +
363G VAL* 4.2 15.9 - - + -
365G LEU* 3.7 24.9 - - + -
412G VAL* 4.3 5.8 - - + +
413G ASP 3.5 1.8 + - - -
414G LYS 3.2 7.0 + - - +
416G ARG* 1.3 77.9 - - - +
418G GLN* 1.3 65.3 + - + +
420G GLY* 3.3 11.3 + - - -
421G ASN 4.4 1.2 + - - -
423G PHE* 4.1 12.2 - + - -
441G LEU* 3.8 27.8 - - + -
442G SER* 3.4 35.0 - - - -
443G LEU* 3.4 46.7 + - + +
444G SER 5.0 0.7 - - - -
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Residues in contact with GLN 418 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358G MET* 3.7 28.2 - - + +
414G LYS* 2.7 49.5 + - + +
415G SER* 3.8 7.5 - - - +
417G TRP* 1.3 75.8 - - + +
419G GLN* 1.4 55.6 + - - +
420G GLY 3.2 4.4 + - - -
443G LEU* 3.4 23.0 - - + +
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Residues in contact with GLN 419 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415G SER* 2.7 24.9 + - - +
416G ARG* 3.6 15.5 - - - +
417G TRP 3.3 0.2 - - - -
418G GLN* 1.4 70.3 - - - +
420G GLY* 1.4 57.9 + - - +
421G ASN* 3.2 28.2 + - - +
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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