Contacts of the helix formed by residues 395 - 409 (chain N) in PDB entry 5KHU
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 395 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394N CYS* 3.8 28.3 - - - +
396N ILE* 3.8 27.8 - - - +
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Residues in contact with ILE 396 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395N ASP* 3.8 25.8 - - - +
397N ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 397 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396N ILE* 3.8 29.4 - - - +
398N THR* 3.8 24.9 - - - +
400N TYR* 4.3 19.3 - - - +
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Residues in contact with THR 398 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N ILE* 3.8 26.2 - - - +
399N LEU* 3.8 29.8 - - - +
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Residues in contact with LEU 399 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398N THR* 3.8 28.9 - - - +
400N TYR* 3.8 24.9 - - - +
402N SER* 4.2 21.3 - - - +
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Residues in contact with TYR 400 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397N ILE* 4.3 19.5 - - - +
399N LEU* 3.8 29.2 - - - +
401N ILE* 3.8 24.0 - - - +
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Residues in contact with ILE 401 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400N TYR* 3.8 25.4 - - - +
402N SER* 3.8 28.5 - - - +
404N ILE* 4.4 18.6 - - - +
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Residues in contact with SER 402 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399N LEU* 4.2 18.4 - - - +
401N ILE* 3.8 29.2 - - - +
403N ALA* 3.8 25.1 - - - +
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Residues in contact with ALA 403 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402N SER* 3.8 28.7 - - - +
404N ILE* 3.8 26.2 - - - +
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Residues in contact with ILE 404 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401N ILE* 4.4 16.8 - - - +
403N ALA* 3.8 29.6 - - - +
405N LYS* 3.8 26.7 - - - +
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Residues in contact with LYS 405 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404N ILE* 3.8 27.8 - - - +
406N ALA* 3.8 29.4 - - - +
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Residues in contact with ALA 406 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405N LYS* 3.8 28.7 - - - +
407N LEU* 3.8 28.7 - - - +
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Residues in contact with LEU 407 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406N ALA* 3.8 25.4 - - - +
408N ARG* 3.8 29.2 - - - +
410N LEU* 4.4 17.9 - - - +
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Residues in contact with ARG 408 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407N LEU* 3.8 29.4 - - - +
409N VAL* 3.8 24.9 - - - +
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Residues in contact with VAL 409 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408N ARG* 3.8 29.2 - - - +
410N LEU* 3.8 26.5 - - - +
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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