Contacts of the helix formed by residues 347 - 351 (chain A) in PDB entry 5NKS
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 ASN 347 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.4 27.6 - - - +
218A THR* 3.8 5.8 + - - -
344A GLY* 3.1 17.7 + - - +
345A LYS 3.5 0.4 + - - -
346A ASP* 1.3 83.4 - - + +
348A PHE* 1.3 60.0 + - - +
349A ALA* 2.9 23.3 + - - +
350A LEU* 2.8 50.7 + - + +
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Residues in contact with PHE 348 (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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209A GLN* 3.8 38.6 - - + -
212A LEU* 4.3 5.4 - - + -
213A LEU* 3.6 18.8 - - + -
217A ILE 3.3 27.4 - - - -
218A THR 3.0 12.3 + - - +
219A GLY 3.3 26.7 - - - +
220A PRO* 4.3 1.8 - - + -
222A GLY* 3.5 24.2 - - - -
223A HIS* 3.5 25.0 + - + +
226A SER* 3.6 13.9 - - - -
302A VAL* 5.0 4.0 - - - +
347A ASN* 1.3 73.1 + - - +
349A ALA* 1.3 60.5 + - + +
350A LEU 3.1 0.2 - - - -
351A ILE* 3.0 41.8 + - + +
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Residues in contact with ALA 349 (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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81A LEU* 4.3 9.7 - - - +
209A GLN* 4.0 30.1 - - - +
213A LEU* 4.6 8.1 - - + -
223A HIS* 6.0 0.4 - - - -
347A ASN* 2.9 17.4 + - - +
348A PHE* 1.3 87.8 - - + +
350A LEU* 1.3 63.5 + - + +
351A ILE 3.4 1.8 - - - +
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Residues in contact with LEU 350 (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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81A LEU* 3.6 16.6 - - + +
343A VAL* 3.4 34.1 - - + +
344A GLY* 3.8 9.0 - - - -
346A ASP* 6.5 0.2 - - + -
347A ASN* 2.8 37.2 + - + +
349A ALA* 1.3 82.6 - - + +
351A ILE* 1.3 63.5 + - - +
352A PRO* 3.5 1.2 - - - +
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Residues in contact with ILE 351 (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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81A LEU* 3.8 5.2 - - - +
218A THR 5.6 0.2 - - - +
220A PRO* 4.1 11.7 - - + -
295A TRP* 3.9 17.3 - - + +
299A ALA* 4.4 2.2 - - + +
302A VAL* 3.8 32.6 - - + +
341A LYS* 3.6 37.0 - - + +
344A GLY* 3.6 22.7 - - - +
348A PHE* 3.0 35.5 + - + +
349A ALA 4.7 1.9 - - - +
350A LEU* 1.3 78.5 - - - +
352A PRO* 1.3 71.3 - - + +
353A GLU* 3.1 11.3 + - - +
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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