Contacts of the helix formed by residues 242 - 252 (chain N) in PDB entry 1K2V
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 242 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182N LEU* 3.6 23.6 + - - +
238N PHE 5.1 1.2 + - - -
239N ASP* 3.8 8.9 - - - +
240N HIS* 3.1 55.9 + - + +
241N ASP* 1.3 73.9 - - - +
243N SER* 1.3 64.7 + - - +
244N LYS* 3.2 4.3 - - - -
245N ASP* 3.1 19.9 + - - +
246N MET* 2.9 32.5 + - - +
268N ARG* 5.4 0.2 + - - -
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Residues in contact with SER 243 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241N ASP* 3.7 2.7 - - - -
242N ASN* 1.3 76.0 - - - +
244N LYS* 1.3 53.8 + - - +
247N ASP* 2.7 50.3 + - - +
268N ARG* 4.2 20.8 - - - +
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Residues in contact with LYS 244 (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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242N ASN* 3.2 1.3 - - - -
243N SER* 1.3 77.7 - - - +
245N ASP* 1.3 62.6 + - - +
247N ASP* 3.7 7.6 + - - +
248N ALA* 3.1 27.5 + - - +
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Residues in contact with ASP 245 (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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182N LEU* 3.5 22.4 - - + +
183N ILE 4.2 14.6 - - - +
184N ASP* 4.2 2.0 - - - +
185N PRO* 3.5 30.0 - - + +
240N HIS* 5.8 0.2 + - - -
242N ASN* 3.1 23.8 + - + +
244N LYS* 1.3 80.6 - - - +
246N MET* 1.3 61.5 + - - +
248N ALA* 3.2 2.9 + - - +
249N LEU* 2.9 25.1 + - - +
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Residues in contact with MET 246 (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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182N LEU* 3.5 33.0 - - - -
237N CYS* 4.1 10.8 - - - -
238N PHE 6.0 0.7 - - - +
239N ASP* 4.0 5.4 - - - +
242N ASN* 2.9 27.7 + - - +
243N SER 3.8 1.6 - - - +
245N ASP* 1.3 76.1 - - - +
247N ASP* 1.3 58.0 + - - +
249N LEU* 3.6 11.3 - - + +
250N MET* 2.9 47.1 + - - +
266N PHE* 4.0 18.6 - - + -
268N ARG* 3.3 59.0 - - + +
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Residues in contact with ASP 247 (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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243N SER* 2.7 38.0 + - - +
244N LYS* 3.7 6.9 + - - +
246N MET* 1.3 71.2 - - - +
248N ALA* 1.3 65.9 + - - +
250N MET* 3.3 9.2 + - - +
251N ALA* 3.1 25.1 + - - +
268N ARG* 4.6 12.1 + - - -
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Residues in contact with ALA 248 (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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185N PRO* 4.0 20.4 - - + -
244N LYS 3.1 15.6 + - - +
245N ASP* 3.6 4.9 - - - +
247N ASP* 1.3 79.7 - - - +
249N LEU* 1.3 64.3 + - - +
251N ALA* 3.5 12.3 + - - +
252N THR* 3.6 13.4 - - - +
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Residues in contact with LEU 249 (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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182N LEU* 3.7 29.6 - - + -
185N PRO* 3.8 16.3 - - + +
188N MET* 4.5 2.7 - - + -
224N ILE* 3.7 32.1 - - + -
245N ASP 2.9 16.6 + - - +
246N MET* 3.6 16.4 - - + +
248N ALA* 1.3 77.3 - - - +
250N MET* 1.3 59.2 + - + +
251N ALA 3.0 4.3 + - - -
252N THR* 2.6 37.2 + - + +
255N TRP* 3.3 44.7 - - + +
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Residues in contact with MET 250 (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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246N MET* 2.9 41.7 + - + +
247N ASP* 3.3 8.3 + - - +
249N LEU* 1.3 74.2 - - + +
251N ALA* 1.3 58.1 + - - +
252N THR 3.4 0.4 - - - -
255N TRP* 3.4 33.3 - - + +
256N GLN* 3.5 20.8 - - - +
266N PHE* 4.1 24.0 - - + -
268N ARG* 4.4 19.3 - - + +
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Residues in contact with ALA 251 (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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247N ASP 3.1 16.0 + - - +
248N ALA* 3.7 8.7 - - - +
249N LEU 3.0 1.2 + - - -
250N MET* 1.3 76.4 - - - +
252N THR* 1.3 62.3 + - + +
253N PRO* 3.6 3.1 - - - +
256N GLN* 3.0 16.7 - - - +
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Residues in contact with THR 252 (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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185N PRO* 6.1 1.1 - - + +
224N ILE* 5.6 0.7 - - - +
248N ALA 3.6 11.4 - - - +
249N LEU* 2.6 28.7 + - + +
251N ALA* 1.3 79.6 - - - +
253N PRO* 1.3 75.3 - - + +
254N LEU* 4.0 9.5 - - - +
255N TRP* 3.2 18.4 + - - +
256N GLN* 3.2 17.3 + - - +
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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