Contacts of the helix formed by residues 206 - 215 (chain A) in PDB entry 1LIK
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 TYR 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.2 0.9 - - - +
168A ALA 4.1 6.5 - - - -
171A LEU* 3.0 54.5 - - + -
172A THR* 2.8 45.2 + - - +
175A PRO* 6.2 2.5 - - + -
201A PHE* 4.4 5.6 - + - -
202A CYS* 2.7 31.1 + - + +
203A VAL 4.5 0.7 - - - -
205A LEU* 1.3 102.9 - - + +
207A LYS* 1.3 56.3 + - - +
208A ASP 3.7 1.1 - - - -
209A ALA* 4.1 9.6 - - + +
210A MET* 2.6 39.5 + - + +
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Residues in contact with LYS 207 (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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203A VAL 4.1 8.8 + - - +
204A GLU 3.4 18.4 - - - +
205A LEU* 2.8 34.2 + - - +
206A TYR* 1.3 78.2 - - - +
208A ASP* 1.3 82.3 + - - +
209A ALA 5.4 0.6 - - - +
210A MET* 3.3 3.7 - - - +
211A GLN* 2.8 30.8 + - - +
233A VAL* 4.6 12.3 - - + -
234A HIS* 4.1 21.1 + - + +
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Residues in contact with ASP 208 (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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206A TYR 3.7 0.2 - - - -
207A LYS* 1.3 101.1 + - - +
209A ALA* 1.3 62.1 + - - +
211A GLN* 3.4 14.0 + - - +
212A SER* 3.3 17.2 + - - -
234A HIS* 6.0 0.2 - - - -
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Residues in contact with ALA 209 (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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171A LEU* 5.2 4.9 - - + -
175A PRO* 3.6 36.6 - - + -
179A LEU* 4.9 8.2 - - + +
206A TYR* 3.5 13.9 + - + +
207A LYS* 3.2 2.0 - - - +
208A ASP* 1.3 76.0 - - - +
210A MET* 1.3 67.1 + - - +
212A SER* 3.1 16.9 + - - -
213A LEU* 3.1 16.1 + - + +
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Residues in contact with MET 210 (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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168A ALA* 4.8 11.7 - - + -
171A LEU* 4.5 11.9 - - + +
195A LEU* 5.0 11.9 - - + -
197A LEU* 4.3 17.7 - - + -
202A CYS 4.5 3.6 - - - +
203A VAL* 3.5 44.6 - - + +
206A TYR* 2.6 24.2 + - + +
207A LYS* 3.4 4.9 - - - +
209A ALA* 1.3 72.7 - - - +
211A GLN* 1.3 63.9 + - - +
213A LEU* 3.2 7.5 + - + +
214A LEU* 2.9 40.9 + - + +
230A LEU* 3.9 25.4 - - + -
234A HIS* 5.0 5.2 - - + +
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Residues in contact with GLN 211 (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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207A LYS 2.8 10.7 + - - +
208A ASP* 3.5 13.3 - - - +
209A ALA 3.1 0.4 - - - -
210A MET* 1.3 78.2 - - - +
212A SER* 1.3 63.1 + - - +
214A LEU* 3.4 15.3 + - + +
215A LEU* 3.5 29.8 + - + +
234A HIS* 3.4 31.1 + - + +
251A HIS* 4.8 4.6 - - + +
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Residues in contact with SER 212 (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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179A LEU* 4.5 17.5 - - - +
208A ASP 3.3 13.0 + - - -
209A ALA* 3.1 7.6 + - - -
211A GLN* 1.3 78.7 - - - +
213A LEU* 1.3 62.5 + - - +
215A LEU* 3.5 18.2 + - - +
216A HIS* 4.0 12.0 + - - +
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Residues in contact with LEU 213 (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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171A LEU* 4.1 19.5 - - + -
178A ALA* 3.7 20.4 - - + -
179A LEU* 3.0 43.8 - - + +
182A ALA* 3.6 19.7 - - + -
193A PHE* 4.1 11.7 - - + -
195A LEU* 4.3 24.5 - - + -
209A ALA 3.1 11.2 + - - +
210A MET* 3.5 12.1 - - + +
212A SER* 1.3 73.2 - - - +
214A LEU* 1.3 58.0 + - - +
216A HIS* 2.7 28.1 + - - +
217A THR* 3.0 11.8 + - - -
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Residues in contact with LEU 214 (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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195A LEU* 4.3 13.5 - - + -
197A LEU* 5.4 2.0 - - + -
210A MET* 2.9 42.5 + - + +
211A GLN* 3.5 10.3 - - + +
212A SER 3.4 0.2 - - - -
213A LEU* 1.3 76.6 - - - +
215A LEU* 1.3 55.5 + - - +
217A THR* 2.8 39.0 + - - +
220A LEU* 3.5 32.5 - - + -
230A LEU* 4.7 18.6 - - + -
234A HIS* 5.4 6.1 - - + +
251A HIS* 4.0 30.5 - - + +
252A ALA* 3.6 16.7 - - + +
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Residues in contact with LEU 215 (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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186A HIS* 5.1 1.9 - - - -
211A GLN* 3.5 25.0 + - + +
212A SER* 4.0 11.9 - - - +
213A LEU 3.2 1.4 - - - -
214A LEU* 1.3 77.2 - - - +
216A HIS* 1.3 71.2 + - + +
217A THR 3.5 0.2 - - - -
250A GLU 4.7 1.1 - - - +
251A HIS* 2.8 30.5 - - - +
252A ALA 3.8 12.3 - - - +
253A VAL 4.5 10.1 - - - +
273A LYS* 2.9 16.7 + - - -
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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