Contacts of the helix formed by residues 207 - 217 (chain F) in PDB entry 3LUE
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 GLU 207 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F SER 5.7 0.6 - - - +
59F GLN* 4.9 13.9 - - + +
203F THR 3.7 0.8 + - - +
204F ALA 2.6 12.5 + - - +
206F ARG* 1.3 90.4 + - - +
208F ILE* 1.3 61.3 + - + +
209F VAL 3.4 1.3 - - - -
210F ARG* 3.1 54.5 + - - +
211F ASP* 3.4 13.3 - - - +
288H ASP* 3.9 6.5 - - - +
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Residues in contact with ILE 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F PHE* 3.7 24.2 - - + -
204F ALA* 3.5 7.5 + - + +
205F GLU* 3.1 36.8 + - + +
207F GLU* 1.3 77.7 - - + +
209F VAL* 1.3 64.7 + - - +
210F ARG 3.3 0.2 - - - -
211F ASP* 3.6 12.3 + - - +
212F ILE* 3.2 29.7 + - + +
240F TYR* 4.8 14.6 - - + +
242F LEU* 4.2 11.2 - - + -
243F PRO* 4.3 28.9 - - + -
248F ILE* 5.1 1.6 - - + -
291H LYS* 5.0 4.7 - - - -
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F THR* 3.4 24.0 - - + +
189F LEU* 3.2 18.3 - - + +
190F MET* 3.8 37.0 - - + +
193F LEU* 4.6 3.1 - - + -
200F PHE* 4.0 33.2 - - + -
205F GLU 3.9 0.9 + - - +
206F ARG 2.9 24.5 - - - +
208F ILE* 1.3 78.6 - - - +
210F ARG* 1.4 63.2 + - - +
212F ILE* 3.0 9.9 + - + -
213F LYS* 2.9 21.3 + - - +
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Residues in contact with ARG 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F SER 5.1 1.8 - - - -
15F GLY* 3.9 34.9 + - - -
16F MET* 4.8 10.5 - - - +
186F THR* 4.0 22.0 - - + +
207F GLU* 3.1 45.2 + - - +
209F VAL* 1.4 80.9 - - - +
211F ASP* 1.3 80.9 + - - +
213F LYS* 3.5 5.3 - - - +
214F GLU* 3.0 71.1 + - - +
215F LYS* 4.7 3.6 - - - +
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Residues in contact with ASP 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207F GLU* 3.4 16.1 - - - +
208F ILE* 3.6 13.6 + - - +
209F VAL 3.2 0.8 - - - -
210F ARG* 1.3 93.7 + - - +
212F ILE* 1.3 59.7 + - - +
214F GLU* 4.3 2.0 - - - +
215F LYS* 2.6 64.3 + - - +
240F TYR* 3.3 24.5 - - + +
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LEU* 4.1 13.0 - - + -
193F LEU* 3.9 19.1 - - + -
200F PHE* 4.4 5.6 - - + -
208F ILE* 3.2 22.0 + - + +
209F VAL* 3.0 14.2 + - - +
211F ASP* 1.3 73.7 - - - +
213F LYS* 1.3 59.1 + - - +
215F LYS 2.8 0.3 + - - -
216F LEU* 2.7 61.2 + - + +
217F CYS* 3.7 2.0 + - - -
240F TYR* 3.8 25.6 - - + -
248F ILE* 3.9 22.4 - - + -
250F ILE* 3.8 18.2 - - + -
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Residues in contact with LYS 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ASP* 5.9 0.2 + - - -
182F GLY* 3.2 20.1 + - - -
185F LEU* 3.6 5.8 - - + +
186F THR* 2.6 44.5 + - - +
189F LEU* 3.6 10.9 - - + +
209F VAL 2.9 15.8 + - - +
210F ARG* 3.5 7.4 - - - +
212F ILE* 1.3 76.9 - - - +
214F GLU* 1.3 89.2 + - - +
217F CYS* 3.2 29.8 + - - +
257F CYS* 4.0 17.3 - - - -
306F TYR* 3.8 26.5 - - - +
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Residues in contact with GLU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F GLY* 5.1 2.6 - - - -
210F ARG* 3.0 69.8 + - - +
211F ASP* 4.3 3.1 - - - +
213F LYS* 1.3 100.2 + - - +
215F LYS* 1.3 66.1 + - + +
217F CYS 4.8 3.1 + - - +
306F TYR* 5.4 5.8 - - - -
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Residues in contact with LYS 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F ARG* 4.7 5.3 - - - +
211F ASP* 2.6 65.7 + - + +
212F ILE* 2.8 3.3 + - - +
214F GLU* 1.3 79.7 + - + +
216F LEU* 1.3 70.6 + - + +
217F CYS 5.1 1.0 - - - +
218F TYR* 5.7 1.7 - - - -
240F TYR* 4.5 14.2 + - + -
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Residues in contact with LEU 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F ILE* 2.7 44.5 + - + +
215F LYS* 1.3 85.6 - - + +
217F CYS* 1.4 65.8 + - - +
218F TYR* 3.1 10.1 - - - -
238F LYS* 3.9 30.7 - - + +
239F SER 5.2 6.1 - - - +
240F TYR* 4.3 13.9 - - + -
250F ILE* 3.7 21.3 - - + -
254F ARG* 2.8 43.7 + - + +
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Residues in contact with CYS 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LEU* 4.5 7.2 - - - -
212F ILE* 3.7 2.0 + - - -
213F LYS* 3.2 33.2 + - - +
214F GLU 5.1 2.8 - - - +
215F LYS 3.9 1.4 - - - -
216F LEU* 1.4 77.4 - - - +
218F TYR* 1.3 70.0 + - - +
253F GLU 4.4 0.2 - - - -
254F ARG* 3.0 26.9 - - - +
257F CYS* 3.7 23.3 - - - -
258F PRO* 3.8 4.0 - - + -
306F TYR* 3.8 23.1 - - + -
307F PRO* 3.8 13.7 - - - +
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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