Contacts of the helix formed by residues 207 - 217 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G SER 5.7 0.8 - - - +
59G GLN* 4.9 13.7 - - + +
203G THR 3.7 0.6 + - - +
204G ALA* 2.6 12.6 + - - +
206G ARG* 1.3 89.8 + - - +
208G ILE* 1.3 61.8 + - + +
209G VAL 3.4 1.6 - - - -
210G ARG* 3.1 54.4 + - - +
211G ASP* 3.4 13.0 - - - +
288I ASP* 3.9 6.3 - - - +
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Residues in contact with ILE 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G PHE* 3.7 24.2 - - + -
204G ALA* 3.5 7.2 + - + +
205G GLU* 3.1 36.3 + - + +
207G GLU* 1.3 78.5 - - + +
209G VAL* 1.3 63.4 + - - +
210G ARG 3.3 0.2 - - - -
211G ASP* 3.6 14.0 + - - +
212G ILE* 3.2 29.6 + - + +
240G TYR* 4.8 13.5 - - + +
242G LEU* 4.2 11.7 - - + -
243G PRO* 4.3 29.6 - - + -
248G ILE* 5.1 1.6 - - + -
291I LYS* 5.0 4.3 - - - -
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Residues in contact with VAL 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186G THR* 3.4 23.6 - - + +
189G LEU* 3.2 16.7 - - + +
190G MET* 3.8 38.6 - - + +
193G LEU* 4.6 2.9 - - + -
200G PHE* 4.0 33.0 - - + -
205G GLU 4.6 0.9 - - - +
206G ARG 2.9 24.5 - - - +
208G ILE* 1.3 77.9 - - - +
210G ARG* 1.4 64.6 + - - +
212G ILE* 3.0 9.7 + - + -
213G LYS* 2.9 21.1 + - - +
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Residues in contact with ARG 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G SER 5.1 2.0 - - - -
15G GLY* 3.9 34.4 + - - -
16G MET* 4.8 10.3 - - - +
186G THR* 4.0 21.8 - - + +
207G GLU* 3.1 45.8 + - - +
209G VAL* 1.4 79.1 - - - +
211G ASP* 1.3 79.1 + - - +
213G LYS* 3.5 5.6 - - - +
214G GLU* 3.0 72.2 + - - +
215G LYS* 4.7 3.0 - - - +
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Residues in contact with ASP 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G GLU* 3.4 16.3 - - - +
208G ILE* 3.6 13.0 + - - +
209G VAL 3.2 0.8 - - - -
210G ARG* 1.3 94.1 + - - +
212G ILE* 1.3 61.3 + - - +
214G GLU* 4.3 2.2 - - - +
215G LYS* 2.6 63.2 + - + +
240G TYR* 3.3 24.9 - - + +
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Residues in contact with ILE 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G LEU* 4.1 13.7 - - + -
193G LEU* 3.9 19.3 - - + -
200G PHE* 4.4 5.4 - - + -
208G ILE* 3.2 21.7 + - + +
209G VAL* 3.0 13.9 + - - +
211G ASP* 1.3 73.5 - - - +
213G LYS* 1.3 57.2 + - - +
215G LYS* 2.8 0.4 + - - -
216G LEU* 2.7 61.7 + - + +
217G CYS* 3.7 1.8 + - - -
240G TYR* 3.8 25.4 - - + -
248G ILE* 3.9 22.0 - - + -
250G ILE* 3.8 18.4 - - + -
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Residues in contact with LYS 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157G ASP* 5.9 0.4 + - - -
182G GLY* 3.2 19.7 + - - -
185G LEU* 3.6 5.2 - - + +
186G THR* 2.6 44.7 + - - +
189G LEU* 3.6 10.9 - - + +
209G VAL 2.9 16.3 + - - +
210G ARG* 3.5 7.1 - - - +
212G ILE* 1.3 75.4 - - - +
214G GLU* 1.3 89.1 + - - +
217G CYS* 3.2 31.1 + - - +
257G CYS* 4.0 16.8 - - - -
303G THR* 5.6 0.6 + - - -
306G TYR* 3.8 27.9 - - - +
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Residues in contact with GLU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G GLY* 5.1 2.6 - - - -
210G ARG* 3.0 70.5 + - - +
211G ASP* 4.3 3.0 - - - +
213G LYS* 1.3 101.0 + - - +
215G LYS* 1.3 65.8 + - + +
217G CYS 4.8 3.1 + - - +
306G TYR* 5.4 5.4 - - + -
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Residues in contact with LYS 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ARG* 4.7 4.9 - - - +
211G ASP* 2.6 65.3 + - + +
212G ILE* 2.8 3.3 + - - +
214G GLU* 1.3 81.0 + - + +
216G LEU* 1.3 71.0 + - + +
217G CYS 5.1 0.7 - - - -
218G TYR* 5.7 2.1 - - - -
240G TYR* 4.5 14.6 + - + -
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Residues in contact with LEU 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G ILE* 2.7 44.1 + - + +
215G LYS* 1.3 85.7 - - + +
217G CYS* 1.4 65.7 + - - +
218G TYR* 3.1 10.5 - - - -
238G LYS* 3.9 30.7 - - + +
239G SER 5.2 5.4 - - - +
240G TYR* 4.3 14.1 - - + -
250G ILE* 3.7 21.3 - - + -
254G ARG* 2.8 44.4 + - + +
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Residues in contact with CYS 217 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189G LEU* 4.5 6.7 - - - -
212G ILE* 4.6 1.6 - - - -
213G LYS* 3.2 33.6 + - - +
214G GLU 5.1 2.6 - - - +
215G LYS 5.1 1.4 - - - -
216G LEU* 1.4 78.5 - - - +
218G TYR* 1.3 69.8 + - - +
250G ILE* 6.3 0.2 - - - -
253G GLU 4.4 0.2 - - - -
254G ARG* 3.0 26.7 - - - +
257G CYS* 3.7 22.7 - - - -
258G PRO* 3.8 3.4 - - + -
306G TYR* 3.8 22.9 - - + -
307G 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