Contacts of the helix formed by residues 207 - 217 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I SER 5.7 0.7 - - - +
59I GLN* 4.9 16.2 - - + +
203I THR 3.7 2.2 + - - +
204I ALA* 2.6 14.7 + - - +
206I ARG* 1.3 90.3 + - - +
208I ILE* 1.3 62.6 + - + +
209I VAL 3.4 1.6 - - - -
210I ARG* 3.1 54.3 + - - +
211I ASP* 3.4 13.2 - - - +
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Residues in contact with ILE 208 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I PHE* 3.7 24.0 - - + -
204I ALA* 3.5 9.6 + - + +
205I GLU* 3.1 36.3 + - + +
207I GLU* 1.3 78.3 - - + +
209I VAL* 1.3 63.3 + - - +
211I ASP* 3.6 14.2 + - - +
212I ILE* 3.2 29.7 + - + +
240I TYR* 4.8 13.4 - - + +
242I LEU* 4.2 11.9 - - + -
243I PRO* 4.3 29.2 - - + -
248I ILE* 5.1 1.6 - - + -
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Residues in contact with VAL 209 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I THR* 3.4 23.8 - - + +
189I LEU* 3.2 17.4 - - + +
190I MET* 3.8 37.2 - - + -
193I LEU* 4.6 2.9 - - + -
200I PHE* 4.0 32.3 - - + -
205I GLU 3.9 0.6 + - - +
206I ARG 2.9 24.0 - - - +
208I ILE* 1.3 77.3 - - - +
210I ARG* 1.4 64.7 + - - +
212I ILE* 3.0 11.5 + - + -
213I LYS* 2.9 21.1 + - - +
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Residues in contact with ARG 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I SER 5.1 2.5 - - - -
15I GLY* 3.9 34.4 + - - -
16I MET* 4.8 9.9 - - - +
186I THR* 4.0 21.5 - - + +
207I GLU* 3.1 46.3 + - - +
208I ILE 3.3 0.2 - - - -
209I VAL* 1.4 80.1 - - - +
211I ASP* 1.3 81.3 + - - +
213I LYS* 3.5 5.3 - - - +
214I GLU* 3.0 72.0 + - - +
215I LYS* 4.7 3.4 - - - +
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Residues in contact with ASP 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207I GLU* 3.4 16.1 - - - +
208I ILE* 3.6 13.2 + - - +
209I VAL 3.2 1.0 - - - -
210I ARG* 1.3 93.1 + - - +
212I ILE* 1.3 59.9 + - - +
214I GLU* 4.3 2.0 - - - +
215I LYS* 2.6 64.4 + - - +
240I TYR* 3.3 25.1 + - + +
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Residues in contact with ILE 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I LEU* 4.1 13.0 - - + -
193I LEU* 3.9 20.0 - - + -
200I PHE* 4.4 5.4 - - + -
208I ILE* 3.2 21.3 + - + +
209I VAL* 3.0 14.2 + - - +
211I ASP* 1.3 72.9 - - - +
213I LYS* 1.3 59.5 + - - +
215I LYS* 2.8 1.0 + - - -
216I LEU* 2.7 60.4 + - + +
217I CYS* 3.7 1.9 + - - -
240I TYR* 3.8 24.2 - - + -
248I ILE* 3.9 23.1 - - + -
250I ILE* 3.8 17.9 - - + -
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Residues in contact with LYS 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I ASP* 5.9 0.2 + - - -
182I GLY* 3.2 19.1 + - - -
185I LEU* 3.6 5.8 - - + +
186I THR* 2.6 44.7 + - - +
189I LEU* 3.6 11.4 - - + +
209I VAL 2.9 15.3 + - - +
210I ARG* 3.5 8.4 - - - +
212I ILE* 1.3 78.1 - - - +
214I GLU* 1.3 88.8 + - - +
217I CYS* 3.2 30.2 + - - +
257I CYS* 4.0 17.0 - - - -
303I THR* 6.0 0.2 - - - -
306I TYR* 3.8 28.3 - - - +
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Residues in contact with GLU 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I GLY* 5.1 2.4 - - - -
210I ARG* 3.0 70.8 + - - +
211I ASP* 4.3 3.0 - - - +
213I LYS* 1.3 98.9 + - - +
215I LYS* 1.3 64.8 + - + +
217I CYS 4.8 2.8 + - - +
306I TYR* 5.4 5.6 - - - -
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Residues in contact with LYS 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210I ARG* 4.7 4.9 - - - +
211I ASP* 2.6 65.5 + - + +
212I ILE* 2.8 3.7 + - - +
214I GLU* 1.3 81.1 + - + +
216I LEU* 1.3 71.3 + - + +
217I CYS 5.1 1.4 - - - +
218I TYR* 5.7 1.7 - - - -
240I TYR* 4.5 14.8 + - + -
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Residues in contact with LEU 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212I ILE* 2.7 44.1 + - + +
215I LYS* 1.3 85.8 - - + +
217I CYS* 1.4 66.2 + - - +
218I TYR* 3.1 10.5 - - - -
238I LYS* 3.9 30.5 - - + +
239I SER 5.2 5.8 - - - +
240I TYR* 4.3 15.3 - - + -
250I ILE* 3.7 20.9 - - + -
254I ARG* 2.8 45.2 + - + +
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Residues in contact with CYS 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I LEU* 4.5 6.3 - - - -
212I ILE* 4.6 2.0 - - - -
213I LYS* 3.2 33.1 + - - +
214I GLU 5.1 1.9 - - - +
215I LYS 3.9 1.4 - - - +
216I LEU* 1.4 76.3 + - - +
218I TYR* 1.3 69.1 - - - +
253I GLU 4.4 0.2 - - - -
254I ARG* 3.0 27.8 - - - +
257I CYS* 3.7 23.3 - - - -
258I PRO* 3.8 4.3 - - + -
306I TYR* 3.8 22.9 - - + -
307I PRO* 3.8 13.9 - - - +
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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