Contacts of the helix formed by residues 209 - 219 (chain I) in PDB entry 5TJ4
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 ASP 209 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150I ASN* 3.6 15.3 - - - +
152I GLN* 3.7 19.1 - - + -
207I ASP 4.3 3.0 - - - +
208I THR* 1.3 78.1 - - - +
210I TYR* 1.3 64.6 + - - +
211I SER* 2.9 23.5 + - - -
212I ILE* 3.1 23.2 + - - +
213I ALA* 3.1 22.7 + - - +
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Residues in contact with TYR 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 ASP* 4.5 14.7 - - + +
150I ASN* 3.5 24.3 - - + +
156I PHE* 4.0 23.6 - + - -
209I ASP* 1.3 76.1 + - - +
211I SER* 1.3 62.3 + - - +
213I ALA* 4.1 2.4 - - - +
214I GLU* 3.1 53.7 + - + +
227I ASN* 3.6 33.6 + - - -
230I TRP* 3.2 32.3 + + - -
231I ALA* 4.0 5.2 - - - +
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Residues in contact with SER 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I ASP* 2.9 14.7 + - - -
210I TYR* 1.3 77.9 - - - +
212I ILE* 1.3 62.3 + - - +
214I GLU* 4.0 4.0 - - - +
215I ALA* 2.9 32.5 + - - +
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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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148I MET* 3.6 24.0 - - + -
207I ASP* 3.7 15.7 - - + +
208I THR* 3.8 5.8 - - + -
209I ASP* 3.1 36.5 + - - +
211I SER* 1.3 75.5 - - - +
213I ALA* 1.3 58.9 + - - +
215I ALA* 3.4 5.2 + - - +
216I ALA* 2.8 30.1 + - + +
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Residues in contact with ALA 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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148I MET* 3.6 34.9 - - - +
149I PHE* 3.6 20.0 - - - +
150I ASN 4.2 1.6 - - - +
208I THR* 4.1 4.9 - - + +
209I ASP 3.1 14.3 + - - +
210I TYR* 4.1 2.2 - - - +
212I ILE* 1.3 78.1 - - - +
214I GLU* 1.3 64.8 + - - +
216I ALA* 3.4 2.0 + - - +
217I PHE* 3.1 24.6 + - - +
222I THR* 4.8 0.7 - - - +
225I THR* 4.2 6.5 + - - +
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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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210I TYR* 3.1 51.0 + - + +
211I SER* 4.0 4.1 - - - +
213I ALA* 1.3 76.1 - - - +
215I ALA* 1.3 64.2 + - - +
217I PHE* 3.4 2.2 + - - -
218I ASN* 3.0 44.3 + - - +
225I THR* 5.1 3.1 + - - -
227I ASN* 5.2 8.9 - - - +
231I ALA* 4.2 12.4 - - + +
234I ASN* 3.5 35.7 + - - +
235I ILE* 5.8 1.6 - - + -
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Residues in contact with ALA 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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211I SER 2.9 20.5 + - - +
212I ILE* 3.5 6.7 - - - +
214I GLU* 1.3 78.0 - - - +
216I ALA* 1.3 58.1 + - - +
218I ASN* 3.3 3.9 + - - +
219I LYS* 2.9 33.0 + - - +
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Residues in contact with ALA 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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148I MET* 3.6 32.1 - - + -
212I ILE* 2.8 22.1 + - + +
213I ALA 3.8 3.4 - - - +
215I ALA* 1.3 72.9 - - - +
217I PHE* 1.3 60.2 + - - +
219I LYS* 3.7 2.4 + - - -
220I GLY 3.3 2.3 + - - -
221I GLU* 2.8 41.0 + - + +
222I THR* 3.4 6.4 + - + -
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Residues in contact with PHE 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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116I ILE* 3.7 31.6 - - + -
117I TYR 3.7 2.5 - - - -
118I ASN* 3.7 23.8 + - + -
213I ALA 3.1 17.0 + - - +
214I GLU* 3.9 3.1 - - - +
216I ALA* 1.3 76.3 - - - +
218I ASN* 1.3 70.9 + - - +
220I GLY* 3.1 15.8 + - - -
222I THR* 3.6 24.0 - - + +
223I ALA 3.6 21.5 - - - -
224I MET* 3.7 24.2 - - - -
225I THR* 3.8 16.4 - - + -
235I ILE* 4.3 22.0 - - + -
240I VAL* 3.6 17.8 - - + +
242I TYR* 4.3 2.0 - - + -
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Residues in contact with ASN 218 (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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214I GLU* 3.0 30.7 + - - +
215I ALA* 4.0 3.4 - - - +
217I PHE* 1.3 80.5 - - - +
219I LYS* 1.3 58.9 + - - +
220I GLY 3.2 2.2 + - - -
234I ASN* 3.2 40.2 + - - +
235I ILE* 3.3 24.0 - - - +
238I SER* 3.9 21.6 - - - +
239I ALA* 4.9 2.6 + - - +
240I VAL* 3.6 17.5 - - - +
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Residues in contact with LYS 219 (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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215I ALA 2.9 18.0 + - - +
216I ALA* 4.1 5.6 - - - +
218I ASN* 1.3 77.1 - - - +
220I GLY* 1.3 60.4 + - - +
221I GLU* 3.5 6.7 + - + +
240I VAL* 5.2 0.2 - - - -
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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