Contacts of the helix formed by residues 209 - 219 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150H ASN* 3.6 15.0 - - - +
152H GLN* 3.7 18.4 - - + -
207H ASP 4.3 3.6 - - - +
208H THR* 1.3 76.8 - - - +
210H TYR* 1.3 64.6 + - - +
211H SER* 2.9 22.7 + - - -
212H ILE* 3.1 24.5 + - - +
213H ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H ASP* 4.3 20.7 + - - -
150H ASN* 3.4 24.0 - - + +
156H PHE* 4.0 23.1 - + - -
209H ASP* 1.3 75.7 + - - +
211H SER* 1.3 63.1 + - - +
213H ALA* 4.1 1.9 - - - +
214H GLU* 3.1 53.8 + - + +
227H ASN* 3.6 33.1 + - - -
230H TRP* 3.2 32.1 + + - -
231H ALA* 4.0 5.4 - - - +
1R GLC 5.9 0.4 - - - -
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Residues in contact with SER 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209H ASP* 2.9 14.2 + - - -
210H TYR* 1.3 77.6 - - - +
212H ILE* 1.3 63.0 + - - +
214H GLU* 4.0 4.1 - - - +
215H ALA* 2.9 31.6 + - - +
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Residues in contact with ILE 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H MET* 3.6 24.2 - - + -
207H ASP* 3.7 16.6 - - + +
208H THR* 3.8 5.6 - - + -
209H ASP* 3.1 37.3 + - - +
211H SER* 1.3 78.8 - - - +
213H ALA* 1.3 57.3 - - - +
215H ALA* 3.4 5.2 + - - +
216H ALA* 2.8 29.8 + - + +
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Residues in contact with ALA 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H MET* 3.6 33.4 - - - +
149H PHE* 3.6 20.0 - - - +
150H ASN 4.1 1.8 - - - +
208H THR* 4.1 4.9 - - + +
209H ASP 3.1 14.9 + - - +
210H TYR* 4.1 2.5 - - - +
212H ILE* 1.3 76.3 - - - +
214H GLU* 1.3 66.5 + - - +
216H ALA* 3.4 1.8 + - - +
217H PHE* 3.1 24.9 + - - +
222H THR* 4.8 0.7 - - - +
225H THR* 4.2 6.5 + - - +
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Residues in contact with GLU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H TYR* 3.1 51.2 + - + +
211H SER* 4.0 4.3 - - - +
213H ALA* 1.3 75.7 - - - +
215H ALA* 1.3 63.6 + - - +
217H PHE* 3.4 2.4 + - - +
218H ASN* 3.0 43.5 + - - +
225H THR* 5.1 3.8 + - - -
227H ASN* 5.1 9.3 - - - +
231H ALA* 4.2 12.1 - - + +
234H ASN* 3.6 32.6 - - - +
235H ILE* 5.8 2.0 - - + -
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Residues in contact with ALA 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211H SER 2.9 20.2 + - - +
212H ILE* 3.5 6.3 - - - +
213H ALA 3.3 0.2 - - - -
214H GLU* 1.3 78.1 - - - +
216H ALA* 1.3 57.7 + - - +
218H ASN* 3.3 3.7 + - - +
219H LYS* 2.9 33.1 + - - +
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Residues in contact with ALA 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H MET* 3.6 31.2 - - + -
212H ILE* 2.8 20.9 + - + +
213H ALA 3.9 3.1 - - - +
215H ALA* 1.3 73.7 - - - +
217H PHE* 1.3 60.2 + - - +
219H LYS 3.7 0.3 + - - -
220H GLY 3.3 2.4 + - - -
221H GLU* 2.8 49.9 + - + +
222H THR* 3.4 6.8 + - + -
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Residues in contact with PHE 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H ILE* 3.7 32.8 - - + -
117H TYR 3.7 2.5 - - - -
118H ASN* 3.7 23.6 + - + -
213H ALA 3.1 17.2 + - - +
214H GLU* 3.9 3.4 - - - +
216H ALA* 1.3 75.7 - - - +
218H ASN* 1.3 71.0 + - - +
220H GLY* 3.1 15.8 + - - -
222H THR* 3.6 24.5 - - + +
223H ALA 3.6 21.3 - - - -
224H MET* 3.7 23.1 - - - -
225H THR* 3.8 15.5 - - + -
235H ILE* 4.3 22.0 - - + -
240H VAL* 3.6 15.0 - - + +
242H TYR* 4.3 4.5 - - + -
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Residues in contact with ASN 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H GLU* 3.0 30.0 + - - +
215H ALA* 4.0 3.8 - - - +
217H PHE* 1.3 80.3 - - - +
219H LYS* 1.3 58.9 + - - +
220H GLY 3.2 2.4 + - - -
234H ASN* 3.2 40.6 + - - +
235H ILE* 3.3 25.2 - - - +
238H SER* 2.8 29.9 + - - +
239H ALA* 5.6 1.6 - - - +
240H VAL* 3.6 8.5 - - - +
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Residues in contact with LYS 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H LYS* 5.7 0.7 + - - -
215H ALA 2.9 17.5 + - - +
216H ALA 4.1 0.9 - - - +
218H ASN* 1.3 75.8 - - - +
220H GLY* 1.3 60.1 + - - +
221H GLU* 3.3 30.2 + - + +
240H 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