Contacts of the helix formed by residues 203 - 213 (chain H) in PDB entry 3AOI
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 203 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198H ARG* 3.8 24.3 + - - +
201H GLY 2.6 23.0 - - - +
202H TYR* 1.3 72.5 - - - +
204H GLN* 1.3 68.2 + - - +
205H GLU* 2.7 26.0 - - + +
206H THR* 2.9 15.3 - - - +
207H LEU* 2.7 25.4 + - - +
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Residues in contact with GLN 204 (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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163D TYR* 5.6 2.0 - - + -
194H VAL* 3.6 26.3 - - - +
198H ARG* 3.4 21.2 + - - +
202H TYR 3.8 6.4 - - - +
203H ASP* 1.3 73.9 - - - +
205H GLU* 1.3 63.0 + - + +
207H LEU* 4.3 5.2 - - - +
208H ALA* 3.0 28.4 + - - +
221H LEU 4.0 5.7 + - - -
222H MET* 4.3 21.0 - - + +
224H GLU* 3.7 10.3 + - - +
228H ALA* 2.6 40.0 - - + +
229H MET* 6.3 1.6 - - - -
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Residues in contact with GLU 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D TYR* 3.9 36.2 - - + -
414D ARG* 3.4 25.9 + - - +
434D ARG* 5.6 4.3 + - - +
203H ASP* 2.7 34.7 - - + +
204H GLN* 1.3 76.3 - - + +
206H THR* 1.3 83.7 + - - +
208H ALA* 4.0 0.7 - - - +
209H ARG* 3.1 45.5 + - - +
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Residues in contact with THR 206 (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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434D ARG* 4.6 17.2 + - - -
202H TYR* 4.1 12.8 - - + -
203H ASP* 2.9 42.4 - - - +
205H GLU* 1.3 93.8 + - - +
207H LEU* 1.3 61.9 + - - +
209H ARG* 2.8 33.4 - - - +
210H GLU* 3.1 20.8 + - - +
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Residues in contact with LEU 207 (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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194H VAL* 4.0 18.2 - - + -
197H LEU* 3.4 39.9 - - + -
202H TYR* 4.1 22.2 - - + +
203H ASP 2.7 19.9 + - - +
204H GLN* 3.7 7.2 - - - +
206H THR* 1.3 76.5 - - - +
208H ALA* 1.3 64.1 + - - +
210H GLU* 3.9 1.7 - - - +
211H LEU* 2.9 56.5 + - + +
221H LEU* 3.4 17.0 - - + -
304H LEU* 6.3 3.1 - - + -
307H LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 208 (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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159D ARG* 2.9 30.0 + - + +
163D TYR* 6.0 2.0 - - + -
204H GLN 3.0 14.3 + - - +
205H GLU* 4.0 2.0 - - - +
207H LEU* 1.3 77.8 - - - +
209H ARG* 1.3 60.7 + - - +
212H GLY* 2.7 29.8 + - - -
213H ALA 3.9 0.2 + - - -
218H VAL* 3.8 7.2 - - - -
222H MET* 3.1 32.8 - - + -
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Residues in contact with ARG 209 (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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159D ARG* 4.5 8.9 - - - +
163D TYR* 2.5 35.7 + - + +
164D GLY* 3.1 25.1 - - - +
165D LYS* 4.4 1.4 - - - +
166D GLN 3.3 4.6 + - - +
414D ARG* 5.0 5.9 - - - +
434D ARG* 3.7 25.5 - - - +
447D VAL* 4.4 3.8 - - - +
449D SER* 3.0 24.7 + - - -
205H GLU* 3.1 43.5 + - - +
206H THR* 2.8 28.6 - - - +
208H ALA* 1.3 81.6 - - - +
210H GLU* 1.3 84.7 + - - +
213H ALA* 3.1 28.6 + - - +
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Residues in contact with GLU 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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166D GLN* 2.8 57.1 + - + +
168D THR* 4.7 10.9 + - - -
434D ARG* 5.6 2.6 + - - -
436D GLU* 5.3 4.4 - - - +
447D VAL* 5.7 1.7 - - - +
206H THR* 3.1 32.0 + - - +
207H LEU* 4.3 1.3 - - - +
209H ARG* 1.3 106.4 - - - +
211H LEU* 1.3 61.8 + - - +
213H ALA* 4.4 2.1 - - - +
214H TYR* 5.1 3.3 - - - -
308H ARG* 4.9 21.5 + - - +
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Residues in contact with LEU 211 (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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207H LEU* 2.9 34.0 + - + +
210H GLU* 1.3 78.6 - - - +
212H GLY* 1.3 57.6 + - - +
213H ALA 3.2 7.3 + - - -
214H TYR* 3.9 21.8 - - - +
215H GLY 4.5 0.2 + - - -
218H VAL* 3.2 11.2 - - + -
221H LEU* 3.0 33.2 - - + -
304H LEU* 6.1 0.9 - - + +
307H LEU* 4.0 22.9 - - + +
308H ARG* 4.3 17.3 - - + +
311H PHE* 3.1 31.5 - - + -
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Residues in contact with GLY 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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156D GLU* 3.7 17.0 - - - +
159D ARG* 3.7 8.4 + - - -
208H ALA 2.7 17.1 + - - -
209H ARG* 5.7 0.2 - - - -
211H LEU* 1.3 72.8 - - - +
213H ALA* 1.3 50.5 + - - -
214H TYR* 2.4 20.9 + - - -
215H GLY* 3.2 14.9 + - - -
216H GLU 4.1 1.4 + - - -
218H VAL* 3.1 22.2 - - - +
311H PHE* 4.9 0.2 - - - -
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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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156D GLU* 5.6 0.2 - - - -
165D LYS* 3.3 24.6 - - + +
166D GLN 3.0 28.9 - - - +
167D GLU* 3.4 28.6 - - + +
168D THR 4.9 0.9 - - - +
209H ARG 3.1 13.2 + - - +
210H GLU 4.4 3.1 - - - +
211H LEU 3.2 3.4 + - - -
212H GLY* 1.3 73.2 - - - +
214H TYR* 1.3 60.0 + - + +
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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