Contacts of the helix formed by residues 206 - 211 (chain D) in PDB entry 3D87
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 PHE 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182D GLU* 3.5 32.1 - - + +
183D SER* 3.5 18.2 - - - -
184D LEU 3.1 39.5 - - - -
185D PRO* 3.3 18.4 - - + -
205D PHE* 1.3 73.4 - - - +
207D ILE* 1.3 68.6 + - - +
208D ARG* 3.3 33.9 - - + -
209D ASP* 3.1 30.1 + - - +
210D ILE* 3.2 11.8 - - - +
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.6 22.9 - - + -
113D ASN 3.7 5.6 - - - +
114D TYR* 4.3 14.8 - - + +
116D GLY* 5.0 14.4 - - - +
118D PHE* 4.1 17.0 - - + -
138D ARG* 4.0 9.2 - - - +
182D GLU* 2.7 21.8 + - - +
186D ILE* 4.4 7.0 - - + -
205D PHE* 4.0 15.7 - - + -
206D PHE* 1.3 70.8 - - - +
208D ARG* 1.3 53.6 + - - +
210D ILE* 2.6 48.3 + - + +
211D ILE* 3.0 24.5 + - + -
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG 5.1 2.8 + - - -
149C SER* 5.3 4.4 - - - +
152C ALA* 3.5 29.9 - - - +
159C ARG* 6.1 0.4 - - - +
114D TYR* 4.2 15.3 + - + +
181D GLU* 4.3 2.2 - - - +
182D GLU* 2.6 67.6 + - - +
206D PHE* 3.3 35.2 - - + -
207D ILE* 1.3 74.3 - - - +
209D ASP* 1.3 64.7 + - - +
210D ILE 3.3 0.3 + - - -
211D ILE* 3.6 13.3 + - - +
293D TYR* 3.2 46.5 + - + -
295D SER* 3.3 23.0 + - - -
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Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG* 5.9 0.9 - - - +
205D PHE* 5.3 2.2 - - + -
206D PHE* 3.1 35.0 + - - +
207D ILE 3.1 1.2 - - - -
208D ARG* 1.3 81.0 + - - +
210D ILE* 1.3 62.3 + - + +
211D ILE 3.6 0.4 + - - -
293D TYR* 2.9 34.9 + - - -
295D SER* 4.4 9.4 - - - -
296D SER* 4.8 5.0 + - - -
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D CYS* 3.6 16.9 - - + +
110D GLU* 3.1 17.7 - - - +
111D ALA* 3.0 28.7 + - + +
118D PHE* 4.5 2.9 - - + -
205D PHE* 3.5 35.4 - - + -
206D PHE 3.2 11.9 - - - +
207D ILE* 2.6 56.4 + - + +
209D ASP* 1.3 74.4 - - + +
211D ILE* 1.3 64.1 + - - +
212D LYS* 3.4 1.2 + - - +
296D SER* 4.6 3.7 + - - -
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Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA* 3.3 7.0 - - + +
113D ASN 2.9 38.4 - - - +
114D TYR* 3.6 30.7 - - + +
207D ILE* 3.0 25.1 + - + +
208D ARG 3.8 10.5 - - - +
209D ASP 3.6 2.0 - - - -
210D ILE* 1.3 74.7 - - - +
212D LYS* 1.3 60.3 + - - +
213D PRO* 4.0 10.5 - - + -
240D TRP* 3.9 24.7 - - + -
290D ASP* 4.7 2.7 - - + -
295D SER* 3.8 12.8 - - - +
296D SER* 2.9 30.5 + - - +
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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