Contacts of the helix formed by residues 206 - 215 (chain D) in PDB entry 5FI6
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 ASN 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173D ARG 3.2 25.9 + - - +
174D LEU* 3.4 19.2 - - + -
176D GLU* 3.2 25.9 + - - -
177D CYS* 3.2 30.5 + - + +
203D VAL 3.1 5.8 + - - -
205D SER* 1.3 87.6 + - - +
207D ILE* 1.3 64.4 + - - +
208D VAL 3.3 2.5 - - - -
209D LEU* 3.3 8.8 + - + +
210D LEU* 3.0 28.1 + - + +
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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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138D LEU* 3.7 28.0 - - + +
139D GLU* 3.7 34.1 - - + +
142D LEU* 3.5 29.4 - - + -
203D VAL* 3.0 20.1 + - + +
204D GLN 3.4 15.0 - - - +
205D SER 3.5 1.4 + - - +
206D ASN* 1.3 76.2 - - - +
208D VAL* 1.3 66.2 + - + +
210D LEU* 3.0 4.3 + - + -
211D THR* 2.7 48.0 + - - +
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 5.1 16.8 - - + -
206D ASN 3.3 0.8 - - - -
207D ILE* 1.3 91.6 - - + +
209D LEU* 1.3 63.3 + - - +
211D THR* 3.3 10.4 + - - +
212D GLN* 3.1 41.6 + - + +
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Residues in contact with LEU 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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167D LEU* 4.5 8.3 - - + -
171D ASP* 4.7 1.1 - - - +
173D ARG* 3.4 69.5 - - + +
174D LEU* 3.8 22.7 - - + -
206D ASN* 3.3 10.6 + - + +
207D ILE 3.2 0.4 - - - -
208D VAL* 1.3 78.3 - - - +
210D LEU* 1.3 65.7 + - - +
212D GLN* 3.6 9.6 + - - +
213D ALA* 3.2 20.4 + - - +
218D PHE* 4.1 20.6 - - + -
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Residues in contact with LEU 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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142D LEU* 4.2 14.1 - - + -
158D PHE* 4.2 9.4 - - + -
162D LEU* 3.5 31.9 - - + -
167D LEU* 5.5 0.7 - - + -
174D LEU* 4.3 14.8 - - + -
177D CYS* 4.3 12.8 - - - -
203D VAL* 3.8 36.8 - - + +
206D ASN* 3.0 24.5 + - + +
207D ILE 3.0 7.9 + - - +
209D LEU* 1.3 77.6 - - - +
211D THR* 1.3 63.9 + - - +
213D ALA* 3.2 5.0 + - + +
214D PHE* 2.9 39.2 + - + +
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Residues in contact with THR 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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138D LEU* 4.2 20.1 + - + +
141D LEU* 5.7 4.9 - - + -
142D LEU* 4.3 8.5 - - + +
207D ILE* 2.7 40.0 + - - +
208D VAL* 3.3 7.3 + - - -
209D LEU 3.2 0.2 - - - -
210D LEU* 1.3 73.9 - - - +
212D GLN* 1.3 55.3 + - + +
214D PHE* 5.0 1.1 - - - -
215D ARG* 2.7 63.8 + - + +
217D LYS* 6.2 0.2 - - + -
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Residues in contact with GLN 212 (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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173D ARG* 5.8 0.2 + - - -
208D VAL* 3.1 34.4 + - + +
209D LEU* 4.1 9.4 - - - +
211D THR* 1.3 73.8 - - + +
213D ALA* 1.3 66.3 + - - +
216D ARG 3.2 2.3 + - - -
217D LYS* 2.9 51.2 + - + +
218D PHE* 3.8 25.4 + - + -
268D ASP* 5.3 2.4 - - - +
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Residues in contact with ALA 213 (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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162D LEU* 5.1 2.9 - - + -
165D THR* 3.0 28.5 - - + +
167D LEU* 3.7 14.4 - - + -
209D LEU 3.2 14.9 + - - +
210D LEU* 3.2 12.3 + - - +
212D GLN* 1.3 80.2 - - - +
214D PHE* 1.3 63.7 + - + +
216D ARG* 3.5 10.4 + - - +
218D PHE* 3.5 29.8 - - + -
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Residues in contact with PHE 214 (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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142D LEU* 3.6 30.1 - - + -
145D THR* 4.6 12.6 - - + +
146D ILE* 3.9 22.9 - - + -
158D PHE* 3.9 17.5 - + - -
161D ALA* 3.2 38.4 - - + -
162D LEU* 3.4 37.0 - - + -
164D SER* 5.4 0.2 - - - -
165D THR* 4.1 7.6 - - + -
210D LEU* 2.9 29.4 + - + +
211D THR 4.2 0.9 - - - +
213D ALA* 1.3 75.0 - - + +
215D ARG* 1.3 62.3 + - - +
216D ARG* 3.2 11.6 + - - +
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Residues in contact with ARG 215 (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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141D LEU* 3.0 38.2 + - - +
142D LEU* 3.3 29.5 - - - +
145D THR* 2.5 36.5 + - - +
211D THR* 2.7 39.3 + - + +
214D PHE* 1.3 72.6 - - - +
216D ARG* 1.3 66.8 + - - +
217D LYS* 2.3 58.8 + - + +
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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