Contacts of the strand formed by residues 181 - 187 (chain F) in PDB entry 6D6Q
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 VAL 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163F THR* 4.0 2.9 - - - +
179F LEU* 5.1 0.4 - - + -
180F VAL* 1.3 81.7 - - - +
182F GLY* 1.3 64.6 + - - +
214F ALA* 3.2 3.1 - - - -
215F LEU* 2.9 34.1 + - + +
217F PRO* 4.4 9.2 - - + -
248F CYS* 3.3 50.5 - - + +
251F LEU* 4.1 17.5 - - + -
252F TYR* 3.9 29.2 - - + -
255F LEU* 4.1 13.2 - - + -
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Residues in contact with GLY 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F ALA* 3.5 21.2 - - - +
162F LEU* 4.8 1.1 - - - -
163F THR* 3.4 15.1 + - - +
180F VAL* 4.2 1.4 - - - +
181F VAL* 1.3 78.9 - - - +
183F CYS* 1.3 65.8 + - - +
213F VAL 3.2 9.6 - - - -
214F ALA* 4.1 5.8 - - - -
248F CYS* 3.4 7.4 - - - -
251F LEU* 4.7 10.6 - - - +
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Residues in contact with CYS 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 5.2 4.0 - - - -
156F SER* 5.7 0.4 - - - -
159F ALA* 3.2 11.8 - - - +
182F GLY* 1.3 76.6 - - - +
184F GLY* 1.3 62.4 + - - +
185F LEU* 4.0 6.5 - - - +
197F LEU* 3.2 35.7 - - - -
198F ASP* 4.8 6.7 - - - -
212F THR* 3.4 2.3 - - - -
213F VAL* 2.9 36.3 + - + +
244F GLY 3.9 10.3 - - - +
247F GLY* 4.7 8.3 - - - -
248F CYS* 3.4 18.4 - - - +
251F LEU* 6.3 1.3 - - + -
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Residues in contact with GLY 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156F SER* 3.9 24.4 + - - -
159F ALA* 4.9 1.1 - - - -
183F CYS* 1.3 74.3 - - - +
185F LEU* 1.3 66.0 + - - +
198F ASP* 2.9 27.5 + - - +
199F PRO* 3.3 8.4 - - - +
211F LEU 3.4 8.5 - - - -
212F THR* 4.4 6.1 - - - -
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Residues in contact with LEU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F CYS* 4.0 10.1 - - - +
184F GLY* 1.3 81.7 - - - +
186F SER* 1.3 64.8 + - - +
195F TRP* 4.5 12.3 - - + -
196F LEU 3.3 8.7 - - - +
197F LEU* 3.7 21.3 - - + -
199F PRO* 4.4 3.1 - - - -
210F GLY* 3.4 3.3 - - - -
211F LEU* 2.9 48.5 + - + +
213F VAL* 5.0 0.2 - - + -
240F ALA* 3.4 38.1 - - + +
243F LEU* 3.7 19.7 - - + -
244F GLY* 3.9 16.2 - - - -
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Residues in contact with SER 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F LEU* 1.3 75.3 - - - +
187F LEU* 1.3 69.9 + - - +
195F TRP* 3.5 12.6 - - - -
196F LEU* 2.9 37.0 + - - +
199F PRO* 4.0 18.4 - - - -
203F GLU 3.3 12.6 + - - -
204F GLU* 4.4 6.0 - - - -
207F ALA* 2.9 28.9 - - - +
209F ALA 3.3 8.5 + - - -
210F GLY* 4.4 1.3 - - - -
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F SER* 1.3 81.2 + - - +
188F ALA* 1.3 92.7 + - - +
189F PRO* 3.4 10.0 - - + +
193F PRO* 3.8 18.2 - - + -
194F THR 4.0 6.1 - - - +
195F TRP* 3.7 34.1 - - + +
196F LEU* 4.6 2.0 - - - -
203F GLU 5.2 0.2 - - - +
207F ALA* 3.7 6.1 - - - +
208F ALA* 3.4 30.0 + - + -
209F ALA* 2.9 28.5 + - + +
231F GLY 4.7 7.4 - - - +
232F GLY* 5.3 5.2 - - - -
236F SER* 5.6 1.6 - - - +
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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