Contacts of the strand formed by residues 158 - 168 (chain F) in PDB entry 6CU0
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 SER 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157F GLY* 1.3 76.9 - - - -
159F GLY* 1.3 60.8 + - - +
185F LEU* 3.7 21.3 - - - +
187F PRO* 4.1 23.6 - - - -
219F GLU 4.0 1.4 - - - +
220F ALA* 4.9 0.3 - - - -
221F ARG* 3.1 42.2 + - - +
222F ALA 5.4 0.5 - - - -
223F ARG* 6.2 0.2 - - - -
226F TRP* 4.2 1.4 - - - +
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Residues in contact with GLY 159 (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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191E GLU 5.7 4.7 - - - -
158F SER* 1.3 78.3 - - - +
160F SER* 1.3 62.8 + - - -
184F ASP* 3.7 4.5 - - - +
185F LEU* 2.8 34.9 + - - +
219F GLU* 3.7 10.1 - - - -
221F ARG* 5.2 2.0 - - - -
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Residues in contact with SER 160 (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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193E ARG* 5.3 12.1 - - - -
159F GLY* 1.3 75.1 - - - -
161F VAL* 1.3 71.4 + - - +
162F SER* 4.0 4.3 + - - -
182F THR* 3.3 22.6 - - - +
183F VAL 3.5 10.1 - - - -
184F ASP* 4.9 2.2 - - - -
185F LEU* 4.2 4.2 - - - +
218F THR* 3.4 3.7 + - - -
219F GLU* 3.0 42.2 + - - +
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Residues in contact with VAL 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 4.0 26.5 - - + -
147F LEU* 4.0 15.5 - - + +
149F LEU* 3.9 20.4 - - + -
160F SER* 1.3 81.1 + - - +
162F SER* 1.3 64.6 + - - +
182F THR* 3.4 1.7 - - - +
183F VAL* 2.9 32.1 + - - +
185F LEU* 3.8 25.6 - - + -
216F LEU* 3.5 26.5 - - + -
217F HIS 3.4 6.7 - - - +
218F THR* 4.2 6.3 - - - +
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Residues in contact with SER 162 (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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147F LEU* 4.8 0.2 - - - -
160F SER* 4.0 3.8 + - - -
161F VAL* 1.3 80.1 + - - +
163F LEU* 1.3 66.1 + - - +
164F ALA* 6.3 0.2 - - - -
181F LEU 3.2 12.3 - - - -
182F THR* 3.6 17.5 + - - +
215F HIS 3.5 1.2 - - - +
216F LEU* 3.3 7.0 - - - +
217F HIS* 2.7 54.4 + - - +
219F GLU 5.9 0.2 + - - -
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Residues in contact with LEU 163 (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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107F LEU* 3.8 19.3 - - + -
109F TRP* 5.6 1.8 - - + -
145F PHE* 3.7 42.6 - - + -
146F GLN 4.2 17.3 - - - +
147F LEU* 3.9 27.8 - - + +
162F SER* 1.3 75.8 - - - +
164F ALA* 1.3 63.1 + - - +
180F ALA* 3.6 2.6 - - - +
181F LEU* 3.1 34.1 + - + +
214F VAL* 4.1 9.9 - - + -
215F HIS 3.5 1.6 - - - -
216F LEU* 3.5 31.6 - - + -
233F THR* 4.3 8.1 - - + -
234F VAL 5.6 0.2 - - - +
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Residues in contact with ALA 164 (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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145F PHE* 4.2 3.1 - - - -
162F SER* 6.3 0.2 - - - -
163F LEU* 1.3 77.5 - - - +
165F LEU* 1.3 61.4 + - - +
166F HIS* 3.7 22.5 + - + +
177F ALA* 4.2 13.0 - - + -
179F LEU 3.6 6.3 - - - -
180F ALA* 4.5 2.5 - - + +
213F GLY 3.7 0.3 - - - +
214F VAL* 3.4 2.6 - - - -
215F HIS* 2.8 40.0 + - + +
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Residues in contact with LEU 165 (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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143F VAL* 4.1 13.5 - - + -
145F PHE* 3.8 8.3 - - + -
164F ALA* 1.3 70.6 - - - +
166F HIS* 1.3 63.2 + - - +
167F LEU* 4.7 5.6 - - + -
177F ALA* 3.6 4.3 - - - -
178F ALA* 2.9 35.1 + - + +
179F LEU* 2.8 32.5 + - + +
204F LEU* 3.8 29.8 - - + -
212F LEU* 4.0 23.3 - - + -
213F GLY 3.5 7.4 - - - +
214F VAL* 3.7 24.7 - - + +
235F LEU* 4.2 14.1 - - + -
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Residues in contact with HIS 166 (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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164F ALA* 3.7 22.7 + - + +
165F LEU* 1.3 75.5 + - - +
167F LEU* 1.3 65.6 + - - +
168F GLN* 4.0 0.5 + - - +
176F ALA 4.4 6.5 + - - -
177F ALA* 3.9 30.5 - - + +
178F ALA 5.0 0.9 - - - +
211F ARG 3.9 0.5 - - - +
212F LEU* 3.7 2.8 - - - +
213F GLY* 2.8 35.3 + - - +
215F HIS* 4.2 22.1 - + + +
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Residues in contact with LEU 167 (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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165F LEU* 4.7 7.0 - - + -
166F HIS* 1.3 78.4 - - - +
168F GLN* 1.3 59.9 + - - +
169F PRO 3.0 11.8 - - - +
170F LEU* 3.1 16.5 + - - +
171F ARG* 4.9 17.5 - - + +
176F ALA 5.9 0.8 + - - -
178F ALA* 4.0 27.1 - - + +
204F LEU* 5.0 2.5 - - + -
205F HIS 5.3 4.5 - - - +
206F LEU* 4.2 24.5 - - + -
210F GLN* 3.9 30.1 - - + +
211F ARG 3.9 1.8 - - - -
212F LEU* 4.5 14.6 - - + -
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Residues in contact with GLN 168 (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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132F GLU* 3.9 18.2 - - - +
166F HIS 4.0 1.0 + - - +
167F LEU* 1.3 72.3 - - - +
169F PRO* 1.3 71.3 - - + +
170F LEU* 3.2 18.9 + - - +
209F GLY 4.7 0.3 - - - +
210F GLN* 3.4 2.9 - - - +
211F ARG* 2.9 47.4 + - + +
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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