Contacts of the strand formed by residues 181 - 188 (chain F) in PDB entry 1I3R
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 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E ASP 5.6 0.7 - - - -
29E ASP* 4.8 1.1 - - - -
147F ASP* 2.9 24.8 + - - -
148F PHE* 3.1 42.6 + - + -
149F TYR* 4.0 20.0 - + - -
150F PRO 3.9 2.0 - - - -
151F GLY* 3.4 33.2 - - - -
173F LEU* 3.6 30.5 - - + -
174F VAL 3.2 15.0 - - - -
175F ARG* 3.7 49.6 - - + -
176F ASN* 3.5 5.2 + - - -
179F TRP 5.6 0.4 - - - -
180F THR* 1.3 76.1 - - - +
182F GLN* 1.3 61.1 + - - +
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Residues in contact with GLN 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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92E LEU* 3.7 16.6 - - - +
93E SER* 2.9 29.6 + - - +
94E ARG* 3.0 14.4 + - - +
95E SER* 4.7 4.2 + - - -
96E PRO* 5.5 1.2 - - - +
145F VAL 3.4 7.6 - - - -
146F SER* 4.1 15.9 - - - -
147F ASP 4.7 0.2 - - - +
148F PHE* 4.0 1.3 - - - -
173F LEU* 4.2 0.3 - - - -
174F VAL* 2.9 47.4 + - + +
176F ASN* 2.8 29.7 + - - +
181F PHE* 1.3 77.3 - - - +
183F THR* 1.3 65.6 + - - +
184F LEU* 5.7 5.2 - - - +
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Residues in contact with THR 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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144F SER* 4.4 0.3 + - - -
145F VAL* 3.0 57.0 + - + +
148F PHE* 3.8 14.4 - - + -
153F ILE* 4.8 9.9 - - + -
155F VAL* 5.2 0.2 - - + -
170F SER* 3.7 9.7 + - - -
171F THR* 3.8 6.7 - - - -
172F GLY 3.1 21.9 + - - -
173F LEU* 4.6 3.6 - - + -
174F VAL* 5.1 0.2 - - - -
182F GLN* 1.3 82.1 + - - +
184F LEU* 1.3 80.5 + - - +
185F VAL* 4.4 10.4 - - + +
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Residues in contact with LEU 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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96E PRO* 6.0 0.4 - - + -
128F TYR* 4.1 10.8 - - - +
142F VAL* 3.8 11.4 - - + -
143F CYS 3.8 1.8 - - - -
144F SER* 3.6 29.2 - - - +
170F SER* 3.1 7.1 + - - -
171F THR* 3.0 51.0 + - + +
182F GLN* 5.7 4.0 - - - +
183F THR* 1.3 87.5 + - - +
185F VAL* 1.3 62.5 + - - +
186F MET* 3.8 25.6 + - + +
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Residues in contact with VAL 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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143F CYS* 3.1 24.6 + - - +
155F VAL* 3.7 48.7 - - + +
157F TRP* 2.9 28.3 + - + +
168F ILE* 4.0 24.0 - - + -
169F VAL 3.5 4.3 - - - +
170F SER* 4.2 12.8 - - - +
183F THR* 4.4 10.5 - - + +
184F LEU* 1.3 73.5 - - - +
186F MET* 1.3 59.5 + - - +
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Residues in contact with MET 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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128F TYR* 5.6 0.2 - - - +
130F THR* 5.2 1.8 - - + +
140F LEU* 3.7 34.8 - - + -
141F LEU 3.3 4.9 - - - +
142F VAL* 3.4 34.1 - - + -
157F TRP* 3.9 1.8 - - - -
167F GLY 3.5 0.7 - - - +
168F ILE* 3.4 6.6 - - - +
169F VAL* 2.6 47.9 + - + +
171F THR* 5.2 2.7 - - + -
184F LEU* 4.1 32.8 - - + +
185F VAL* 1.3 76.7 - - - +
187F LEU* 1.3 60.2 + - - +
188F GLU 4.1 0.2 - - - -
313G NAG 5.9 2.5 - - - -
20H VAL* 4.9 16.8 - - - -
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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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140F LEU* 3.0 4.2 - - - +
141F LEU* 2.8 37.1 + - + +
157F TRP* 3.7 40.1 - - + +
158F PHE 5.4 0.4 - - - +
164F GLU* 4.2 17.9 - - + -
166F THR 3.9 11.4 - - - +
167F GLY 3.4 3.6 - - - +
168F ILE* 3.4 21.8 - - + -
186F MET* 1.3 74.1 - - - +
188F GLU* 1.3 64.0 + - - +
189F THR* 3.5 26.2 + - + +
197F TYR* 4.0 27.8 - - + -
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Residues in contact with GLU 188 (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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138F HIS* 5.9 5.4 - - + -
139F ASN 4.3 3.4 - - - +
140F LEU* 3.4 22.2 - - + +
166F THR 5.2 0.2 - - - +
167F GLY* 2.7 41.0 + - - +
169F VAL* 3.3 28.4 - - + +
187F LEU* 1.3 70.7 - - - +
189F THR* 1.3 70.1 + - - +
313G NAG 4.6 8.8 - - - +
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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