Contacts of the strand formed by residues 179 - 185 (chain F) in PDB entry 1LWU
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 179 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168F TYR 3.6 0.3 - - - +
169F TYR* 3.2 9.7 - - - -
170F ILE* 2.9 39.5 + - + +
172F PRO* 3.4 40.2 - - + -
175F ALA* 4.5 6.5 - - + -
177F GLN 3.9 11.2 - - - +
178F PRO* 1.3 73.5 - - + +
180F LEU* 1.3 62.6 + - - +
181F VAL* 3.2 38.0 + - + -
228F LEU* 4.2 6.3 - - + -
232F LYS* 3.6 60.8 - - + +
235F LEU* 5.3 1.6 - - + -
236F LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 180 (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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224E VAL* 3.7 29.6 - - + -
247E TYR* 5.9 2.0 - - + -
146F ILE* 3.6 44.6 - - + -
167F LEU* 3.9 22.2 - - + -
168F TYR 3.4 12.3 - - - +
169F TYR* 3.7 26.9 - - + +
179F PHE* 1.3 76.8 - - - +
181F VAL* 1.3 67.7 + - - +
218F LEU* 3.5 26.0 - - + +
228F LEU* 3.9 6.6 - - - +
232F LYS* 4.5 2.4 + - - -
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Residues in contact with VAL 181 (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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154F CYS* 4.0 15.3 - - - -
167F LEU* 3.4 7.7 - - - -
168F TYR 2.9 34.1 + - - +
170F ILE* 3.4 38.6 - - + -
179F PHE* 3.2 35.2 - - + -
180F LEU* 1.3 80.4 - - - +
182F PHE* 1.3 61.0 + - - +
183F CYS* 3.7 1.7 + - - -
192F THR* 5.1 1.8 - - - +
193F VAL 5.0 4.0 - - - +
218F LEU* 4.3 6.1 - - - -
228F LEU* 3.8 18.6 - - + -
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Residues in contact with PHE 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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154F CYS* 4.4 1.1 - - - -
165F SER* 4.1 14.6 - - - -
166F GLY* 3.3 12.1 - - - -
167F LEU* 4.1 7.0 - - + -
181F VAL* 1.3 74.1 - - - +
183F CYS* 1.3 78.7 + - - +
184F GLU* 4.0 11.9 - - + -
192F THR* 4.1 0.3 - - - -
193F VAL* 3.2 45.8 + - + +
218F LEU* 4.3 14.1 - - + +
219F ALA 3.3 19.1 - - - -
220F PRO 3.7 8.5 - - - -
221F THR* 3.4 13.9 - - - -
222F LEU* 3.2 52.9 - - + -
226F PHE* 4.9 1.3 - - + -
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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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154F CYS* 2.0 56.5 - - + -
157F VAL* 4.4 5.8 - - - -
165F SER* 3.2 6.4 - - - -
166F GLY 2.7 30.4 + - - -
168F TYR* 3.7 40.2 - - + -
181F VAL* 3.7 5.4 + - - -
182F PHE* 1.3 76.8 - - - +
184F GLU* 1.3 59.0 + - - +
185F ILE* 4.5 10.1 - - + -
191F TRP 3.4 0.2 - - - -
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Residues in contact with GLU 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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165F SER* 3.3 7.9 - - - +
182F PHE* 3.8 11.8 + - + -
183F CYS* 1.3 72.5 - - - +
185F ILE* 1.3 66.2 + - - +
186F GLU* 4.0 18.9 - - + +
189F ASN 3.1 1.9 - - - +
190F GLY 3.7 0.3 - - - -
191F TRP* 2.7 54.3 + - + +
193F VAL* 4.6 6.2 - - + +
222F LEU* 4.5 14.0 - - - +
247F ASP* 4.9 1.0 - - - +
381F THR* 5.2 1.7 + - - +
383F LYS* 3.1 36.4 + - - -
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Residues in contact with ILE 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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157F VAL* 5.2 1.6 - - + -
158F VAL* 3.7 33.0 - - + -
162F GLY* 3.9 13.2 - - - +
163F LYS* 3.5 28.6 - - - +
164F ASP 3.4 22.9 - - - +
165F SER* 2.7 19.6 + - - +
168F TYR* 3.9 10.8 - - + +
183F CYS* 4.4 11.0 - - + +
184F GLU* 1.3 76.7 - - - +
186F GLU* 1.3 72.9 + - - +
188F GLY* 4.7 1.6 - - - +
189F ASN 3.1 10.3 - - - +
190F GLY* 4.7 0.7 - - - -
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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