Contacts of the strand formed by residues 179 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C TYR 3.6 0.2 - - - +
169C TYR* 3.1 10.7 - - - -
170C ILE* 2.9 39.0 + - + +
172C PRO* 3.4 40.6 - - + -
175C ALA* 4.6 6.7 - - + -
177C GLN 3.9 11.4 - - - +
178C PRO* 1.3 73.7 - - - +
180C LEU* 1.3 64.1 + - - +
181C VAL* 3.2 37.8 + - + -
228C LEU* 4.2 6.1 - - + -
232C LYS* 3.6 63.9 - - + +
235C LEU* 5.3 1.8 - - + -
236C LEU* 5.1 2.2 - - + -
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B VAL* 3.7 39.7 - - + -
247B TYR* 5.9 1.8 - - + -
146C ILE* 3.6 30.3 - - + -
167C LEU* 3.9 15.9 - - + -
168C TYR 3.4 12.1 - - - +
169C TYR* 3.6 38.1 - - + +
179C PHE* 1.3 76.5 - - - +
181C VAL* 1.3 67.1 + - - +
218C LEU* 3.5 25.2 - - + +
228C LEU* 3.9 6.2 - - - +
232C LYS* 4.5 3.0 + - - +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C CYS* 4.1 14.1 - - - -
167C LEU* 3.4 8.1 - - - -
168C TYR 2.9 39.5 + - - +
170C ILE* 3.4 32.1 - - + -
179C PHE* 3.2 34.8 - - + -
180C LEU* 1.3 80.7 - - - +
182C PHE* 1.3 61.0 + - - +
183C CYS* 3.7 1.5 + - - -
192C THR* 5.1 2.9 - - - +
193C VAL 5.0 4.0 - - - +
218C LEU* 4.3 6.5 - - - -
228C LEU* 3.8 17.9 - - + -
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C CYS* 4.4 1.1 - - - -
165C SER* 4.1 14.4 - - - -
166C GLY* 3.3 11.0 - - - -
167C LEU* 4.1 7.0 - - + -
181C VAL* 1.3 72.7 - - - +
183C CYS* 1.3 79.1 + - - +
184C GLU* 4.0 10.5 - - + -
192C THR* 4.2 0.2 - - - -
193C VAL* 3.2 45.6 + - + +
218C LEU* 4.3 14.6 - - + +
219C ALA 3.3 21.1 - - - -
220C PRO 3.7 5.4 - - - -
221C THR* 3.3 14.1 - - - -
222C LEU* 3.1 56.8 - - + -
226C PHE* 4.9 0.9 - - + -
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Residues in contact with CYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C CYS* 2.0 55.9 - - + +
157C VAL* 4.5 5.6 - - - -
165C SER* 3.2 6.1 - - - -
166C GLY 2.7 30.5 + - - -
168C TYR* 3.7 40.8 - - + -
181C VAL* 3.7 5.4 + - - -
182C PHE* 1.3 75.9 - - - +
184C GLU* 1.3 59.0 + - - +
185C ILE* 4.5 10.3 - - + -
191C TRP 3.4 0.2 - - - -
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Residues in contact with GLU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C SER* 3.4 8.1 - - - +
182C PHE* 3.8 11.8 + - + -
183C CYS* 1.3 71.9 - - - +
185C ILE* 1.3 66.3 + - - +
186C GLU* 4.0 18.2 - - + +
189C ASN 3.1 2.1 - - - +
190C GLY 3.7 0.3 - - - -
191C TRP* 2.6 54.2 + - + +
193C VAL* 4.6 6.4 - - + +
222C LEU* 4.5 14.4 - - + +
247C ASP* 4.9 1.0 - - - +
381C THR* 5.2 1.4 + - - +
383C LYS* 3.1 35.8 + - - -
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Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C VAL* 5.2 1.8 - - + -
158C VAL* 3.7 33.0 - - + -
162C GLY* 3.9 13.2 - - - +
163C LYS* 3.5 27.7 - - - +
164C ASP 3.4 24.2 - - - +
165C SER* 2.7 20.6 + - - +
168C TYR* 3.9 10.3 - - + +
183C CYS* 4.5 11.0 - - + +
184C GLU* 1.3 78.2 - - - +
186C GLU* 1.3 72.5 + - - +
188C GLY* 4.7 2.0 - - - +
189C ASN 3.1 9.9 - - - +
190C 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