Contacts of the strand formed by residues 179 - 185 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168L TYR 3.6 0.2 - - - +
169L TYR* 3.1 9.5 - - - -
170L ILE* 2.9 40.1 + - + +
172L PRO* 3.4 40.6 - - + -
175L ALA* 4.5 6.3 - - + -
177L GLN 3.9 11.7 - - - +
178L PRO* 1.3 73.1 - - - +
180L LEU* 1.3 66.4 + - - +
181L VAL* 3.2 36.7 + - + -
228L LEU* 4.1 6.7 - - + -
232L LYS* 3.6 62.1 - - + +
235L LEU* 5.3 2.7 - - + -
236L LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K VAL* 3.6 41.3 - - + -
247K TYR* 6.0 1.6 - - + -
146L ILE* 3.6 41.1 - - + -
167L LEU* 3.9 15.7 - - + -
168L TYR 3.4 12.6 - - - +
169L TYR* 3.6 26.7 - - + +
179L PHE* 1.3 79.9 - - - +
181L VAL* 1.3 67.0 + - - +
218L LEU* 3.5 25.1 - - + +
228L LEU* 3.9 6.1 - - - +
232L LYS* 4.6 2.8 + - - -
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Residues in contact with VAL 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L CYS* 4.0 15.3 - - - -
167L LEU* 3.4 7.2 - - - -
168L TYR 2.9 33.1 + - - +
170L ILE* 3.4 39.3 - - + -
179L PHE* 3.2 34.5 - - + -
180L LEU* 1.3 81.5 - - - +
182L PHE* 1.3 61.3 + - - +
183L CYS* 3.7 1.7 + - - -
192L THR* 5.1 2.5 - - - +
193L VAL 5.0 4.3 - - - +
218L LEU* 4.2 7.0 - - - -
228L LEU* 3.8 17.5 - - + -
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Residues in contact with PHE 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L CYS* 4.4 0.7 - - - -
165L SER* 4.1 15.0 - - - -
166L GLY* 3.4 11.4 - - - -
167L LEU* 4.2 7.0 - - + -
181L VAL* 1.3 73.6 - - - +
183L CYS* 1.3 79.3 + - - +
184L GLU* 4.0 12.3 - - + -
192L THR 4.1 0.3 - - - -
193L VAL* 3.2 46.7 + - + +
218L LEU* 4.3 14.5 - - + +
219L ALA 3.3 20.9 - - - -
220L PRO 3.7 6.3 - - - -
221L THR* 3.4 13.9 - - - -
222L LEU* 3.1 53.2 - - + -
226L PHE* 4.8 0.7 - - + -
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Residues in contact with CYS 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L CYS* 2.0 57.7 - - + +
157L VAL* 4.5 5.4 - - - -
165L SER* 3.2 4.7 - - - -
166L GLY 2.7 30.1 + - - -
168L TYR* 3.7 40.4 - - + -
181L VAL* 3.7 5.1 + - - -
182L PHE* 1.3 77.9 - - - +
184L GLU* 1.3 60.0 + - - +
185L ILE* 4.5 9.9 - - + -
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Residues in contact with GLU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165L SER* 3.4 7.4 - - - +
182L PHE* 3.8 12.2 + - + -
183L CYS* 1.3 72.2 - - - +
185L ILE* 1.3 63.2 + - - +
186L GLU* 4.0 18.7 - - + +
189L ASN 3.1 1.6 - - - +
190L GLY 3.7 0.3 - - - -
191L TRP* 2.6 54.9 + - + +
193L VAL* 4.6 6.8 - - + +
222L LEU* 4.5 14.6 - - - +
247L ASP* 4.9 0.7 - - - +
381L THR* 5.2 1.7 + - - +
383L LYS* 3.1 36.0 + - - -
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Residues in contact with ILE 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L VAL* 5.2 2.0 - - + -
158L VAL* 3.7 33.2 - - + -
162L GLY* 3.9 13.5 - - - +
163L LYS* 3.5 24.6 - - - +
164L ASP 3.4 22.9 - - - +
165L SER* 2.7 20.1 + - - +
168L TYR* 3.9 14.4 - - + +
183L CYS* 4.5 10.8 - - + +
184L GLU* 1.3 78.0 - - - +
186L GLU* 1.3 72.5 + - - +
188L GLY* 4.7 1.6 - - - +
189L ASN 3.1 10.1 - - - +
190L GLY* 4.6 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