Contacts of the strand formed by residues 166 - 170 (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 GLY 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C LYS 5.3 2.0 - - - -
164C ASP 3.5 2.8 + - - -
165C SER* 1.3 74.9 - - - +
167C LEU* 1.3 64.1 + - - -
168C TYR* 3.2 11.7 - - - -
182C PHE* 3.3 8.6 - - - -
183C CYS 2.7 38.1 + - - -
220C PRO* 4.2 15.0 - - - -
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Residues in contact with LEU 167 (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* 4.2 10.8 - - + -
142C THR* 4.6 3.4 - - + -
145C LYS 4.1 6.6 + - - +
146C ILE* 3.7 25.8 - - + -
147C SER 3.3 20.6 + - - -
166C GLY* 1.3 68.8 - - - -
168C TYR* 1.3 72.5 + - - +
180C LEU* 3.9 24.9 - - + -
181C VAL 3.4 10.8 - - - +
182C PHE* 4.1 10.5 - - + -
218C LEU* 3.7 14.1 - - + -
219C ALA* 3.0 50.0 - - - +
220C PRO* 4.3 10.0 - - + +
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE* 4.7 3.1 - - - -
147C SER* 3.2 36.7 - - - -
149C ILE* 3.8 15.2 - - + +
157C VAL* 3.4 31.9 - - + -
162C GLY* 4.3 4.7 - - - -
163C LYS 4.1 4.3 + - - -
164C ASP* 2.5 35.0 + - - +
166C GLY* 3.2 24.7 - - - -
167C LEU* 1.3 88.6 - - - +
169C TYR* 1.3 63.9 + - - +
170C ILE* 4.7 0.4 - - + -
180C LEU* 3.4 7.5 - - - -
181C VAL* 2.9 34.9 + - - +
183C CYS* 3.7 28.3 - - + -
185C ILE* 3.9 6.4 - - + +
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Residues in contact with TYR 169 (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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247B TYR* 4.0 18.7 - - - +
255B GLU* 5.5 6.5 - - - -
256B PRO* 3.7 41.3 + - + +
146C ILE* 3.8 18.6 - - + +
147C SER 4.9 5.2 + - - +
149C ILE 3.8 4.4 + - - +
150C THR* 2.8 37.3 - - + +
168C TYR* 1.3 75.0 - - - +
170C ILE* 1.3 61.7 + - - +
178C PRO* 4.0 19.1 - - + -
179C PHE* 3.1 22.0 - - - -
180C LEU* 3.6 36.8 - - + +
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Residues in contact with ILE 170 (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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150C THR* 3.9 1.3 - - - -
151C GLY 3.3 12.6 - - - +
152C LYS 4.6 1.3 - - - +
153C ASP* 4.1 30.1 - - - -
154C CYS* 4.2 3.6 - - - +
157C VAL* 4.2 11.7 - - + -
168C TYR 4.3 2.2 - - - +
169C TYR* 1.3 79.6 - - - +
171C LYS* 1.3 60.3 + - - +
172C PRO* 3.8 5.1 - - + +
178C PRO* 3.4 2.3 - - - +
179C PHE* 2.9 51.9 + - + -
181C VAL* 3.4 41.1 - - + -
183C CYS* 4.6 0.4 - - - -
192C THR* 4.3 13.0 - - - +
236C LEU* 4.3 8.5 - - + -
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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