Contacts of the strand formed by residues 166 - 170 (chain B) in PDB entry 3LXC
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 LEU 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B THR* 4.1 2.9 - - + -
88B TYR* 3.7 27.6 - - + -
90B CYS* 4.3 10.1 - - + -
131B LEU 3.1 2.8 + - - -
132B GLY* 3.8 15.7 - - - -
133B ILE* 2.9 24.8 + - - +
164B VAL* 3.1 12.6 - - - +
165B ASP* 1.3 81.2 - - - +
167B LEU* 1.3 75.7 + - - +
168B LYS* 3.7 11.2 - - + +
198B ILE* 4.0 1.6 - - - -
199B VAL* 3.3 32.1 - - + +
201B SER* 5.1 4.3 - - - -
225B HIS* 4.7 3.6 - - + -
295B PHE* 3.9 26.7 - - + -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 3.4 22.0 - - + +
135B ALA* 3.9 12.1 - - + +
159B PHE* 3.7 28.5 - - + -
164B VAL* 5.3 0.9 - - + -
166B LEU* 1.3 78.5 - - - +
168B LYS* 1.3 71.5 + - - +
169B PHE* 4.3 7.6 - - + +
187B MET* 4.0 23.1 - - + -
191B LEU* 3.9 30.1 - - + -
198B ILE* 3.8 12.3 - - + +
199B VAL 2.8 10.7 + - - +
200B TYR* 3.8 7.8 - - + -
201B SER* 2.9 27.7 + - - +
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.1 20.7 - - + +
90B CYS* 6.4 0.7 - - + -
91B ILE 5.7 1.1 - - - +
92B ASP* 3.0 20.8 + - - +
133B ILE 2.8 14.3 + - - +
134B TYR* 3.3 19.1 - - + -
135B ALA 3.0 25.6 + - - +
166B LEU* 3.7 9.1 - - + +
167B LEU* 1.3 73.1 - - - +
169B PHE* 1.3 62.0 + - - +
170B ASP* 4.9 3.6 - - - -
201B SER* 3.7 19.5 - - - +
203B SER* 4.7 11.7 - - - +
227B ARG* 4.2 23.1 - - - +
266B ASP* 5.1 0.8 + - - -
267B MET* 4.9 5.7 - - - +
802B GOL 2.6 33.4 + - - -
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 3.3 25.4 - - + -
136B ASP 3.4 22.7 - - - -
137B VAL* 3.4 36.6 - - + -
148B SER* 4.0 1.3 - - - -
152B TYR* 3.8 7.9 - + - -
167B LEU* 4.3 9.6 - - + -
168B LYS* 1.3 71.8 - - - +
170B ASP* 1.3 61.5 + - - +
183B GLY 4.3 2.0 - - - -
184B TYR* 2.8 31.2 + + + -
187B MET* 3.6 42.4 - - + -
200B TYR* 3.6 31.2 - + + -
201B SER 2.8 16.6 + - - +
203B SER* 3.3 17.3 + - - -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B TYR* 2.9 38.3 + - + +
135B ALA 2.8 7.5 + - - +
136B ASP* 3.4 8.1 - - - +
137B VAL* 2.9 26.2 + - - +
142B CYS* 3.1 12.5 - - - -
168B LYS* 4.0 3.9 + - - -
169B PHE* 1.3 71.1 - - - +
171B GLY* 1.3 66.0 + - - +
184B TYR* 3.2 8.5 + - - -
203B SER* 3.4 11.0 + - - -
207B TYR* 3.0 19.8 + - - -
227B ARG* 5.9 0.7 + - - -
802B GOL 2.8 30.1 + - - -
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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
------------------------------------------------------------
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