Contacts of the strand formed by residues 167 - 173 (chain B) in PDB entry 3UX9
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 ALA 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER* 3.8 17.7 - - - +
30A LEU* 3.5 30.5 - - + -
166B TYR* 1.3 78.8 - - - +
168B MET* 1.3 59.4 + - - +
185B ILE 3.4 15.3 - - - +
187B GLY 4.0 3.1 - - - +
206B ARG* 3.6 0.9 - - - +
232B ARG 3.7 0.3 - - - -
233B TYR* 2.8 48.4 + - + -
235B ASP 5.1 0.7 - - - +
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.9 23.3 - - + -
156B CYS* 4.4 2.5 - - - -
161B PHE* 4.6 4.3 - - - -
163B PHE* 3.8 27.1 - - + -
166B TYR 4.2 2.2 - - - +
167B ALA* 1.3 75.3 - - - +
169B SER* 1.3 62.5 + - - +
184B ALA* 3.4 2.8 - - - -
185B ILE* 3.0 31.8 + - - -
206B ARG* 3.3 20.4 - - - +
213B LEU* 3.7 34.8 - - + -
230B CYS* 4.1 4.7 - - - -
231B ALA 3.3 30.7 - - - +
232B ARG* 3.8 20.0 - - - -
233B TYR* 3.4 7.5 - - - -
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Residues in contact with SER 169 (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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168B MET* 1.3 72.6 - - - +
170B TRP* 1.3 67.1 + - - +
171B VAL* 4.0 4.5 - - - +
181B TRP* 4.0 4.9 - - - -
183B SER 3.4 11.7 - - - -
184B ALA* 4.1 0.9 - - - +
204B ILE* 4.7 1.1 - - - -
213B LEU* 3.9 2.5 - - - +
230B CYS* 3.3 7.8 - - - +
231B ALA* 2.9 48.4 + - - +
233B TYR* 3.1 32.3 - - - -
240B MET* 3.6 12.1 - - - -
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Residues in contact with TRP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 4.1 11.9 - - + -
154B LEU* 3.8 31.6 - - + -
155B SER 3.6 21.8 - - - -
156B CYS* 3.8 9.0 - - + -
169B SER* 1.3 72.2 - - - +
171B VAL* 1.3 66.7 + - - +
181B TRP* 3.8 0.7 - - - -
182B VAL* 3.2 32.8 + - + +
183B SER* 3.1 11.5 + - - +
204B ILE* 3.6 22.0 - - + -
213B LEU* 3.3 42.1 - - + +
214B TYR 2.9 18.5 + - - -
215B LEU* 3.4 31.8 - - + +
228B TYR* 4.3 15.7 - - + -
229B TYR 3.3 22.0 - - - -
230B CYS* 3.8 13.2 - - + -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 4.1 20.4 - - + -
169B SER* 4.0 15.0 - - - +
170B TRP* 1.3 80.3 - - - +
172B ARG* 1.3 69.8 + - - +
179B LEU* 4.0 13.5 - - + -
180B GLU 3.4 22.2 - - - +
181B TRP* 4.2 10.1 - - + -
182B VAL* 4.3 0.4 - - - -
228B TYR* 4.6 1.3 - - - -
229B TYR* 2.7 42.2 + - + +
231B ALA* 5.2 0.9 - - + -
240B MET* 4.5 3.4 - - - -
243B TRP* 3.9 32.3 - - + -
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Residues in contact with ARG 172 (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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171B VAL* 1.3 78.2 - - - +
173B GLN* 1.3 62.8 + - - +
174B ALA* 5.2 1.3 - - + +
179B LEU* 3.7 1.9 - - - -
180B GLU* 2.8 67.0 + - + +
182B VAL* 3.5 17.3 - - + +
197B SER* 4.0 19.8 - - - -
198B VAL* 4.1 7.0 - - - +
201B ARG* 5.3 0.4 - - - +
202B PHE* 3.9 10.9 - - - -
223B GLU* 4.1 12.7 + - - +
224B ASP* 3.0 33.7 + - - +
226B ALA* 3.8 13.7 - - + +
227B VAL 3.2 10.8 - - - +
228B TYR* 3.0 38.1 + - + -
229B TYR* 5.1 0.2 - - - -
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Residues in contact with GLN 173 (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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41B GLN* 3.1 40.0 + - - -
88B ASP* 5.1 2.4 + - - -
90B TYR* 3.3 15.8 + - - -
172B ARG* 1.3 72.8 - - - +
174B ALA* 1.3 68.3 + - - +
177B LYS 2.8 31.7 + - - +
178B GLY* 3.7 8.6 - - - -
179B LEU* 3.5 14.8 - - + +
226B ALA* 2.9 13.1 - - - +
227B VAL* 3.0 24.8 + - + +
229B TYR* 4.2 13.5 + - + -
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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