Contacts of the helix formed by residues 177 - 188 (chain C) in PDB entry 1UN6
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 TRP 177 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C TYR* 3.4 20.8 - + + -
176C THR* 1.3 67.7 - - - +
178C THR* 1.3 68.7 + - - +
180C TYR* 3.2 28.2 + + - +
181C LEU* 2.9 53.4 + - + +
10E C 2.8 30.7 + - - +
11E A 3.1 75.1 + + - +
13E A 3.2 33.6 + + - -
14E C 3.3 27.6 - - - -
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Residues in contact with THR 178 (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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176C THR* 3.2 1.5 - - - -
177C TRP* 1.3 79.3 - - - +
179C LEU* 1.3 63.0 + - + +
181C LEU* 2.9 11.2 + - - +
182C LYS* 2.9 53.8 + - + +
8E G 6.0 1.6 - - - +
9E C 3.6 16.6 + - - +
10E C 3.0 34.4 + - - +
13E A 4.0 6.6 - - - -
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Residues in contact with LEU 179 (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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172C PHE* 4.4 7.0 - - + -
174C GLY* 4.7 2.9 - - - -
175C LYS* 4.5 15.7 - - + +
176C THR* 3.0 38.0 + - + +
178C THR* 1.3 81.5 - - + +
180C TYR* 1.3 65.9 + - - +
182C LYS* 3.2 26.4 + - + +
183C HIS* 3.0 22.5 + - - +
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Residues in contact with TYR 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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162C TYR* 4.1 32.5 - - + +
163C PRO 4.4 4.3 - - - -
164C CYS* 3.9 29.2 - - + -
165C LYS 5.0 2.6 + - - -
166C LYS* 4.2 16.8 + - - +
172C PHE* 4.2 12.8 - + - -
174C GLY* 4.7 1.2 - - - -
176C THR 2.8 16.8 + - - +
177C TRP* 3.2 31.6 + + - +
179C LEU* 1.3 73.1 - - - +
181C LEU* 1.3 86.4 + - + +
183C HIS* 3.2 12.9 - + - +
184C VAL* 3.3 30.1 + - + +
14E C 5.9 0.9 - - - -
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Residues in contact with LEU 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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177C TRP* 2.9 52.8 + - + +
178C THR* 2.9 12.8 + - - +
180C TYR* 1.3 99.0 - - + +
182C LYS* 1.3 61.0 + - + +
183C HIS 3.1 2.0 - - - -
184C VAL* 3.1 9.3 + - + +
185C ALA* 2.8 27.1 + - - +
13E A 4.1 2.5 - - - +
14E C 3.8 33.7 - - - +
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Residues in contact with LYS 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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178C THR* 2.9 37.1 + - + +
179C LEU* 3.2 22.5 + - + +
181C LEU* 1.3 75.2 - - + +
183C HIS* 1.3 65.9 + - - +
185C ALA* 2.8 25.1 + - + +
186C GLU* 3.2 21.8 + - - +
6E C 5.8 1.2 + - - -
7E G 3.1 35.9 + - - -
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Residues in contact with HIS 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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164C CYS* 3.5 10.8 - - + -
170C CYS* 3.3 6.0 - - - -
172C PHE* 3.3 58.4 - + + +
179C LEU 3.0 8.0 + - - +
180C TYR* 3.2 11.4 - + - +
182C LYS* 1.3 79.8 - - - +
184C VAL* 1.3 65.7 + - + +
186C GLU* 3.5 6.3 - - - +
187C CYS* 2.9 53.3 + - + +
188C HIS* 3.6 2.8 + + - -
206C ZN 2.3 35.7 - - - -
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Residues in contact with VAL 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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164C CYS* 4.7 1.1 - - - -
166C LYS* 4.2 31.6 - - + +
180C TYR* 3.3 39.9 + - + +
181C LEU* 3.1 11.9 + - + +
183C HIS* 1.3 83.2 - - + +
185C ALA* 1.3 57.9 + - - +
186C GLU 3.1 1.0 + - - -
188C HIS* 3.2 32.9 + - + +
189C GLN* 2.9 18.2 + - - -
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Residues in contact with ALA 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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181C LEU 2.8 13.5 + - - +
182C LYS* 2.8 20.3 + - - +
184C VAL* 1.3 73.0 - - - +
186C GLU* 1.3 55.0 + - + +
189C GLN* 2.5 30.9 + - - +
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Residues in contact with GLU 186 (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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182C LYS* 3.2 25.2 - - - +
183C HIS* 3.5 5.1 - - - +
185C ALA* 1.3 81.9 - - + +
187C CYS* 1.3 78.9 + - - +
188C HIS 3.2 3.0 + - - -
189C GLN* 3.4 16.5 + - - +
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Residues in contact with CYS 187 (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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183C HIS* 2.9 51.1 + - + +
186C GLU* 1.3 84.2 - - - +
188C HIS* 1.3 75.5 + - + +
189C GLN 4.0 0.7 + - - -
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Residues in contact with HIS 188 (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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164C CYS* 3.8 2.4 - - - -
166C LYS* 4.0 32.5 + - + +
167C ASP* 5.0 8.2 - - + +
169C SER* 5.7 1.3 - - - -
170C CYS* 4.0 13.5 - - + -
183C HIS* 3.6 4.0 + - - -
184C VAL* 3.2 28.4 + - + +
186C GLU 3.2 1.2 + - - -
187C CYS* 1.3 92.3 + - + +
189C GLN* 1.3 71.1 + - - +
190C ASP* 4.4 0.3 + - - +
206C ZN 2.2 35.8 - - - -
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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