Contacts of the helix formed by residues 156 - 165 (chain C) in PDB entry 3UO9
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 VAL 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE 3.6 1.8 + - - -
155C PRO* 1.4 69.0 - - - +
157C HIS* 1.3 64.8 + - - +
159C PHE* 3.1 9.3 + - + +
160C ILE* 3.0 34.7 + - + +
182C LEU* 4.5 15.7 - - + -
185C THR* 5.9 0.2 - - - +
186C LEU* 4.2 35.9 - - + -
193C VAL 3.4 25.1 + - - +
195C LEU* 3.7 30.7 - - + +
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Residues in contact with HIS 157 (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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155C PRO* 3.5 27.2 - - + +
156C VAL* 1.3 80.6 - - - +
158C LYS* 1.3 78.8 + - - +
160C ILE* 3.8 6.1 - - - +
161C THR* 2.9 38.2 + - - +
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ILE* 3.4 37.6 + - + +
149C GLU* 3.8 24.1 + - - -
154C ILE* 4.5 5.2 - - + -
155C PRO* 3.0 29.7 + - + +
157C HIS* 1.3 88.0 - - - +
159C PHE* 1.3 65.1 + - - +
161C THR* 4.0 4.4 - - - -
162C ALA* 3.2 37.4 + - - +
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Residues in contact with PHE 159 (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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143C LEU* 5.0 1.6 - - + -
147C ILE* 3.8 23.1 - - + -
154C ILE* 4.2 12.3 - - + +
155C PRO 3.3 7.1 + - - +
156C VAL* 3.1 11.5 + - - +
158C LYS* 1.3 81.3 - - - +
160C ILE* 1.3 73.6 + - + +
162C ALA* 3.4 3.6 + - - +
163C LEU* 3.0 39.8 + - + +
178C CYS* 4.3 8.5 - - - -
182C LEU* 4.2 25.6 - - + -
195C LEU* 5.4 4.9 - - + -
200C PHE* 3.7 30.7 - + + -
204C VAL* 4.1 18.2 - - + -
211C LEU* 4.2 19.3 - - + -
215C PHE* 4.2 12.3 - + - -
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Residues in contact with ILE 160 (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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156C VAL* 3.0 29.3 + - + +
157C HIS* 3.8 6.7 - - - +
159C PHE* 1.3 89.5 - - + +
161C THR* 1.3 60.0 + - - +
163C LEU* 3.3 4.9 + - + +
164C LYS* 3.0 54.5 + - - +
170C THR* 4.0 21.3 - - + -
179C MET* 4.2 9.4 - - + -
182C LEU* 4.0 16.8 - - + -
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Residues in contact with THR 161 (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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157C HIS* 2.9 22.4 + - - +
158C LYS* 4.0 5.4 - - - +
160C ILE* 1.3 75.6 - - - +
162C ALA* 1.3 66.2 + - - +
164C LYS* 3.3 9.9 + - - +
165C SER* 3.1 22.7 + - - -
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Residues in contact with ALA 162 (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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147C ILE* 4.9 4.7 - - + -
158C LYS* 3.2 31.4 + - - +
159C PHE* 3.7 4.9 - - - +
160C ILE 3.4 0.2 - - - -
161C THR* 1.3 77.5 - - - +
163C LEU* 1.3 62.9 + - - +
165C SER* 2.8 26.0 + - - -
166C THR* 3.6 9.0 - - - +
215C PHE* 3.6 24.8 - - + -
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Residues in contact with LEU 163 (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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159C PHE* 3.0 30.8 + - + +
160C ILE* 3.5 5.8 - - + +
162C ALA* 1.3 77.1 - - - +
164C LYS* 1.3 61.6 + - - +
166C THR* 2.8 27.2 + - - +
168C LEU* 3.8 28.3 + - + +
170C THR* 4.3 15.0 - - + -
175C LEU* 4.0 13.9 - - + -
179C MET* 3.9 28.5 - - + -
211C LEU* 3.7 25.1 - - + -
214C ALA* 5.1 1.6 - - + -
215C PHE* 3.6 16.3 - - + -
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Residues in contact with LYS 164 (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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160C ILE* 3.0 39.7 + - + +
161C THR* 3.3 7.6 + - - +
163C LEU* 1.3 76.1 - - + +
165C SER* 1.3 57.0 + - - +
166C THR 3.1 0.2 - - - -
167C GLY* 2.9 22.7 + - - -
168C LEU 3.5 16.3 - - - +
169C ARG* 5.4 1.1 - - - -
170C THR* 4.1 24.2 - - + +
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Residues in contact with SER 165 (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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161C THR* 3.1 15.0 + - - -
162C ALA* 2.8 23.2 + - - -
164C LYS* 1.3 75.5 - - - +
166C THR* 1.3 59.0 + - - +
167C GLY 3.2 1.7 + - - -
217C ARG* 5.8 2.1 + - - -
224C PHE* 4.5 7.5 + - - +
225C MET* 3.6 45.8 + - - +
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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