Contacts of the helix formed by residues 157 - 168 (chain Q) in PDB entry 3HOU
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 SER 157 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71Q LYS* 4.0 24.9 - - - -
72Q PHE* 3.7 20.6 - - - -
156Q LEU* 1.3 75.9 - - - +
158Q SER* 1.3 54.6 + - - +
159Q ASP* 2.6 30.9 + - - +
160Q GLU* 2.5 59.8 + - - +
161Q LYS* 3.0 5.7 + - - +
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Residues in contact with SER 158 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Q LEU 3.3 3.6 + - - -
157Q SER* 1.3 70.8 - - - +
159Q ASP* 1.3 68.6 + - - +
161Q LYS* 3.9 10.8 - - - +
162Q ARG* 3.0 41.3 + - - +
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Residues in contact with ASP 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Q LYS 5.1 2.9 - - - +
157Q SER* 2.6 20.7 + - - +
158Q SER* 1.3 82.9 + - - +
160Q GLU* 1.3 66.1 + - + +
161Q LYS 2.9 1.5 + - - -
162Q ARG* 3.0 22.5 + - - +
163Q GLU* 2.9 25.9 + - - +
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Residues in contact with GLU 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006M ILE* 4.9 2.1 - - - +
71Q LYS* 3.3 37.0 + - - +
72Q PHE* 5.0 0.3 - - - -
154Q ILE* 5.9 0.3 - - - +
155Q ARG 3.8 2.8 - - - +
156Q LEU* 2.9 34.3 - - + +
157Q SER* 2.5 56.2 + - - +
159Q ASP* 1.3 72.9 - - + +
161Q LYS* 1.3 56.2 + - - +
163Q GLU* 3.5 7.3 - - - +
164Q LEU* 3.1 24.4 + - - +
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Residues in contact with LYS 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Q LEU* 4.3 10.2 - - + +
157Q SER 3.0 8.9 + - - +
158Q SER* 3.9 12.8 - - - +
159Q ASP 2.9 0.6 - - - -
160Q GLU* 1.3 74.4 - - - +
162Q ARG* 1.3 68.7 + - + +
163Q GLU 2.9 4.5 - - - -
164Q LEU* 2.8 20.2 + - + +
165Q LEU* 2.9 32.1 + - + +
172Q GLU* 2.7 36.1 + - - +
193Q GLY* 2.7 26.3 + - - +
194Q GLU* 5.1 1.6 - - - -
195Q VAL* 3.5 34.1 - - + +
213Q ILE* 4.4 0.6 - - - +
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Residues in contact with ARG 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158Q SER* 3.0 28.7 + - - +
159Q ASP* 3.0 23.4 + - - +
161Q LYS* 1.3 84.8 - - + +
163Q GLU* 1.3 56.5 + - - +
165Q LEU* 3.7 13.3 + - + +
166Q LYS* 3.0 26.5 + - - +
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Residues in contact with GLU 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004M ASN* 5.1 2.3 - - - +
1005M GLU* 5.8 1.2 + - - +
1006M ILE* 3.0 30.6 + - + +
159Q ASP 2.9 15.2 + - - +
160Q GLU* 3.5 8.5 - - - +
162Q ARG* 1.3 74.2 - - - +
164Q LEU* 1.3 57.8 + - - +
165Q LEU 3.1 1.6 - - - -
166Q LYS* 2.9 21.9 + - - +
167Q ARG* 2.7 64.9 + - - +
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Residues in contact with LEU 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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866M PHE* 5.5 0.4 - - + -
1006M ILE* 3.7 13.6 - - + +
156Q LEU* 4.8 2.2 - - + -
160Q GLU 3.1 14.0 + - - +
161Q LYS* 2.8 14.6 + - + +
163Q GLU* 1.3 72.0 - - - +
165Q LEU* 1.3 62.8 + - + +
168Q TYR* 3.3 40.8 + - + +
170Q LEU* 4.7 3.0 - - + +
175Q LEU* 3.8 21.1 - - + -
195Q VAL* 4.3 12.3 - - + -
211Q TYR* 3.2 72.5 - - + +
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Residues in contact with LEU 165 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161Q LYS* 2.9 42.9 + - + +
162Q ARG* 3.7 15.5 - - + +
164Q LEU* 1.3 78.4 - - + +
166Q LYS* 1.3 62.9 + - - +
168Q TYR 3.4 0.2 + - - -
169Q ARG* 3.0 20.4 + - - -
170Q LEU* 3.1 35.3 + - + +
171Q LYS 4.3 5.8 - - - +
172Q GLU* 4.5 13.9 - - + +
175Q LEU* 3.4 33.2 - - + -
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Residues in contact with LYS 166 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162Q ARG 3.0 17.7 + - - +
163Q GLU* 2.9 21.6 + - - +
165Q LEU* 1.3 76.8 - - - +
167Q ARG* 1.3 104.6 + - - +
168Q TYR 3.1 1.4 + - - -
169Q ARG* 3.2 16.0 + - - +
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Residues in contact with ARG 167 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003M LYS 5.0 3.0 + - - -
1004M ASN* 3.0 47.8 + - - +
1006M ILE* 3.6 28.7 - - + -
1007M ILE* 3.8 15.2 - - + +
163Q GLU* 2.7 44.9 + - - +
164Q LEU 4.3 1.6 - - - +
166Q LYS* 1.3 107.6 - - - +
168Q TYR* 1.3 66.2 + - + +
169Q ARG* 3.6 1.1 - - - +
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Residues in contact with TYR 168 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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853M ASP* 5.8 5.4 - - - -
855M THR* 4.7 13.9 - - - -
857M ARG* 3.3 15.2 + - - +
866M PHE* 3.7 32.1 - + - +
867M ILE* 4.1 16.6 - - + +
1000M LEU* 5.3 0.7 - - - +
1006M ILE* 3.9 24.2 - - + +
1007M ILE* 4.2 16.5 - - + +
1010M ALA* 3.9 22.5 - - - +
164Q LEU* 3.3 31.2 + - + +
166Q LYS 3.1 0.6 - - - -
167Q ARG* 1.3 84.2 - - + +
169Q ARG* 1.3 73.2 + - - +
170Q LEU* 3.0 32.1 + - + +
211Q TYR* 4.8 5.5 - + - -
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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