Contacts of the helix formed by residues 147 - 162 (chain V) in PDB entry 6QXT
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 ASN 147 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144V ASP* 3.6 18.0 + - - +
145V PRO 3.4 3.9 - - - +
146V SER* 1.3 79.4 - - - +
148V ARG* 1.3 59.9 + - - +
149V GLU* 3.1 4.2 + - - +
150V GLY* 3.3 7.5 + - - +
151V HIS* 3.0 26.6 + - - +
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Residues in contact with ARG 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136V LEU* 3.9 34.7 - - + +
139V GLY 5.2 2.5 - - - -
140V LEU* 5.0 12.3 - - + +
144V ASP* 5.7 1.2 - - - +
146V SER* 3.2 12.4 - - - +
147V ASN* 1.3 77.0 - - - +
149V GLU* 1.3 56.8 + - - +
151V HIS* 3.9 8.4 - - - +
152V SER* 2.9 28.9 + - - -
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Residues in contact with GLU 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110V ILE* 5.2 15.3 - - + -
147V ASN* 3.1 1.5 - - - -
148V ARG* 1.3 76.6 - - - +
150V GLY* 1.3 61.1 + - - +
152V SER* 3.2 6.7 + - - -
153V ALA* 2.9 27.9 + - - +
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Residues in contact with GLY 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147V ASN* 3.3 9.6 + - - +
149V GLU* 1.3 79.3 - - - +
151V HIS* 1.3 57.3 + - - +
153V ALA* 3.3 7.2 + - - +
154V ARG* 2.9 29.3 + - - +
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Residues in contact with HIS 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136V LEU* 6.0 2.2 - - + -
146V SER 5.4 1.3 - - - +
147V ASN 3.0 17.0 + - - +
148V ARG* 4.0 7.9 - - - +
150V GLY* 1.3 72.4 - - - +
152V SER* 1.3 61.2 + - - +
154V ARG* 3.9 5.6 - - - +
155V ILE* 2.9 32.2 + - - +
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Residues in contact with SER 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114V ILE* 4.9 15.9 - - - -
117V GLN* 6.1 2.7 - - - -
133V ILE* 4.7 21.5 - - - +
136V LEU* 4.8 9.8 - - - +
148V ARG 2.9 21.0 + - - -
149V GLU* 3.2 7.4 + - - -
151V HIS* 1.3 77.4 - - - +
153V ALA* 1.3 57.7 + - - +
155V ILE* 3.9 3.4 - - - +
156V TYR* 2.9 30.5 + - - +
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Residues in contact with ALA 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149V GLU 2.9 15.9 + - - +
150V GLY* 3.7 7.9 - - - +
151V HIS 3.2 0.2 - - - -
152V SER* 1.3 75.6 - - - +
154V ARG* 1.3 60.0 + - - +
156V TYR* 3.5 5.0 - - - +
157V PHE* 2.9 32.6 + - - +
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Residues in contact with ARG 154 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150V GLY 2.9 17.9 + - - +
151V HIS* 3.4 6.5 + - - +
153V ALA* 1.3 77.5 - - - +
155V ILE* 1.3 57.4 + - - +
157V PHE* 4.5 2.1 - - - +
158V ASN* 2.9 34.6 + - - +
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Residues in contact with ILE 155 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128V GLU 5.9 1.1 - - - +
129V LYS* 4.6 13.2 - - - +
132V SER* 6.2 2.7 - - - -
133V ILE* 6.2 1.8 - - + -
151V HIS 2.9 18.3 + - - +
152V SER* 4.3 4.0 - - - +
154V ARG* 1.3 74.1 - - - +
156V TYR* 1.3 61.2 + - - +
158V ASN* 4.4 4.0 - - - -
159V THR* 2.9 32.9 + - - -
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Residues in contact with TYR 156 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117V GLN* 5.2 13.9 - - + -
129V LYS* 5.6 3.6 - - - -
133V ILE* 6.3 1.3 - - + -
152V SER 2.9 22.0 + - - +
153V ALA* 3.2 7.8 + - - +
155V ILE* 1.3 77.6 - - - +
157V PHE* 1.3 57.5 + - - +
159V THR* 3.8 2.9 - - - -
160V LEU* 2.9 30.1 + - - +
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Residues in contact with PHE 157 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153V ALA 2.9 16.0 + - - +
154V ARG* 4.5 2.0 - - - +
156V TYR* 1.3 77.8 - - - +
158V ASN* 1.3 59.2 + - - +
160V LEU* 4.5 4.5 - - - +
161V PHE* 2.9 35.7 + - + +
162V GLY 4.1 0.7 - - - +
165V PHE* 4.5 4.5 - - + +
166V THR* 6.0 3.8 - - - -
167V ARG* 5.8 9.9 - - + +
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Residues in contact with ASN 158 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154V ARG 2.9 21.8 + - - +
155V ILE* 4.3 4.3 - - - +
157V PHE* 1.3 78.0 - - - +
159V THR* 1.3 58.2 + - - +
162V GLY* 2.9 38.8 + - - +
163V ASN* 3.4 11.5 + - - +
165V PHE 4.9 8.1 - - - +
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Residues in contact with THR 159 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129V LYS* 3.4 30.7 - - - -
155V ILE 2.9 20.9 + - - -
156V TYR 3.9 2.0 - - - -
158V ASN* 1.3 79.1 - - - +
160V LEU* 1.3 64.2 + - - +
162V GLY* 4.2 2.3 + - - -
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Residues in contact with LEU 160 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156V TYR 2.9 18.4 + - - +
157V PHE* 4.1 4.0 - - - +
159V THR* 1.3 80.9 - - - +
161V PHE* 1.3 61.0 + - + +
162V GLY 3.7 0.2 + - - -
231V TYR* 5.5 10.8 - - + -
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Residues in contact with PHE 161 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157V PHE* 2.9 18.8 + - + +
160V LEU* 1.3 74.8 - - + +
162V GLY* 1.3 59.6 + - - +
165V PHE* 3.6 22.3 + - + +
173V ILE* 6.2 4.5 - - + -
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Residues in contact with GLY 162 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158V ASN* 2.9 23.7 + - - +
159V THR 4.2 2.8 + - - -
160V LEU 3.4 3.0 + - - -
161V PHE* 1.3 78.1 - - - +
163V ASN* 1.3 67.2 + - - -
164V ASP 3.2 2.5 - - - -
165V PHE* 3.1 17.5 + - - +
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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