Contacts of the helix formed by residues 143 - 155 (chain F) 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 THR 143 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E LYS* 5.3 7.4 - - - -
141F SER 3.7 2.4 + - - -
142F CYS* 1.3 75.9 - - - +
144F VAL* 1.3 56.2 + - - +
145F PHE* 3.2 8.3 - - - -
146F GLU* 3.1 12.0 + - - +
147F LYS* 2.8 34.0 + - - +
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Residues in contact with VAL 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E ALA* 5.0 16.5 + - + +
32E VAL* 6.5 1.1 - - + -
33E LYS* 5.4 5.3 - - + +
65F ILE* 5.2 12.4 - - + +
66F LEU* 6.3 4.5 - - + -
143F THR* 1.3 72.9 - - - +
145F PHE* 1.3 58.0 + - - +
147F LYS* 3.2 8.9 + - - +
148F ILE* 2.9 30.1 + - - +
172F TYR* 4.9 17.0 - - + -
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Residues in contact with PHE 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F THR* 3.2 6.1 - - - -
144F VAL* 1.3 79.2 - - - +
146F GLU* 1.3 56.9 + - - +
148F ILE* 3.4 5.2 + - - +
149F PHE* 2.9 29.5 + - - +
173F PHE* 5.8 6.1 - - + -
177F GLU* 5.1 15.3 - - + -
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Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F CYS* 4.3 10.9 - - + +
143F THR* 3.1 21.9 + - - +
145F PHE* 1.3 80.4 - - - +
147F LYS* 1.3 56.4 + - - +
149F PHE* 3.7 7.7 - - - +
150F GLU* 2.9 29.8 + - - +
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Residues in contact with LYS 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE* 4.8 19.3 - - + +
66F LEU* 5.5 4.3 - - + -
139F THR* 5.9 5.8 - - - -
142F CYS* 4.6 10.0 - - + +
143F THR 2.8 14.5 + - - +
144F VAL* 3.4 12.6 - - - +
145F PHE 3.2 0.2 - - - -
146F GLU* 1.3 74.9 - - - +
148F ILE* 1.3 60.9 + - - +
150F GLU* 3.3 7.0 + - - +
151F ILE* 2.9 27.8 + - - +
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Residues in contact with ILE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F ILE* 5.6 9.3 - - + +
144F VAL 2.9 15.8 + - - +
145F PHE* 3.9 4.5 - - - +
147F LYS* 1.3 77.2 - - - +
149F PHE* 1.3 58.4 + - - +
151F ILE* 3.2 8.8 + - - +
152F LEU* 2.9 27.9 + - - +
169F SER* 6.5 1.3 - - - -
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Residues in contact with PHE 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F PHE 2.9 18.3 + - - +
146F GLU* 3.7 8.1 - - - +
147F LYS 3.2 0.2 - - - -
148F ILE* 1.3 77.4 - - - +
150F GLU* 1.3 56.2 + - - +
152F LEU* 3.2 8.2 + - - +
153F GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 5.9 8.1 - - + -
137F ILE* 6.0 6.3 - - + -
146F GLU 2.9 18.7 + - - +
147F LYS* 3.3 7.2 + - - +
149F PHE* 1.3 76.5 - - - +
151F ILE* 1.3 57.2 + - - +
153F GLN* 3.2 8.9 + - - +
154F ILE* 2.9 30.1 + - - +
118G ASP* 6.3 3.4 - - + +
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Residues in contact with ILE 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 6.1 4.9 - - + -
147F LYS 2.9 13.8 + - - +
148F ILE* 3.5 12.3 - - - +
149F PHE 3.2 0.2 - - - -
150F GLU* 1.3 78.7 - - - +
152F LEU* 1.3 58.0 + - - +
154F ILE* 3.4 4.4 + - - +
155F PHE* 3.0 29.3 + - - +
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Residues in contact with LEU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ILE 2.9 13.8 + - - +
149F PHE* 3.6 10.8 - - - +
151F ILE* 1.3 76.9 - - - +
153F GLN* 1.3 60.7 + - - +
154F ILE 3.5 0.2 - - - -
155F PHE* 3.8 14.0 + - - +
156F LYS* 4.4 3.8 + - - +
184F TYR* 6.3 3.8 - - + -
185F THR* 6.3 3.8 - - - -
188F SER* 4.9 15.7 - - - -
190F ALA* 5.6 2.8 - - - +
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Residues in contact with GLN 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F PHE 2.9 15.9 + - - +
150F GLU* 3.5 9.6 - - - +
151F ILE 3.2 0.2 - - - -
152F LEU* 1.3 78.3 - - - +
154F ILE* 1.3 59.9 + - - +
155F PHE 3.6 0.3 + - - -
156F LYS* 3.9 13.7 + - - +
157F TYR* 4.4 1.9 + - - +
116G GLU* 6.1 0.9 - - + +
117G LEU* 5.0 17.9 - - + -
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Residues in contact with ILE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F ILE* 5.4 13.0 - - + +
75F VAL* 5.5 8.1 - - + +
150F GLU 2.9 15.5 + - - +
151F ILE* 3.4 4.7 + - - +
153F GLN* 1.3 73.0 - - - +
155F PHE* 1.3 61.0 + - - +
156F LYS 3.2 2.2 - - - -
157F TYR* 3.0 27.0 + - + +
158F LEU* 3.1 12.6 + - - +
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Residues in contact with PHE 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE 3.0 17.5 + - - +
152F LEU* 3.9 11.9 - - - +
153F GLN 3.3 0.6 - - - -
154F ILE* 1.3 78.0 - - - +
156F LYS* 1.3 60.4 + - - +
158F LEU* 3.3 24.6 + - - +
161F LYS* 5.3 2.8 - - - +
164F LEU* 5.3 13.5 - - + -
190F ALA* 5.0 14.1 - - + -
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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