Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 1QI9
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 ASP 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B THR 3.3 5.7 + - - -
158B ASP* 1.3 75.1 + - - +
160B ILE* 1.3 62.3 + - - +
162B VAL* 4.4 7.4 - - - +
163B THR* 2.7 43.0 + - - -
382B ARG* 2.9 27.7 + - - -
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Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 3.8 11.2 - - + -
146B LEU* 3.5 44.9 - - + +
147B ALA* 3.8 11.4 - - + +
150B VAL* 4.1 13.5 - - + -
158B ASP* 2.8 24.5 + - - +
159B ASP* 1.3 73.3 - - - +
161B THR* 1.3 56.9 + - - +
163B THR* 3.9 0.2 - - - -
164B ALA* 3.0 24.8 + - + +
382B ARG* 3.9 21.3 - - - +
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.7 28.9 - - + -
150B VAL* 4.3 7.9 - - + -
155B TYR* 2.7 58.7 + - + -
158B ASP* 3.2 12.0 + - - +
160B ILE* 1.3 73.1 - - - +
162B VAL* 1.3 64.9 + - - +
163B THR 3.3 0.7 - - - -
164B ALA* 3.7 4.9 - - - -
165B ALA* 3.1 24.3 + - - +
190B PRO* 4.1 2.5 - - - +
194B LEU* 3.7 20.9 - - + +
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Residues in contact with VAL 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR 3.7 2.2 - - - +
156B GLY* 3.2 33.7 - - - +
157B THR 4.2 4.7 - - - +
158B ASP 2.9 19.8 + - - +
159B ASP* 4.2 7.0 - - - +
161B THR* 1.3 79.7 - - - +
163B THR* 1.3 64.3 + - - +
165B ALA* 3.6 3.5 + - - +
166B ALA* 3.4 18.8 + - + +
190B PRO* 4.2 12.2 - - + +
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 4.0 4.7 - - + -
159B ASP* 2.7 37.6 + - - -
160B ILE 3.9 2.2 - - - -
162B VAL* 1.3 75.4 - - - +
164B ALA* 1.4 55.8 + - - +
166B ALA* 3.1 5.4 + - + +
167B ASN* 2.7 37.9 + - + +
378B GLU* 3.4 44.6 - - + +
382B ARG* 3.6 9.1 + - - +
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 3.5 41.0 - - + +
147B ALA* 5.8 0.4 - - + -
160B ILE* 3.0 19.7 + - + +
161B THR* 3.8 10.3 - - + +
162B VAL 3.4 0.4 - - - -
163B THR* 1.4 74.7 - - - +
165B ALA* 1.4 57.5 + - - +
167B ASN* 3.7 0.3 - - - +
168B LEU* 2.8 39.3 + - - +
194B LEU* 4.1 13.7 - - + -
195B PHE* 4.9 2.7 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B THR 3.1 14.9 + - - +
162B VAL 3.8 4.5 - - - +
164B ALA* 1.4 81.3 - - - +
166B ALA* 1.3 57.5 + - - +
168B LEU* 4.1 1.5 - - - +
169B ALA* 3.1 28.2 + - - +
188B VAL* 3.4 40.9 + - + +
190B PRO* 3.9 12.8 - - + -
194B LEU* 4.0 14.1 - - + +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B VAL 3.4 10.1 + - - +
163B THR* 3.1 9.0 + - - +
165B ALA* 1.3 78.3 - - - +
167B ASN* 1.3 67.7 + - - +
169B ALA* 3.4 5.9 + - - +
170B GLY* 3.1 19.8 + - - -
188B VAL 6.0 0.4 - - - +
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B TRP* 2.9 34.7 + - + -
163B THR* 2.7 21.8 + - + +
164B ALA 3.8 0.9 - - - +
166B ALA* 1.3 72.1 - - - +
168B LEU* 1.3 62.6 + - - +
170B GLY* 3.1 12.3 + - - -
171B MET* 3.4 15.8 + - - +
376B ASN* 2.8 43.3 + - - +
378B GLU* 3.7 17.1 - - + +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ALA 4.1 2.9 - - - +
139B ALA* 4.1 9.4 - - + -
140B GLU* 3.7 42.8 - - + +
143B TRP* 3.7 22.0 - - + -
164B ALA 2.8 24.4 + - - +
165B ALA* 4.1 2.2 - - - +
167B ASN* 1.3 73.4 - - - +
169B ALA* 1.3 62.3 + - - +
171B MET* 3.0 16.0 + - - +
174B PHE* 3.0 57.1 - - + +
188B VAL* 5.5 0.4 - - + -
194B LEU* 4.0 22.2 - - + -
195B PHE* 4.4 4.3 - - + -
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ALA 3.1 20.0 + - - +
166B ALA* 3.4 6.5 + - - +
168B LEU* 1.3 76.7 - - - +
170B GLY* 1.3 61.3 - - - +
171B MET 3.3 4.7 + - - +
174B PHE* 3.9 14.8 - - - +
175B PRO* 5.0 7.3 - - - +
182B ILE* 5.0 1.4 - - + +
186B GLY 3.6 25.8 - - - +
187B THR* 4.4 2.2 - - - -
188B VAL* 4.1 15.0 - - + +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ALA 3.1 14.1 + - - -
167B ASN 3.1 5.1 + - - -
168B LEU 3.1 0.6 - - - -
169B ALA* 1.3 77.6 - - - +
171B MET* 1.3 62.0 + - - +
172B GLU* 3.5 2.6 + - - -
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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