Contacts of the helix formed by residues 125 - 133 (chain B) in PDB entry 2IWI
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 LEU 125 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B GLN 3.9 1.4 + - - -
124B ASP* 1.3 71.2 - - - +
126B PHE* 1.3 62.8 + - - +
128B TYR* 4.0 15.5 - - + -
129B ILE* 2.9 41.3 + - + +
135B LEU* 4.1 20.0 - - + -
143B PHE* 4.9 8.5 - - + -
147B VAL* 6.2 0.2 - - + -
166B ASP* 3.3 24.9 + - + +
169B ILE* 3.1 34.6 + - + +
171B ILE* 4.4 17.9 - - + +
227B LEU* 5.0 3.6 - - + -
231B MET* 4.1 27.8 - - + -
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Residues in contact with PHE 126 (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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124B ASP* 3.1 10.7 - - - +
125B LEU* 1.3 78.2 - - - +
127B ASP* 1.3 71.0 + - - +
129B ILE* 3.5 3.3 + - - +
130B THR* 2.9 42.9 + - - -
166B ASP* 3.3 40.3 + - - +
167B GLU* 3.6 31.2 - - + +
203B TYR* 5.5 1.8 - - - -
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Residues in contact with ASP 127 (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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123B GLN* 3.9 17.1 - - + +
124B ASP* 2.9 34.6 + - - +
126B PHE* 1.3 94.7 - - - +
128B TYR* 1.3 68.7 + - - +
130B THR* 3.4 8.9 + - - -
131B GLU* 3.2 21.1 + - - +
1288B HB1 5.4 1.7 - - - -
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Residues in contact with TYR 128 (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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123B GLN* 3.5 27.3 - - + +
124B ASP 2.8 13.3 + - - +
125B LEU* 3.1 17.7 + - + +
127B ASP* 1.3 75.7 - - - +
129B ILE* 1.3 67.6 + - - +
131B GLU* 2.9 14.6 + - - +
132B LYS* 2.9 47.3 + - + +
133B GLY 4.4 1.3 - - - -
134B PRO 5.6 0.2 - - - -
135B LEU* 3.6 37.5 - - + -
143B PHE* 6.2 3.6 - + - -
171B ILE* 5.1 9.0 - - + -
173B LEU* 4.6 17.0 - - + -
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Residues in contact with ILE 129 (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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125B LEU* 2.9 35.5 + - + +
126B PHE* 3.7 4.7 - - - +
128B TYR* 1.3 75.7 - - - +
130B THR* 1.3 61.2 + - - +
133B GLY* 2.6 44.2 + - - +
135B LEU* 4.0 9.9 - - + -
166B ASP* 4.3 3.4 - - + +
230B ASP* 3.3 48.0 - - - +
231B MET* 4.0 11.0 - - - +
234B GLY* 4.0 26.2 - - - +
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Residues in contact with THR 130 (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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126B PHE* 2.9 38.7 + - + -
127B ASP* 3.6 12.5 + - - -
128B TYR 3.1 0.4 + - - -
129B ILE* 1.3 78.1 - - - +
131B GLU* 1.3 66.6 + - - +
133B GLY 4.6 0.4 + - - -
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Residues in contact with GLU 131 (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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123B GLN* 5.6 4.9 - - - +
127B ASP 3.2 11.4 + - - +
128B TYR* 2.9 4.7 + - - +
130B THR* 1.3 88.9 - - - +
132B LYS* 1.3 71.5 + - + +
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Residues in contact with LYS 132 (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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123B GLN* 5.8 0.7 - - - +
128B TYR* 2.9 54.7 + - + +
131B GLU* 1.3 91.6 - - + +
133B GLY* 1.3 60.5 + - - +
134B PRO* 4.4 3.5 - - - +
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Residues in contact with GLY 133 (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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129B ILE* 2.6 42.9 + - - -
131B GLU 3.8 0.4 - - - -
132B LYS* 1.3 77.4 - - - +
134B PRO* 1.3 80.9 - - - +
135B LEU* 3.5 6.9 + - - +
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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