Contacts of the helix formed by residues 140 - 146 (chain B) in PDB entry 1IL0
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 GLN 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B SER 4.0 1.0 + - - -
139B LEU* 1.3 71.7 - - - +
141B ILE* 1.3 66.5 + - - +
142B THR* 3.8 15.0 + - - +
143B SER* 3.0 44.0 + - - +
144B ILE* 3.5 8.1 + - - +
201B ASP* 2.8 38.8 + - - +
203B PRO* 5.7 12.4 - - + +
205B PHE* 5.3 0.7 - - - -
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Residues in contact with ILE 141 (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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134B SER* 4.4 9.6 - - - +
136B THR* 3.6 29.2 - - + -
140B GLN* 1.3 71.2 - - - +
142B THR* 1.3 61.8 + - - +
144B ILE* 3.0 7.7 + - + +
145B ALA* 2.9 20.8 + - - +
154B PHE* 3.8 10.8 - - + -
155B ALA* 3.7 24.9 - - - -
156B GLY* 3.6 19.7 - - - +
172B ILE* 3.7 17.9 - - + +
174B THR* 3.4 22.2 - - + -
201B ASP* 2.7 23.2 + - - +
205B PHE* 3.8 9.0 - - + -
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Residues in contact with THR 142 (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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140B GLN* 3.2 14.7 - - - +
141B ILE* 1.3 77.1 - - - +
143B SER* 1.3 61.6 + - - +
145B ALA* 3.9 4.0 - - - +
146B ASN* 2.8 46.6 + - - +
174B THR* 3.4 23.7 - - - +
175B PRO* 3.6 12.0 - - + +
176B MET* 4.2 11.9 - - + -
201B ASP* 3.2 15.2 + - - -
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Residues in contact with SER 143 (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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112B LEU* 4.1 23.5 - - - +
116B ASN* 3.1 19.4 - - - +
140B GLN* 3.0 34.6 + - - +
142B THR* 1.3 77.5 - - - +
144B ILE* 1.3 61.2 + - - +
146B ASN* 4.2 12.6 + - - +
147B ALA 4.7 0.9 + - - -
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Residues in contact with ILE 144 (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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112B LEU* 3.6 18.8 - - + -
115B LYS* 3.9 22.0 - - + -
116B ASN* 3.4 12.8 - - - +
119B PHE* 3.4 21.6 - - + +
134B SER* 3.6 24.7 - - - +
136B THR* 4.2 14.1 - - + -
139B LEU* 4.3 7.2 - - + -
140B GLN 3.9 8.7 - - - +
141B ILE* 3.0 7.7 + - - +
143B SER* 1.3 75.5 - - - +
145B ALA* 1.3 67.9 + - - +
146B ASN 3.1 2.0 - - - -
147B ALA* 3.1 19.6 + - - +
148B THR* 4.4 1.6 + - - +
154B PHE* 3.3 26.8 - - + -
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Residues in contact with ALA 145 (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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141B ILE 2.9 14.0 + - - +
142B THR* 3.5 8.3 + - - +
144B ILE* 1.3 79.0 - - - +
146B ASN* 1.3 55.7 + - - +
147B ALA 3.1 0.2 - - - -
148B THR* 2.6 32.4 + - - +
151B GLN* 3.4 18.0 - - + +
154B PHE* 3.5 39.9 - - + -
174B THR* 4.9 5.4 - - + +
176B MET* 4.6 4.9 - - + -
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Residues in contact with ASN 146 (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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142B THR* 2.8 36.8 + - - +
143B SER* 4.4 9.5 - - - +
144B ILE 3.1 1.2 - - - -
145B ALA* 1.3 73.3 - - - +
147B ALA* 1.3 56.6 + - - +
148B THR 3.0 13.7 + - - +
151B GLN* 3.7 16.4 + - - +
176B MET* 4.0 12.9 - - - +
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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