Contacts of the strand formed by residues 133 - 138 (chain B) in PDB entry 2X06
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 ILE 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.4 38.6 - - + -
239A ILE* 4.3 10.5 - - + -
127B ALA* 3.9 2.6 - - - +
132B MSE 1.3 74.1 - - - +
134B GLY* 1.3 61.9 + - - +
135B ILE* 4.2 18.8 - - + +
161B ILE* 4.6 2.2 - - + -
162B ALA 3.5 9.4 - - - +
163B PHE* 4.0 8.1 - - + -
265B ILE 3.8 0.3 - - - +
266B ALA* 3.4 6.8 - - - +
267B ILE* 2.9 59.4 + - + +
269B PRO* 4.4 7.2 - - + -
278B PHE* 3.9 31.4 - - + -
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Residues in contact with GLY 134 (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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94B MSE 4.4 0.4 - - - -
124B SER* 3.0 20.4 + - - -
127B ALA* 3.5 21.3 - - - +
133B ILE* 1.3 73.6 - - - +
135B ILE* 1.3 63.2 + - - +
161B ILE* 3.1 5.4 - - - +
162B ALA 2.9 35.7 + - - -
265B ILE 3.7 3.4 - - - -
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Residues in contact with ILE 135 (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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236A LEU* 4.4 20.0 - - + -
265A ILE* 6.4 1.6 - - + -
94B MSE 3.7 1.3 - - - +
133B ILE* 4.5 6.7 - - + +
134B GLY* 1.3 79.5 - - - +
136B THR* 1.3 65.6 + - - +
137B ILE* 4.6 7.4 - - + -
159B ILE* 4.6 13.5 - - + -
160B ALA 3.3 6.7 - - - +
161B ILE* 4.3 22.2 - - + -
263B LEU 3.7 0.5 - - - +
264B PHE* 3.5 2.6 - - - -
265B ILE* 2.7 64.2 + - + +
267B ILE* 4.4 22.9 - - + -
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Residues in contact with THR 136 (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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94B MSE 3.4 15.9 - - - +
117B PHE* 3.7 25.4 - - + -
120B ALA* 4.1 17.6 - - + +
123B TYR* 3.7 10.1 - - + +
124B SER* 3.2 15.6 + - - -
135B ILE* 1.3 75.1 - - - +
137B ILE* 1.3 65.0 + - - +
158B PRO 4.0 0.3 - - - +
159B ILE* 3.5 4.2 - - - -
160B ALA* 3.0 30.9 + - - +
263B LEU 3.4 4.5 - - - +
264B PHE* 3.6 26.4 - - + -
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Residues in contact with ILE 137 (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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135B ILE* 4.6 8.7 - - + -
136B THR* 1.3 82.8 - - - +
138B THR* 1.3 65.5 + - - +
158B PRO 3.5 7.2 - - - +
159B ILE* 3.6 29.2 - - + -
233B ILE* 4.2 18.4 - - + +
236B LEU* 3.7 35.0 - - + -
237B SER* 3.5 15.9 + - - +
262B ASP* 3.6 2.1 - - - +
263B LEU* 3.0 52.3 + - + +
265B ILE* 5.8 3.6 - - + -
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Residues in contact with THR 138 (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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117B PHE* 3.3 29.8 - - + -
120B ALA* 5.0 0.7 - - + -
137B ILE* 1.3 76.8 - - - +
139B ASN* 1.3 77.2 + - - +
157B ASN* 3.3 26.7 - - - -
158B PRO* 3.1 35.8 + - + +
233B ILE* 3.5 5.9 - - - +
237B SER* 3.1 10.6 + - - -
260B LYS* 3.6 8.1 - - - +
261B GLY 3.4 3.6 + - - -
262B ASP* 3.2 23.5 + - - -
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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