Contacts of the strand formed by residues 133 - 138 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LEU* 3.9 32.8 - - + -
239C ILE* 4.1 13.7 - - + -
127D ALA* 3.9 3.0 - - - +
132D MSE 1.3 74.4 - - - +
134D GLY* 1.3 61.1 + - - +
135D ILE* 4.1 20.1 + - + -
161D ILE* 4.8 1.6 - - + -
162D ALA 3.4 7.6 - - - +
163D PHE* 4.0 8.3 - - + -
265D ILE 3.8 0.2 - - - +
266D ALA* 3.3 6.8 - - - -
267D ILE* 2.8 57.9 + - + +
269D PRO* 4.2 10.5 - - + -
278D PHE* 3.7 35.9 - - + -
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Residues in contact with GLY 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D MSE 4.4 0.7 - - - -
124D SER* 3.3 15.2 + - - -
127D ALA* 3.5 22.0 - - - +
132D MSE 4.0 0.2 + - - -
133D ILE* 1.3 71.2 - - - +
135D ILE* 1.3 65.0 + - - +
161D ILE* 3.2 6.8 - - - +
162D ALA 2.8 40.1 + - - -
265D ILE 3.6 3.6 - - - -
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LEU* 4.0 25.8 - - + -
265C ILE* 6.1 2.5 - - + -
94D MSE 3.7 0.7 - - - +
133D ILE* 4.3 9.0 - - + -
134D GLY* 1.3 78.9 - - - +
136D THR* 1.3 67.4 + - - +
137D ILE* 4.9 5.2 - - + -
159D ILE* 4.8 11.0 - - + -
160D ALA 3.3 6.5 - - - +
161D ILE* 4.2 20.0 - - + -
263D LEU 4.1 0.7 - - - +
264D PHE* 3.8 0.3 - - - -
265D ILE* 2.8 63.5 + - + +
267D ILE* 4.2 19.5 - - + -
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D MSE 3.2 21.1 - - - +
117D PHE* 4.1 19.5 - - + -
120D ALA* 4.0 18.7 - - + +
123D TYR* 3.9 1.8 - - + +
124D SER* 3.1 22.6 + - - -
135D ILE* 1.3 70.4 - - - +
137D ILE* 1.3 72.2 + - - +
158D PRO 4.6 0.2 - - - -
159D ILE* 3.4 1.7 - - - -
160D ALA* 2.9 34.5 + - - +
263D LEU 3.6 4.5 - - - +
264D PHE* 3.6 28.5 - - + -
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA* 5.9 0.4 - - - -
135D ILE* 4.9 6.5 - - + -
136D THR* 1.3 84.3 - - - +
138D THR* 1.3 64.2 + - - +
158D PRO* 3.8 8.1 - - - +
159D ILE* 3.7 25.6 - - + -
233D ILE* 3.9 20.6 - - + -
236D LEU* 3.5 35.0 - - + -
237D SER* 3.5 14.6 - - - +
262D ASP* 3.1 6.2 - - - +
263D LEU* 2.9 53.2 + - + +
265D ILE* 6.1 1.6 - - + -
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Residues in contact with THR 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PHE* 3.7 20.8 - - + -
137D ILE* 1.3 76.0 - - - +
139D ASN* 1.3 72.9 + - - +
140D THR* 4.9 3.6 - - + -
157D ASN* 3.3 22.9 - - - -
158D PRO* 3.4 28.2 + - + +
233D ILE* 3.5 4.0 - - - +
237D SER* 3.0 11.9 + - - -
260D LYS* 3.5 6.8 - - - +
261D GLY 3.0 7.6 + - - -
262D ASP* 2.9 25.9 + - - -
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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