Contacts of the strand formed by residues 133 - 138 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ALA* 4.0 1.8 - - - +
132A MSE 1.3 78.0 - - - +
134A GLY* 1.3 62.6 + - - +
135A ILE* 4.3 8.8 - - + +
161A ILE* 4.2 12.6 - - + -
162A ALA 3.3 9.4 - - - +
163A PHE* 3.9 19.5 - - + -
265A ILE 3.8 0.3 - - - +
266A ALA* 3.3 6.4 - - - +
267A ILE* 2.9 57.4 + - + +
269A PRO* 4.6 7.2 - - + -
278A PHE* 4.0 20.9 - - + -
236B LEU* 3.5 37.7 - - + -
239B ILE* 4.5 11.0 - - + -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MSE 4.3 0.7 - - - -
124A SER* 3.2 18.1 + - - -
127A ALA* 3.6 19.5 - - - +
133A ILE* 1.3 72.3 - - - +
135A ILE* 1.3 65.4 + - - +
161A ILE* 3.2 6.9 - - - +
162A ALA 2.9 32.9 + - - -
265A ILE 3.5 5.8 - - - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MSE 3.7 1.3 - - - +
124A SER* 3.4 0.2 + - - -
133A ILE* 4.3 6.1 - - + +
134A GLY* 1.3 79.6 - - - +
136A THR* 1.3 69.0 + - - +
137A ILE* 4.9 3.6 - - + -
159A ILE* 4.1 17.7 - - + -
160A ALA 3.1 8.5 - - - +
161A ILE* 3.9 22.0 - - + -
263A LEU 3.8 0.5 - - - +
264A PHE* 3.7 1.0 - - - -
265A ILE* 2.8 63.4 + - + +
267A ILE* 4.5 18.4 - - + -
236B LEU* 4.5 21.3 - - + -
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MSE 3.6 9.7 - - - +
117A PHE* 3.8 24.2 - - + -
120A ALA* 3.9 17.9 - - + +
123A TYR* 3.7 3.0 - - + +
124A SER* 3.0 26.5 + - - -
135A ILE* 1.3 74.6 - - - +
137A ILE* 1.3 67.4 + - - +
158A PRO 3.8 0.7 - - - +
159A ILE* 3.2 4.3 - - - -
160A ALA* 2.8 34.6 + - - +
263A LEU 3.5 5.6 - - - +
264A PHE* 3.5 28.7 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ALA* 5.8 0.2 - - - -
135A ILE* 4.9 4.7 - - + -
136A THR* 1.3 76.8 - - - +
138A THR* 1.3 64.6 + - - +
158A PRO 3.3 7.6 - - - +
159A ILE* 3.3 38.6 - - + -
233A ILE* 4.0 19.5 - - + +
236A LEU* 3.6 34.3 - - + -
237A SER* 3.2 17.3 - - - +
262A ASP* 3.6 1.4 - - - -
263A LEU* 3.1 51.8 + - + +
265A ILE* 5.8 4.5 - - + -
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Residues in contact with THR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.8 23.5 - - + -
120A ALA* 5.6 0.4 - - + -
137A ILE* 1.3 74.8 - - - +
139A ASN* 1.3 75.3 + - - +
140A THR* 5.2 0.7 - - - +
157A ASN* 3.4 10.7 - - - +
158A PRO* 3.1 49.1 + - + +
233A ILE* 3.6 3.8 - - - +
237A SER* 3.0 15.1 + - - -
260A LYS* 3.7 6.8 - - + +
261A GLY 3.1 3.8 + - - -
262A ASP* 2.4 27.6 + - - -
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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