Contacts of the strand formed by residues 159 - 164 (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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU* 4.3 15.3 - - + -
120B ALA* 4.8 0.2 - - - -
135B ILE* 4.6 6.1 - - + -
136B THR 3.5 4.5 - - - +
137B ILE* 3.6 21.8 - - + -
157B ASN 3.8 0.2 + - - -
158B PRO* 1.3 74.1 - - - +
160B ALA* 1.3 67.6 + - - +
161B ILE* 4.3 25.4 - - + -
172B LEU* 3.9 2.3 - - + +
173B ASP* 3.6 1.8 - - - +
174B MSE 2.8 62.5 + - + +
176B THR* 4.9 5.4 - - + -
233B ILE* 3.8 21.5 - - + -
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Residues in contact with ALA 160 (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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120B ALA* 3.6 19.1 - - + -
121B GLY* 3.7 11.9 - - - +
124B SER* 2.9 21.8 + - - +
135B ILE* 3.3 3.8 - - - +
136B THR* 3.0 22.4 + - - +
159B ILE* 1.3 77.2 - - - +
161B ILE* 1.3 63.9 + - - +
172B LEU* 2.9 10.8 - - - +
173B ASP* 3.3 21.8 - - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 4.8 9.4 - - + -
232A ALA* 4.2 22.0 - - + -
236A LEU* 4.5 13.5 - - + -
124B SER* 4.4 0.4 - - - -
133B ILE* 4.6 2.2 - - + -
134B GLY 3.1 7.0 - - - +
135B ILE* 4.3 20.0 - - + -
159B ILE* 4.3 24.7 - - + -
160B ALA* 1.3 79.7 - - - +
162B ALA* 1.3 64.7 + - - +
163B PHE* 4.3 13.2 - - + -
170B PHE* 3.4 21.1 - - + -
172B LEU* 2.7 45.2 + - + -
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Residues in contact with ALA 162 (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 SER* 3.7 29.2 - - - +
125B GLU* 4.0 17.3 - - + -
128B MSE 4.0 8.0 - - + +
132B MSE 3.8 1.0 - - - +
133B ILE* 3.5 1.0 - - - -
134B GLY 2.9 31.8 + - - -
161B ILE* 1.3 77.6 - - - +
163B PHE* 1.3 69.5 + - - +
170B PHE* 3.0 11.4 - - - +
171B SER* 4.1 5.6 - - - +
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Residues in contact with PHE 163 (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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231A LEU* 5.1 1.3 - - + -
232A ALA* 4.5 7.9 - - - -
235A MSE 3.9 31.0 - - + -
236A LEU* 4.2 15.3 - - + -
128B MSE 3.6 10.7 - - - +
132B MSE 3.9 13.0 - - - +
133B ILE* 4.0 17.7 - - + -
161B ILE* 4.3 7.2 - - + -
162B ALA* 1.3 80.2 - - - +
164B LYS* 1.3 59.3 + - - +
170B PHE* 2.7 77.6 + + + +
278B PHE* 4.0 23.1 - + + -
282B VAL* 3.9 19.3 - - + -
285B LEU* 6.1 0.7 - - + -
286B LEU* 5.2 3.4 - - + -
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Residues in contact with LYS 164 (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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128B MSE 3.3 29.1 + - + +
129B ASN* 2.8 35.3 + - - +
131B ASP* 4.1 18.9 - - - +
132B MSE 5.0 0.8 + - - -
163B PHE* 1.3 78.4 - - - +
165B GLY* 1.3 67.2 + - - +
168B TYR 3.4 14.4 - - - +
169B LYS* 3.7 31.5 - - + +
278B PHE* 4.1 11.5 - - - -
279B LYS* 3.8 19.7 - - - +
282B VAL* 4.0 9.4 - - - -
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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