Contacts of the strand formed by residues 235 - 242 (chain B) in PDB entry 1I0E
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 LEU 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLY* 3.3 3.6 - - - -
135B ARG* 2.9 41.3 + - + +
137B ILE* 3.7 15.5 - - + -
158B SER* 3.6 24.2 - - - +
162B LEU* 5.6 0.9 - - + -
227B VAL* 4.1 19.5 - - + -
228B TRP 3.4 10.1 - - - +
229B VAL* 4.3 4.5 - - + -
233B ASP* 4.1 6.6 - - - +
234B HIS* 1.3 84.9 - - - +
236B ARG* 1.3 62.3 + - - +
237B VAL* 3.8 7.0 - - + +
260B ILE* 4.3 6.3 - - + -
264B PHE* 3.8 14.8 - - + -
271B PHE* 3.8 31.9 - - + -
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Residues in contact with ARG 236 (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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132B ARG* 3.1 46.7 - - - +
133B THR 3.4 11.9 - - - +
134B GLY* 4.8 4.3 - - - -
226B LEU 4.1 0.3 - - - +
227B VAL* 3.9 0.9 - - - +
228B TRP* 3.0 75.1 + - + +
231B GLU* 2.9 25.9 + - + +
232B GLU* 3.4 24.7 + - + -
233B ASP* 5.0 9.9 - - - +
235B LEU* 1.3 75.6 - - - +
237B VAL* 1.3 62.4 + - - +
238B ILE* 3.5 23.4 + - + +
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Residues in contact with VAL 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL 4.1 0.3 - - - +
132B ARG* 3.6 0.5 - - - -
133B THR* 3.0 38.0 + - + +
135B ARG* 4.7 9.9 - - + -
225B PHE* 3.4 31.2 - - + -
226B LEU 3.5 5.2 - - - +
227B VAL* 4.0 17.2 - - + +
235B LEU* 5.2 7.2 - - + -
236B ARG* 1.3 70.2 - - - +
238B ILE* 1.3 77.1 + - - +
253B PHE* 4.4 5.2 - - + -
257B LEU* 3.2 35.0 - - + -
260B ILE* 6.2 2.0 - - + -
271B PHE* 6.5 0.2 - - + -
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Residues in contact with ILE 238 (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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130B ARG* 5.4 1.8 - - + -
131B VAL 3.6 2.2 - - - -
132B ARG* 3.2 56.3 - - + +
133B THR 4.1 1.6 - - - +
225B PHE* 3.4 5.6 - - - -
226B LEU* 2.7 52.8 + - + +
228B TRP* 5.8 0.7 - - + -
236B ARG* 3.5 26.0 + - - +
237B VAL* 1.3 96.2 - - - +
239B SER* 1.3 65.1 + - - +
240B MET* 4.1 30.7 + - + +
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Residues in contact with SER 239 (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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131B VAL* 3.0 24.4 + - - -
224B SER 3.6 10.5 + - - -
225B PHE* 3.9 15.3 - - - -
238B ILE* 1.3 72.7 - - - +
240B MET* 1.3 59.0 + - - +
249B VAL* 2.8 39.0 + - - +
252B ARG* 4.0 9.4 + - - +
253B PHE* 3.9 27.6 + - - -
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Residues in contact with MET 240 (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 SER* 5.9 2.5 - - - +
129B SER 3.6 5.8 - - - +
130B ARG* 3.1 27.6 - - + -
191B HIS* 3.7 39.5 - - + +
192B PHE* 5.2 0.9 - - + -
223B LYS 4.1 11.4 - - - +
224B SER* 3.0 23.3 + - - +
226B LEU* 3.6 33.7 - - + -
238B ILE* 4.0 11.2 - - + -
239B SER* 1.3 75.5 - - - +
241B GLU* 1.3 69.5 - - - +
242B LYS* 6.4 1.1 - - + -
249B VAL* 4.1 0.7 - - - -
252B ARG* 3.6 4.7 + - - -
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Residues in contact with GLU 241 (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 SER* 3.3 13.9 - - - -
129B SER* 3.1 18.2 + - - +
224B SER* 5.1 4.5 - - - -
240B MET* 1.3 79.6 - - - +
242B LYS* 1.3 73.8 + - - +
245B ASN* 3.9 25.9 - - - +
248B GLU* 4.4 8.8 - - - +
249B VAL* 4.1 13.8 - - + +
252B ARG* 2.7 39.3 + - - +
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Residues in contact with LYS 242 (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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127B LEU 4.2 7.2 - - - +
128B SER* 4.0 12.4 - - - -
191B HIS* 3.5 31.8 + - - +
240B MET* 6.4 1.1 - - + -
241B GLU* 1.3 92.4 - - - +
243B GLY* 1.3 65.6 + - - +
244B GLY 3.5 2.9 + - - -
245B ASN* 4.8 2.3 + - - +
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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