Contacts of the strand formed by residues 235 - 242 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLY* 3.3 3.6 - - - -
135A ARG* 2.8 42.9 + - + +
137A ILE* 3.7 23.1 - - + -
158A SER* 3.6 24.9 - - - +
162A LEU* 5.6 1.1 - - + -
227A VAL* 4.1 18.4 - - + -
228A TRP 3.4 9.9 - - - +
229A VAL* 4.4 4.7 - - + -
233A ASP* 4.1 6.1 - - - +
234A HIS* 1.3 83.6 - - - +
236A ARG* 1.3 61.7 + - - +
237A VAL* 3.8 7.4 - - + +
260A ILE* 4.3 7.0 - - + -
264A PHE* 3.8 23.1 - - + -
271A PHE* 3.8 15.5 - - + -
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Residues in contact with ARG 236 (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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132A ARG* 3.1 47.1 - - - +
133A THR 3.5 11.9 - - - +
134A GLY* 4.8 4.7 - - - -
226A LEU 4.1 0.3 - - - +
227A VAL* 3.9 0.9 - - - +
228A TRP* 3.0 75.2 + - + +
231A GLU* 2.8 25.2 + - + +
232A GLU* 3.4 24.6 + - + -
233A ASP* 5.0 11.4 - - - +
235A LEU* 1.3 76.0 - - - +
237A VAL* 1.3 62.4 + - - +
238A ILE* 3.5 22.9 + - + +
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Residues in contact with VAL 237 (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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131A VAL 4.1 0.3 - - - +
132A ARG* 3.6 0.7 - - - -
133A THR* 2.9 46.8 + - + +
135A ARG* 4.7 10.3 - - + -
225A PHE* 3.4 31.9 - - + -
226A LEU 3.5 4.9 - - - -
227A VAL* 3.9 16.7 - - + +
235A LEU* 5.1 6.3 - - + -
236A ARG* 1.3 74.0 - - - +
238A ILE* 1.3 65.5 + - - +
253A PHE* 4.5 5.4 - - + -
257A LEU* 3.2 34.8 - - + -
260A ILE* 6.2 1.8 - - + -
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Residues in contact with ILE 238 (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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130A ARG* 5.4 1.6 - - + -
131A VAL 3.6 2.5 - - - -
132A ARG* 3.2 56.1 - - + +
133A THR 4.1 1.6 - - - +
225A PHE* 3.4 4.8 - - - -
226A LEU* 2.7 51.9 + - + +
228A TRP* 5.9 0.4 - - + -
236A ARG* 3.5 25.8 - - - +
237A VAL* 1.3 96.4 - - - +
239A SER* 1.3 64.6 + - - +
240A MET* 4.1 30.5 + - + +
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Residues in contact with SER 239 (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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131A VAL 2.9 25.0 + - - -
224A SER 3.6 11.0 + - - -
225A PHE* 3.9 15.3 - - - -
238A ILE* 1.3 72.9 - - - +
240A MET* 1.3 58.4 - - - +
249A VAL* 2.8 39.2 + - - +
252A ARG* 4.1 8.8 + - - -
253A PHE* 3.8 27.7 + - - -
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Residues in contact with MET 240 (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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128A SER* 5.9 2.2 - - - +
129A SER 3.6 4.5 - - - +
130A ARG* 3.1 27.6 - - + -
191A HIS* 3.8 40.4 - - + +
192A PHE* 5.2 0.4 - - + -
223A LYS 4.1 11.4 - - - +
224A SER* 3.0 25.7 + - - +
226A LEU* 3.6 33.9 - - + -
238A ILE* 4.0 10.7 - - + -
239A SER* 1.3 73.9 - - - +
241A GLU* 1.3 70.6 + - - +
242A LYS* 6.4 1.1 - - + -
249A VAL* 4.1 0.7 - - - -
252A ARG* 3.6 2.8 + - - -
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Residues in contact with GLU 241 (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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128A SER* 3.3 14.0 - - - -
129A SER* 3.1 18.8 + - - +
224A SER* 5.1 4.5 - - - -
240A MET* 1.3 80.0 - - - +
242A LYS* 1.3 74.6 + - - +
245A ASN* 3.9 25.3 - - + +
248A GLU* 4.4 8.2 - - - +
249A VAL* 4.0 14.4 - - + +
252A ARG* 2.6 38.1 + - - +
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Residues in contact with LYS 242 (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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127A LEU 4.2 6.3 - - - +
128A SER* 4.0 12.0 + - - -
191A HIS* 3.5 32.6 + - - +
240A MET* 6.4 1.1 - - + -
241A GLU* 1.3 91.5 - - - +
243A GLY* 1.3 65.3 + - - +
244A GLY 3.5 3.3 + - - -
245A 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