Contacts of the strand formed by residues 231 - 238 (chain B) in PDB entry 3HI6
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 THR 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B ASN 3.2 16.5 + - - -
130B VAL* 3.5 12.8 - - + +
131B ASP 2.9 25.6 + - - +
229B ASP 3.8 1.9 + - - -
230B ALA* 1.3 70.7 - - - +
232B LYS* 1.3 61.8 + - - +
233B VAL* 3.7 11.7 + - + -
255B ILE* 3.8 29.8 - - + -
302B LEU 5.8 0.2 - - - +
303B GLN 5.5 3.9 + - - +
304B LYS 5.2 3.6 - - - +
305B LYS* 5.1 18.1 + - + +
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Residues in contact with LYS 232 (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 ASP* 3.6 7.4 - - + +
216B ALA 5.4 3.0 + - - -
220B PHE* 3.7 58.1 + - + +
227B ARG 5.9 3.4 - - - +
230B ALA 3.5 9.1 + - - +
231B THR* 1.3 73.2 - - - +
233B VAL* 1.3 63.5 + - - +
253B ASP* 4.7 8.3 + - + +
254B ILE* 3.9 23.4 - - + +
255B ILE* 3.0 26.7 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 4.0 13.2 - - + -
131B ASP 3.0 9.9 + - - +
132B LEU* 3.2 29.4 - - + -
133B VAL 2.8 25.5 + - - -
220B PHE* 3.7 3.9 - - - -
231B THR* 4.1 15.3 - - + -
232B LYS* 1.3 78.6 - - - +
234B LEU* 1.3 65.4 + - - +
235B ILE* 4.6 1.6 - - + -
254B ILE* 4.2 2.2 - - - -
255B ILE* 3.3 19.5 - - + +
257B TYR* 4.0 23.3 - - + -
302B LEU* 3.8 20.6 - - + +
304B LYS 5.7 0.2 - - - +
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Residues in contact with LEU 234 (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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133B VAL* 3.3 30.3 - - + +
135B LEU* 3.6 29.2 - - + -
212B ILE* 4.4 22.2 - - + +
215B VAL* 3.9 23.1 - - + -
220B PHE* 5.1 1.8 - - + -
233B VAL* 1.3 73.9 - - - +
235B ILE* 1.3 62.5 + - - +
236B ILE* 3.8 16.2 - - + -
254B ILE* 3.7 24.4 - - + +
255B ILE 2.8 11.1 + - - +
256B ARG* 3.5 11.1 - - + -
257B TYR* 2.9 30.5 + - - +
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Residues in contact with ILE 235 (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 LEU* 3.7 36.3 - - + -
133B VAL 2.8 11.9 + - - +
134B PHE* 3.6 18.6 - - + -
135B LEU 2.9 26.3 + - - +
153B PHE* 4.2 12.6 - - + -
157B VAL* 5.1 1.1 - - + -
233B VAL* 4.6 1.8 - - + -
234B LEU* 1.3 74.2 - - - +
236B ILE* 1.3 60.9 + - - +
237B ILE* 3.6 17.8 + - + +
257B TYR* 3.7 7.2 - - + -
259B ILE* 3.3 31.9 - - + -
292B PHE* 5.3 2.5 - - + -
302B LEU* 3.9 26.2 - - + -
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Residues in contact with ILE 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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135B LEU* 3.4 19.3 - - + +
173B PHE* 4.7 1.8 - - + -
208B THR* 4.2 23.3 - - + -
212B ILE* 3.7 26.0 - - + -
234B LEU* 3.8 26.9 - - + -
235B ILE* 1.3 71.3 - - - +
237B ILE* 1.3 62.8 + - - +
238B THR* 4.6 13.0 - - + -
256B ARG* 4.4 7.9 - - + -
257B TYR 2.9 9.9 + - - +
258B ILE* 3.3 31.3 - - + +
259B ILE 2.8 26.3 + - - +
277B PHE* 4.3 10.3 - - + +
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Residues in contact with ILE 237 (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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134B PHE* 4.2 5.2 - - + -
135B LEU 2.8 10.6 + - - +
136B PHE* 4.2 8.1 - - + -
137B ASP* 3.1 26.7 + - - +
150B ILE* 3.7 38.3 - - + +
153B PHE* 4.0 13.2 - - + -
154B MET* 3.9 28.3 - - + -
173B PHE* 4.1 0.7 - - - -
235B ILE* 3.7 28.7 - - + +
236B ILE* 1.3 74.6 - - - +
238B THR* 1.3 61.8 + - - +
259B ILE* 3.4 18.2 - - + +
261B ILE* 5.1 2.9 - - + -
289B LEU* 4.2 15.3 - - + -
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Residues in contact with THR 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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137B ASP* 2.6 28.3 + - - -
142B LEU* 5.4 0.7 - - - -
150B ILE* 5.2 1.1 - - - +
173B PHE* 4.0 11.4 - - - -
206B THR* 4.5 4.2 - - - +
208B THR* 4.5 5.7 + - + -
236B ILE* 4.6 9.9 - - + -
237B ILE* 1.3 77.7 - - - +
239B ASP* 1.3 64.0 + - - +
240B GLY 3.7 20.5 + - - +
258B ILE* 4.3 22.9 - - + -
259B ILE 3.2 8.2 + - - +
260B GLY* 3.5 4.2 - - - -
261B ILE* 3.2 25.1 + - - +
265B PHE* 3.7 1.4 - - + -
274B LEU* 4.3 6.7 - - + -
277B PHE* 5.6 3.1 - - + -
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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