Contacts of the helix formed by residues 233 - 244 (chain B) in PDB entry 3IIV
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 ASP 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B PHE* 5.7 4.7 - - - -
42B ILE* 5.7 4.0 - - - +
230B ARG* 4.6 14.0 + - - +
231B GLU 4.3 0.6 + - - -
232B ILE* 1.3 75.1 - - - +
234B VAL* 1.3 60.5 + - - +
235B ARG* 3.2 15.2 + - - +
236B GLU* 3.0 53.0 + - - +
237B LEU* 2.8 30.1 + - - +
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Residues in contact with VAL 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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6B ILE* 5.2 4.9 - - + -
23B PHE* 6.1 0.4 - - + -
39B TYR* 4.3 15.5 - - + -
42B ILE* 4.1 15.5 - - + +
43B GLY* 3.7 37.5 - - - +
44B ILE* 3.7 31.9 - - + +
227B PHE* 4.0 21.8 - - + -
232B ILE 3.8 0.9 + - - +
233B ASP* 1.3 73.9 + - - +
235B ARG* 1.3 60.0 + - - +
237B LEU* 3.3 7.5 + - - +
238B LYS* 2.9 32.3 + - + +
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Residues in contact with ARG 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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111A SER* 4.2 13.1 + - - -
115A GLN* 6.0 0.6 - - - +
42B ILE* 4.4 9.1 + - + +
233B ASP* 3.2 10.9 + - - +
234B VAL* 1.3 78.5 - - - +
236B GLU* 1.3 66.0 + - - +
238B LYS* 3.2 2.4 + - - +
239B GLU* 2.9 53.6 + - - +
253B LEU* 3.8 30.8 - - + +
254B GLY* 3.6 20.3 - - - +
257B GLU* 2.5 45.8 + - - -
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Residues in contact with GLU 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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207B THR* 6.0 3.8 - - + -
232B ILE* 6.1 0.2 - - + -
233B ASP* 3.0 39.2 + - + +
235B ARG* 1.3 77.0 - - + +
237B LEU* 1.3 58.8 + - - +
239B GLU* 3.4 13.5 + - - +
240B TYR* 2.9 31.1 + - - +
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Residues in contact with LEU 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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6B ILE* 4.1 14.1 - - + -
207B THR* 3.9 24.8 - - - +
210B PHE* 3.7 57.0 - - + -
227B PHE* 3.9 23.1 - - + -
232B ILE* 4.0 8.0 - - + +
233B ASP 2.8 14.6 + - - +
234B VAL* 3.5 9.2 - - - +
236B GLU* 1.3 76.4 - - - +
238B LYS* 1.3 59.1 + - + +
240B TYR* 3.3 6.3 + - + +
241B LEU* 2.9 46.6 + - + +
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Residues in contact with LYS 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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6B ILE* 4.0 22.2 - - + -
43B GLY* 2.7 26.3 + - - +
45B ASP* 2.6 41.0 + - - -
234B VAL* 2.9 20.0 + - + +
235B ARG 3.2 3.6 + - - +
237B LEU* 1.3 76.6 - - + +
239B GLU* 1.3 57.5 + - - +
241B LEU* 3.2 5.6 + - + -
242B LYS* 2.9 30.5 + - - +
248B VAL* 3.6 13.0 - - + +
249B ARG* 2.7 33.3 + - - +
250B LEU* 4.2 11.2 - - + -
252B GLY 6.0 0.6 - - - +
253B LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 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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235B ARG* 2.9 47.8 + - + +
236B GLU* 3.7 14.2 - - - +
238B LYS* 1.3 75.5 - - - +
240B TYR* 1.3 57.9 + - - +
242B LYS* 3.5 6.7 + - - +
243B LYS* 2.9 30.4 + - - +
250B LEU* 5.2 2.2 - - + -
253B LEU* 4.4 12.0 - - + +
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Residues in contact with TYR 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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207B THR* 3.5 27.1 - - + +
208B GLU* 3.3 34.3 - - + +
211B LEU* 3.6 35.7 - - + +
236B GLU 2.9 18.1 + - - +
237B LEU* 3.5 4.0 - - + +
239B GLU* 1.3 74.0 - - - +
241B LEU* 1.3 77.3 + - + +
243B LYS* 3.2 9.7 + - + +
244B HIS* 3.2 57.7 + + + -
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Residues in contact with LEU 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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6B ILE* 3.8 29.6 - - + -
210B PHE* 4.2 5.2 - - + -
211B LEU* 3.7 39.0 - - + +
214B PHE* 4.0 12.3 - - + -
237B LEU* 2.9 35.1 + - + +
238B LYS* 3.7 5.2 - - - +
240B TYR* 1.3 87.0 - - + +
242B LYS* 1.3 63.4 + - - +
244B HIS* 3.2 7.7 + - - -
245B GLY 3.3 0.3 + - - -
246B VAL* 3.0 39.6 + - + +
248B VAL* 3.9 19.1 - - + -
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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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108A GLU* 5.0 9.3 + - - -
238B LYS 2.9 16.8 + - - +
239B GLU* 3.6 6.7 - - - +
241B LEU* 1.3 76.7 - - - +
243B LYS* 1.3 64.1 + - - +
245B GLY* 3.1 14.0 + - - -
246B VAL 3.8 16.2 + - - +
247B ASN* 5.4 6.1 + - - +
248B VAL* 3.9 16.7 + - + +
250B LEU* 4.2 31.8 - - + +
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Residues in contact with LYS 243 (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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239B GLU 2.9 18.8 + - - +
240B TYR* 3.2 11.4 + - + +
242B LYS* 1.3 77.6 - - - +
244B HIS* 1.3 86.6 + - + +
245B GLY 3.5 2.3 + - - -
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Residues in contact with HIS 244 (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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211B LEU* 4.6 22.1 - - + +
240B TYR* 3.2 61.9 + + + +
241B LEU* 3.2 2.9 + - - +
242B LYS 3.2 0.6 - - - -
243B LYS* 1.3 108.9 + - + +
245B GLY* 1.3 58.5 + - - +
246B VAL* 3.5 7.3 + - - +
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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