Contacts of the helix formed by residues 236 - 247 (chain B) in PDB entry 1H5Y
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 SER 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B GLU* 5.0 9.0 - - - -
230B PHE* 4.2 2.9 - - - -
233B ARG* 4.1 22.9 - - - +
235B LEU* 1.3 77.2 - - - +
237B ILE* 1.3 65.8 + - - +
238B ALA* 3.3 10.7 + - - +
239B GLN* 2.9 37.6 + - - +
240B VAL* 3.1 21.5 + - - +
242B ARG* 4.9 0.5 + - - -
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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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7B ILE* 4.0 17.5 - - + -
9B PRO* 3.7 32.5 - - + -
42B TYR* 4.0 20.4 - - + +
45B GLU* 3.6 12.8 + - + +
46B GLY* 3.6 26.0 - - - +
47B ALA* 3.8 17.7 - - + +
230B PHE* 3.6 29.3 - - + -
236B SER* 1.3 73.6 - - - +
238B ALA* 1.3 57.7 + - - +
240B VAL* 3.1 5.2 + - - +
241B LYS* 2.9 34.6 + - + +
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Residues in contact with ALA 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 3.6 16.9 + - + +
236B SER* 3.1 9.7 + - - +
237B ILE* 1.3 78.7 - - - +
239B GLN* 1.3 64.1 + - - +
241B LYS* 3.3 7.6 + - - +
242B ARG* 2.9 49.3 + - - +
253B ILE* 5.3 3.5 - - + +
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL* 4.6 2.1 - - - +
234B VAL 4.7 1.1 + - - +
235B LEU* 3.4 26.3 - - + +
236B SER* 2.9 43.2 + - - +
238B ALA* 1.3 79.0 - - - +
240B VAL* 1.3 61.8 + - - +
242B ARG* 3.4 26.2 + - - +
243B TYR* 3.0 23.7 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 4.2 17.0 - - + -
210B VAL* 4.0 8.2 - - + +
213B PHE* 3.6 44.2 - - + -
230B PHE* 3.9 12.8 - - + -
235B LEU* 4.0 17.9 - - + -
236B SER 3.1 13.3 + - - +
237B ILE* 3.1 10.2 + - - +
239B GLN* 1.3 77.2 - - - +
241B LYS* 1.3 59.9 + - - +
243B TYR* 3.2 3.3 + - - +
244B LEU* 2.9 45.5 + - + +
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Residues in contact with LYS 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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7B ILE* 3.9 20.9 - - + -
46B GLY* 2.7 33.2 + - - +
48B ASP* 2.8 32.6 + - - -
237B ILE* 2.9 22.3 + - + +
238B ALA* 3.8 5.6 - - - +
240B VAL* 1.3 77.2 - - - +
242B ARG* 1.3 57.9 + - - +
244B LEU* 3.2 3.8 + - - +
245B LYS* 2.8 33.2 + - - +
251B VAL* 3.6 15.7 - - + +
252B ARG* 2.7 43.2 + - - +
253B ILE* 3.9 18.2 - - + -
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Residues in contact with ARG 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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236B SER* 4.9 0.4 + - - -
238B ALA* 2.9 38.7 + - - +
239B GLN* 3.5 32.3 - - - +
241B LYS* 1.3 76.1 - - - +
243B TYR* 1.3 63.7 + - - +
245B LYS* 3.6 7.4 + - - +
246B GLU* 3.1 24.8 + - - +
253B ILE* 5.0 11.4 - - + +
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Residues in contact with TYR 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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210B VAL* 3.5 54.7 - - + -
211B GLU* 3.4 18.0 - - + +
214B TYR* 4.1 13.7 - - + -
239B GLN 3.0 14.3 + - - +
240B VAL 3.5 6.7 - - - +
241B LYS 3.2 0.2 - - - -
242B ARG* 1.3 78.7 - - - +
244B LEU* 1.3 69.9 + - + +
246B GLU* 3.3 9.9 + - + +
247B ARG* 3.0 63.8 + - + +
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Residues in contact with LEU 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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5B LEU* 3.8 14.8 - - + -
7B ILE* 3.8 20.4 - - + -
213B PHE* 4.1 5.8 - - + -
214B TYR* 3.7 41.1 - - + +
240B VAL* 2.9 38.9 + - + +
241B LYS* 3.8 2.9 - - - +
243B TYR* 1.3 86.2 - - + +
245B LYS* 1.3 63.7 + - - +
247B ARG* 2.9 14.1 + - - +
248B GLY 3.2 0.2 + - - -
249B VAL* 3.0 38.4 + - + +
251B VAL* 4.0 13.2 - - + -
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Residues in contact with LYS 245 (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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121A ARG* 4.1 27.8 - - - +
241B LYS 2.8 17.9 + - - +
242B ARG* 3.8 6.5 - - - +
244B LEU* 1.3 76.8 - - - +
246B GLU* 1.3 65.7 + - - +
248B GLY* 2.9 14.7 + - - -
249B VAL 3.5 14.1 + - - +
251B VAL* 4.1 15.2 - - + +
253B ILE* 4.0 32.8 - - + -
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Residues in contact with GLU 246 (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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242B ARG 3.1 18.8 + - - +
243B TYR* 3.6 8.9 - - + +
245B LYS* 1.3 78.8 - - - +
247B ARG* 1.3 69.4 + - - +
248B GLY 3.4 2.6 + - - -
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Residues in contact with ARG 247 (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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3B MET* 5.6 0.7 - - - +
211B GLU* 5.1 4.9 - - - +
214B TYR* 3.4 70.1 + - + +
215B GLU* 5.4 2.4 + - - -
243B TYR* 3.0 51.6 + - + +
244B LEU* 2.9 10.9 + - - +
246B GLU* 1.3 87.2 - - - +
248B GLY* 1.3 61.1 + - - +
249B VAL 3.3 1.2 + - - -
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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