Contacts of the helix formed by residues 235 - 246 (chain B) in PDB entry 4AOR
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 TYR 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B HIS* 3.7 33.7 - + - -
106B ASN* 2.5 42.6 + - - -
108B ILE* 3.9 31.2 - - + -
182B ASN* 3.1 26.9 + - + +
230B THR* 3.9 15.0 - - + +
231B LYS 3.2 30.7 - - - -
232B VAL* 2.8 12.3 + - - +
234B ASN* 1.3 89.1 - - + +
236B VAL* 1.3 60.7 + - - +
237B SER 3.3 2.7 - - - -
238B TRP* 3.2 12.6 + + + +
239B ILE* 2.9 32.2 + - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 4.4 20.1 - - + +
129B PRO* 3.4 38.6 - - + +
232B VAL* 4.0 9.0 - - + +
233B CYS* 3.8 15.4 + - - +
234B ASN 3.6 1.6 - - - -
235B TYR* 1.3 77.5 - - - +
237B SER* 1.3 63.7 + - - +
239B ILE* 3.3 6.8 + - + +
240B LYS* 3.0 28.2 + - + +
6D PRO* 3.8 28.3 - - + -
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ASN 5.3 1.0 + - - -
235B TYR 3.3 0.2 - - - -
236B VAL* 1.3 78.5 - - - +
238B TRP* 1.3 58.0 + - - +
240B LYS* 3.4 8.2 + - - +
241B GLN* 2.9 31.2 + - - +
1254B MES 3.7 34.3 - - - -
4D CYS* 4.8 0.5 - - - -
6D PRO* 5.4 4.2 - - - +
21D CYS* 3.6 29.3 - - - +
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Residues in contact with TRP 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE* 3.7 31.5 - - + +
96B HIS* 3.6 48.2 - + + +
97B PRO* 3.5 20.5 - - + +
108B ILE* 4.1 23.6 - - + -
110B LEU* 3.8 27.6 - - + -
235B TYR* 3.2 20.0 + - + +
237B SER* 1.3 78.1 - - - +
239B ILE* 1.3 74.9 + - + +
241B GLN* 3.4 5.6 + - + +
242B THR* 2.7 57.1 + - - -
1254B MES 3.3 29.9 + - + +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ILE* 3.6 26.9 - - + -
59B VAL* 4.4 9.9 - - + -
108B ILE* 4.3 15.7 - - + -
110B LEU* 3.9 14.6 - - + -
128B LEU* 3.9 35.0 - - + -
232B VAL* 4.4 8.1 - - + -
235B TYR* 2.9 26.0 + - + +
236B VAL* 3.7 4.7 - - - +
238B TRP* 1.3 94.5 - - + +
240B LYS* 1.3 62.7 + - - +
242B THR* 3.3 1.9 + - - -
243B ILE* 2.9 33.5 + - + +
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 5.7 0.9 - - + +
236B VAL* 3.0 21.2 + - + +
237B SER* 3.8 7.2 - - - +
239B ILE* 1.3 77.4 - - - +
241B GLN* 1.3 63.7 + - - +
243B ILE* 3.5 5.9 + - - +
244B ALA* 3.0 25.2 + - + +
7D SER* 3.1 31.4 + - - +
22D SER* 5.5 4.4 - - - -
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Residues in contact with GLN 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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237B SER 2.9 18.3 + - - +
238B TRP* 3.9 5.8 - - + +
240B LYS* 1.3 78.2 - - - +
242B THR* 1.3 58.1 + - - +
244B ALA* 3.3 8.8 + - - +
245B SER* 2.7 46.6 + - - +
1254B MES 3.4 35.1 - - + +
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Residues in contact with THR 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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57B TRP* 4.7 2.2 - - + -
94B ILE* 3.6 39.9 - - + -
110B LEU* 3.8 23.1 - - + -
238B TRP* 2.7 46.7 + - + -
241B GLN* 1.3 79.7 - - - +
243B ILE* 1.3 63.3 + - - +
245B SER* 3.3 5.5 + - - -
246B ASN* 3.0 35.1 + - - +
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Residues in contact with ILE 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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53B ILE* 3.8 25.6 - - + -
54B ASN* 3.8 24.2 - - - +
57B TRP* 3.7 46.0 + - + +
110B LEU* 4.7 2.5 - - + -
128B LEU* 6.2 0.2 - - + -
239B ILE* 2.9 26.6 + - + +
240B LYS* 3.9 4.9 - - - +
242B THR* 1.3 75.6 - - - +
244B ALA* 1.3 63.4 + - - +
245B SER 3.3 0.5 + - - -
246B ASN* 3.4 18.4 + - - +
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Residues in contact with ALA 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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240B LYS* 3.0 19.8 + - + +
241B GLN* 3.6 12.1 - - - +
242B THR 3.2 0.2 - - - -
243B ILE* 1.3 81.1 - - - +
245B SER* 1.3 57.4 + - - +
246B ASN* 3.8 1.4 + - - +
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B GLN* 2.7 37.8 + - - +
242B THR* 3.3 9.7 + - - -
243B ILE 3.2 0.2 - - - -
244B ALA* 1.3 76.7 - - - +
246B ASN* 1.3 72.6 + - - +
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Residues in contact with ASN 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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57B TRP* 3.8 19.8 + - + -
92B LYS* 3.0 39.3 + - + +
94B ILE* 3.6 16.1 - - + +
112B LYS* 3.0 25.3 + - - +
242B THR* 3.0 37.7 + - - +
243B ILE 3.4 12.9 + - - +
244B ALA 4.7 1.9 - - - +
245B SER* 1.3 97.3 + - - +
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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