Contacts of the helix formed by residues 226 - 230 (chain B) in PDB entry 2I65
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 GLN 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.7 23.2 - - + +
193B SER* 3.1 45.3 + - - +
196B PHE* 4.4 6.1 - - - +
197B ALA* 3.5 15.2 - - + +
221B THR 3.1 10.0 + - - +
222B PHE* 3.1 25.5 + - + +
225B VAL* 1.3 72.1 - - - +
227B VAL* 1.3 66.8 + - - +
229B ASN 3.0 10.4 + - - -
230B LEU* 3.2 16.7 + - - +
301B NAD 2.8 47.6 + - - +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 4.0 4.9 - - + -
222B PHE* 2.8 52.9 + - + +
223B GLY* 3.0 30.3 - - - +
226B GLN* 1.3 72.6 - - - +
228B HIS* 1.3 76.7 + - + +
229B ASN 3.4 0.5 + - - -
230B LEU* 3.6 21.5 + - - +
238B LEU* 4.9 1.1 - - + -
262B LEU* 3.7 16.8 - - + -
265B ILE* 4.3 13.7 - - + -
266B ILE* 4.8 8.0 - - + +
269B ARG* 3.4 17.1 - - - -
271B ILE* 5.5 0.2 - - - +
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Residues in contact with HIS 228 (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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218B LYS* 5.0 4.9 - - + -
223B GLY 3.0 26.1 + - - -
224B SER* 3.0 27.7 + - - +
225B VAL 3.5 5.6 + - - +
226B GLN 3.1 1.0 - - - -
227B VAL* 1.3 87.1 - - + +
229B ASN* 1.3 67.6 + - - +
230B LEU 3.6 0.2 - - - -
231B GLN* 5.1 0.5 + - - -
265B ILE* 3.9 27.4 - - + +
269B ARG* 3.2 29.1 + - - +
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Residues in contact with ASN 229 (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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194B ARG* 3.5 33.1 - - + +
197B ALA* 4.3 4.7 - - + -
198B GLU* 3.6 43.8 - - + +
224B SER 5.3 0.2 + - - -
225B VAL* 2.6 29.0 + - - +
226B GLN 3.0 6.1 + - - +
228B HIS* 1.3 86.2 - - - +
230B LEU* 1.3 62.4 + - - +
231B GLN* 3.3 19.0 + - - +
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Residues in contact with LEU 230 (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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124B LEU* 4.2 15.5 - - + -
197B ALA* 3.7 25.1 - - + +
200B ALA* 4.4 5.4 - - + -
204B VAL* 4.3 15.7 - - + -
222B PHE* 5.3 0.2 - - + -
226B GLN 3.2 13.9 + - - +
227B VAL* 3.8 18.6 - - + +
228B HIS 3.6 0.4 - - - -
229B ASN* 1.3 75.5 - - - +
231B GLN* 1.3 58.6 + - - +
232B PRO* 3.4 0.2 - - - +
235B VAL* 4.3 7.4 - - + -
238B LEU* 3.8 38.8 - - + -
266B ILE* 5.2 3.4 - - + -
269B ARG* 2.4 36.9 + - - -
271B ILE* 3.8 18.6 - - + -
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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