Contacts of the strand formed by residues 225 - 227 (chain F) in PDB entry 2I2X
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 GLY 225 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ASN* 3.9 1.8 - - - +
207F PHE* 3.5 14.8 - - - -
209F CYS* 5.0 2.0 - - - -
219F VAL* 4.0 15.9 - - - +
222F PHE* 3.1 18.6 + - - -
223F ALA 3.3 0.2 - - - -
224F LEU* 1.3 77.5 - - - +
226F VAL* 1.3 62.4 + - - +
248F VAL* 3.5 0.9 - - - +
252F ARG* 3.0 30.6 + - - -
256F HIS* 4.6 1.0 + - - -
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Residues in contact with VAL 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F PRO* 4.3 8.1 - - + -
207F PHE 3.0 8.0 + - - +
208F ALA* 3.1 12.6 - - - +
209F CYS 2.7 31.6 + - - -
219F VAL* 4.3 4.0 - - - +
224F LEU 4.0 8.7 - - - +
225F GLY* 1.3 79.5 - - - +
227F TYR* 1.3 63.6 + - - +
237F ILE* 3.6 31.9 - - + -
248F VAL* 4.0 13.9 - - + +
251F LEU* 4.2 25.8 - - + -
252F ARG* 4.7 2.5 - - + +
255F PHE* 4.6 7.0 - - + -
256F HIS* 3.9 14.8 - - + +
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Residues in contact with TYR 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F ALA* 6.1 0.2 - - - -
209F CYS 3.3 15.3 - - - -
210F GLY* 4.6 1.8 - - - -
211F GLY 5.0 1.2 + - - -
214F VAL* 2.9 47.4 + - + -
215F ASN* 3.6 8.7 - - + +
216F GLN* 3.7 18.2 - - + -
219F VAL* 3.4 22.8 - - + +
226F VAL* 1.3 76.3 - - - +
228F GLY* 1.3 66.8 + - - +
229F GLU* 3.5 34.8 + - + +
233F ASP* 5.5 0.3 - - - +
255F PHE* 4.7 9.2 - - - +
256F HIS* 3.2 21.5 + - + +
258F HIS* 3.6 36.1 + + - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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