Contacts of the strand formed by residues 226 - 231 (chain g) in PDB entry 5FLX
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 HIS 226 (chain g).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220D THR* 5.9 3.3 - - + +
221D THR* 4.9 14.4 - - + +
217g MET* 3.4 23.4 - - + +
218g LEU 3.4 15.5 + - - -
219g TRP* 3.5 31.1 - + + -
225g LYS* 1.3 79.2 - - - +
227g LEU* 1.3 72.1 + - - +
228g TYR* 3.8 16.5 - - - -
229g THR* 3.0 28.7 + - - -
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Residues in contact with LEU 227 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206g LEU* 3.9 27.6 - - + -
218g LEU* 4.0 18.8 + - + +
220g ASP* 4.6 24.7 - - + +
225g LYS* 4.7 2.7 - - + +
226g HIS* 1.3 91.4 + - - +
228g TYR* 1.3 86.0 + - + +
261g LEU* 6.3 1.6 - - + -
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Residues in contact with TYR 228 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218g LEU* 3.5 38.9 + - + +
226g HIS* 3.8 8.5 + - - -
227g LEU* 1.3 97.7 - - + +
229g THR* 1.3 66.2 + - - +
230g LEU* 3.5 28.4 - - + +
260g ASP 4.7 1.6 + - - -
261g LEU* 2.5 46.3 + - + +
262g GLU* 4.8 0.3 - - - -
264g LYS* 4.3 35.4 - - + +
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Residues in contact with THR 229 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D THR* 5.8 1.0 - - - +
215g GLN* 3.7 18.8 - - + +
216g ALA 3.6 10.5 - - - +
217g MET* 3.2 27.9 - - + +
226g HIS* 3.0 27.4 + - - -
228g TYR* 1.3 75.9 - - - +
230g LEU* 1.3 75.7 + - - +
231g ASP 4.3 0.7 + - - -
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Residues in contact with LEU 230 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215g GLN* 2.9 11.9 - - - +
216g ALA* 2.5 55.1 + - + +
218g LEU* 4.4 12.8 - - + -
228g TYR* 3.5 35.9 - - + +
229g THR* 1.3 74.3 - - - +
231g ASP* 1.3 60.3 + - - +
248g LEU* 5.3 5.8 - - + -
259g TRP* 3.5 55.6 - - + -
260g ASP 5.1 5.6 - - - +
264g LYS* 6.6 0.2 - - - -
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Residues in contact with ASP 231 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213g ASP 5.2 0.2 - - - +
215g GLN* 2.8 30.3 + - - +
229g THR 4.3 0.4 + - - -
230g LEU* 1.3 71.3 - - - +
232g GLY* 1.3 59.8 + - - +
233g GLY* 3.2 19.6 + - - -
259g TRP* 4.1 17.8 - - - -
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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