Contacts of the strand formed by residues 204 - 208 (chain D) in PDB entry 2XLR
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 THR 204 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LYS 1.3 68.0 - - - -
205D VAL* 1.3 61.2 + - - +
206D LEU 4.2 0.2 - - - -
227D LYS* 4.7 14.0 + - - +
228D LYS* 3.1 30.5 - - + +
230D ILE* 4.0 23.6 - - + -
268D GLU* 5.4 0.7 - - - +
269D LYS* 3.6 25.9 + - - +
270D VAL* 4.1 3.8 - - + -
271D ASP* 2.3 60.3 + - - +
272D ALA 3.4 2.1 + - - +
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D PHE* 3.7 35.7 - - + +
203D LYS* 4.1 11.9 - - + +
204D THR* 1.3 79.9 - - - +
206D LEU* 1.3 71.2 + - - +
207D LEU* 4.1 10.1 + - + +
221D CYS* 4.7 5.8 - - - -
226D ALA* 4.7 2.0 - - + -
228D LYS 3.0 7.0 + - - +
229D LEU* 3.4 18.8 - - + +
230D ILE* 3.0 25.1 + - - +
270D VAL* 5.3 0.2 - - - -
272D ALA* 3.5 11.7 - - + +
274D ILE* 3.8 29.4 - - + -
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D THR 4.2 0.4 + - - -
205D VAL* 1.3 77.1 - - - +
207D LEU* 1.3 63.4 + - - +
208D VAL* 4.1 12.7 + - + -
230D ILE* 3.3 22.4 - - + +
232D CYS* 3.6 23.6 - - - -
252D LEU* 4.2 25.6 - - + -
260D ALA* 4.3 11.7 - - + -
262D PHE* 3.9 13.2 - - + -
270D VAL* 4.2 14.7 - - + +
272D ALA 2.9 13.8 + - - +
273D ILE* 3.5 24.4 - - + -
274D ILE* 2.8 31.7 + - - +
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Residues in contact with LEU 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D VAL* 4.3 7.9 - - + -
206D LEU* 1.3 73.9 - - - +
208D VAL* 1.3 63.4 + - - +
209D GLY 4.2 1.0 - - - +
214D ALA* 4.2 12.6 - - + +
217D ILE* 4.3 8.5 - - + +
218D GLY* 3.5 37.2 - - - +
221D CYS* 5.3 1.3 - - - -
229D LEU* 4.7 14.4 - - + -
230D ILE 2.8 16.7 + - - +
231D SER* 3.1 12.4 - - - -
232D CYS* 2.9 25.1 + - - +
246D TRP* 4.3 13.2 - - + -
274D ILE* 3.5 33.0 - - + +
276D CYS* 4.3 13.5 - - - -
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D PHE* 4.1 14.1 - - + -
206D LEU* 4.2 7.0 - - + -
207D LEU* 1.3 74.6 - - - +
209D GLY* 1.3 61.5 + - - +
232D CYS* 3.9 15.7 - - - -
251D ASN* 4.2 6.7 - - - +
252D LEU* 4.5 8.1 - - + -
273D ILE* 4.0 19.7 - - + -
274D ILE 3.0 6.3 + - - +
275D LEU* 3.9 28.5 - - + -
276D CYS* 2.7 37.0 + - - +
277D THR* 4.4 3.1 - - + -
501D NAP 3.4 28.3 - - + +
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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