Contacts of the strand formed by residues 255 - 261 (chain B) in PDB entry 1XDD
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 ILE 255 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B THR* 3.8 24.9 - - + -
232B LYS 3.1 13.4 + - - +
233B VAL* 3.4 14.9 - - + +
234B LEU 2.8 31.9 + - - +
253B ASP 4.2 1.5 - - - +
254B ILE* 1.3 70.6 - - - +
256B ARG* 1.3 56.0 + - - +
257B TYR* 4.2 11.9 - - + -
279B SER* 3.6 6.1 - - - +
285B PHE* 3.7 28.9 - - + -
501B AAY 4.5 21.8 - - + +
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Residues in contact with ARG 256 (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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212B ILE* 4.8 3.4 - - - -
234B LEU* 3.5 28.0 - - + +
236B ILE* 4.9 6.5 - - + -
248B ILE* 3.9 17.6 - - - +
251B ALA* 3.2 35.7 + - - -
252B LYS* 3.9 29.4 + - - +
254B ILE* 3.4 17.0 + - + +
255B ILE* 1.3 76.2 - - - +
257B TYR* 1.3 62.8 + - - +
276B LYS 4.6 1.2 + - - -
277B PHE 3.0 35.7 + - - +
278B ALA* 3.2 24.7 + - - -
279B SER* 2.9 38.2 + - - +
285B PHE* 3.5 10.3 - - - +
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Residues in contact with TYR 257 (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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233B VAL* 4.6 12.8 - - + -
234B LEU 3.0 10.6 + - - +
235B ILE* 4.5 10.3 - - + -
236B ILE* 2.9 30.2 + - - +
255B ILE* 4.2 11.7 - - + -
256B ARG* 1.3 74.9 - - - +
258B ILE* 1.3 61.2 + - - +
259B ILE* 5.4 2.5 - - + -
278B ALA* 5.0 0.2 - - - -
284B GLU* 2.7 36.9 + - - -
285B PHE* 3.3 44.0 - + - -
287B LYS* 4.3 7.0 - - + -
501B AAY 3.1 79.6 + - + +
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Residues in contact with ILE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B THR* 5.3 2.0 - - + -
236B ILE* 3.3 29.4 - - + +
238B THR* 4.0 22.7 - - + -
256B ARG 4.3 0.4 + - - -
257B TYR* 1.3 74.8 - - - +
259B ILE* 1.3 65.0 + - - +
260B GLY 3.9 0.4 - - - -
274B LEU* 3.7 37.7 - - + +
277B PHE* 4.0 31.6 - - + -
278B ALA* 3.9 8.7 - - + +
285B PHE 2.9 8.2 + - - +
286B VAL* 3.8 22.8 - - + +
287B LYS* 3.0 27.4 + - - +
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Residues in contact with ILE 259 (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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153B PHE* 4.1 17.3 - - + -
235B ILE* 4.0 24.9 - - + -
236B ILE 2.7 13.2 + - - +
237B ILE* 3.5 9.3 - - + -
238B THR* 2.9 29.5 + - - +
257B TYR* 5.4 3.4 - - + -
258B ILE* 1.3 78.3 - - - +
260B GLY* 1.3 58.8 + - - +
261B ILE* 4.1 11.1 - - + +
287B LYS* 3.4 14.4 - - + +
289B LEU* 3.9 31.4 - - + -
295B LEU* 4.4 5.4 - - + -
298B LEU* 3.7 24.5 - - + -
501B AAY 4.5 8.1 - - + -
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Residues in contact with GLY 260 (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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238B THR* 3.3 7.2 - - - -
258B ILE 3.9 1.8 - - - -
259B ILE* 1.3 72.0 - - - +
261B ILE* 1.3 60.2 + - - +
262B GLY 4.4 0.2 - - - -
265B PHE* 3.8 11.4 - - - -
274B LEU* 3.8 25.7 - - - +
287B LYS 2.9 9.8 + - - +
288B ILE* 3.4 7.1 - - - +
289B LEU* 2.9 26.2 + - - +
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Residues in contact with ILE 261 (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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150B ILE* 4.9 0.4 - - + -
237B ILE* 3.8 27.4 - - + -
238B THR 2.9 13.8 + - - +
239B ASP* 3.3 27.9 - - - +
259B ILE* 4.1 13.2 - - + +
260B GLY* 1.3 78.1 - - - +
262B GLY* 1.3 67.7 + - - +
264B HIS* 5.3 0.3 + - - -
265B PHE* 3.7 6.6 - - - -
289B LEU* 3.4 10.1 - - + +
291B THR 3.6 31.6 - - - +
292B PHE* 3.8 41.3 - - + +
295B LEU* 4.1 22.0 - - + -
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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