Contacts of the helix formed by residues 289 - 301 (chain B) in PDB entry 1XR2
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 ASP 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288B VAL* 1.3 74.8 - - + +
290B LEU* 1.3 65.4 + - - +
291B ARG* 3.4 21.3 + - - +
292B LYS* 3.1 26.3 + - + +
293B VAL* 3.4 12.1 + - - +
357B PRO 4.3 8.3 - - - +
358B ASN* 5.2 1.5 - - - -
359B VAL* 3.6 37.7 + - - +
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Residues in contact with LEU 290 (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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280B ILE* 4.1 15.3 - - + -
288B VAL* 3.0 32.0 + - + +
289B ASP* 1.3 72.4 + - - +
291B ARG* 1.3 58.0 + - - +
293B VAL* 3.7 4.8 - - + +
294B ALA* 2.8 30.1 + - - +
341B GLU* 3.8 22.0 - - + +
344B MET* 3.7 44.0 - - + -
345B LEU* 3.7 23.5 - - + +
348B PHE* 5.5 0.6 - - - -
356B LEU* 4.1 20.0 - - + -
357B PRO* 5.0 6.7 + - + +
359B VAL* 5.1 0.2 - - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 3.1 13.4 + - - +
290B LEU* 1.3 79.2 - - - +
292B LYS* 1.3 58.2 + - - +
294B ALA* 3.6 7.5 + - - +
295B SER* 3.1 25.3 + - - -
348B PHE* 5.4 8.3 - - + -
356B LEU* 4.6 12.4 - - + +
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Residues in contact with LYS 292 (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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288B VAL* 6.2 0.9 - - + -
289B ASP* 3.1 24.0 + - + +
291B ARG* 1.3 77.2 - - - +
293B VAL* 1.3 65.5 + - + +
295B SER* 3.3 8.9 + - - -
296B LEU* 3.2 19.6 + - - +
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Residues in contact with VAL 293 (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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279B VAL* 3.5 48.7 - - + +
280B ILE* 4.5 2.7 - - + -
288B VAL* 3.8 29.4 - - + -
289B ASP 3.7 11.9 - - - +
290B LEU* 3.3 10.4 + - + +
292B LYS* 1.3 74.9 - - + +
294B ALA* 1.3 68.3 + - - +
296B LEU* 3.0 8.6 + - + +
297B VAL* 2.9 26.3 + - + +
345B LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 294 (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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290B LEU 2.8 18.0 + - - +
291B ARG 3.6 6.3 - - - +
293B VAL* 1.3 77.5 - - - +
295B SER* 1.3 56.8 + - - +
297B VAL* 3.2 7.5 + - - +
298B GLU* 2.9 37.9 + - - +
345B LEU* 4.0 12.8 - - + +
348B PHE* 3.8 35.2 - - + -
349B LEU* 4.4 7.6 - - + -
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Residues in contact with SER 295 (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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291B ARG 3.1 15.4 + - - -
292B LYS* 3.4 13.2 - - - -
293B VAL 3.1 0.2 - - - -
294B ALA* 1.3 76.9 - - - +
296B LEU* 1.3 57.1 + - - +
298B GLU* 3.4 12.8 + - - +
299B LYS* 2.9 30.7 + - - +
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Residues in contact with LEU 296 (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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254B PHE* 4.3 21.1 - - + +
261B LEU* 3.8 26.9 - - + -
279B VAL* 3.9 25.8 - - + -
292B LYS 3.2 8.0 + - - +
293B VAL* 3.0 12.1 + - - +
295B SER* 1.3 78.4 - - - +
297B VAL* 1.3 63.2 + - - +
299B LYS* 3.4 5.0 + - + +
300B LEU* 3.1 46.9 + - + +
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Residues in contact with VAL 297 (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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1B THR* 5.7 1.3 - - + -
277B ALA* 5.0 1.8 - - + -
279B VAL* 4.2 13.2 - - + -
293B VAL* 2.9 29.1 + - + +
294B ALA* 3.4 9.0 - - - +
296B LEU* 1.3 77.0 - - - +
298B GLU* 1.3 57.8 - - - +
300B LEU* 3.4 7.4 + - - +
301B GLY* 3.0 21.5 + - - -
302B ALA* 3.3 28.4 + - + +
305B ILE* 3.9 25.6 - - + -
345B LEU* 4.6 1.1 - - + -
349B LEU* 3.8 27.6 - - + -
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Residues in contact with GLU 298 (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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294B ALA* 2.9 25.9 + - - +
295B SER* 3.7 13.7 + - - +
297B VAL* 1.3 73.9 - - - +
299B LYS* 1.3 66.8 + - - +
300B LEU 3.1 2.0 - - - -
301B GLY* 3.0 14.2 + - - +
348B PHE* 4.6 10.7 - - - -
349B LEU* 3.7 23.5 - - + +
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Residues in contact with LYS 299 (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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295B SER* 2.9 17.9 + - - +
296B LEU* 3.4 8.9 + - + +
298B GLU* 1.3 77.8 - - - +
300B LEU* 1.3 66.8 + - + +
301B GLY* 3.5 0.3 + - - -
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Residues in contact with LEU 300 (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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254B PHE* 3.7 37.2 - - + -
261B LEU* 3.6 25.8 - - + -
264B LEU* 4.6 16.7 - - + +
265B GLU* 5.8 1.8 - - + +
275B LEU* 4.2 18.1 - - + +
277B ALA* 4.5 10.1 - - + -
296B LEU* 3.1 37.3 + - + +
297B VAL* 3.6 5.6 - - - +
298B GLU 3.1 0.2 - - - -
299B LYS* 1.3 82.9 - - + +
301B GLY* 1.3 60.0 + - - +
302B ALA* 3.0 9.9 + - + +
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Residues in contact with GLY 301 (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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297B VAL 3.0 3.8 + - - -
298B GLU* 3.0 17.3 + - - -
299B LYS 3.3 0.6 + - - -
300B LEU* 1.3 78.0 - - - +
302B ALA* 1.3 67.1 + - - +
303B SER* 3.5 2.6 + - - -
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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