Contacts of the helix formed by residues 289 - 300 (chain B) in PDB entry 2XWU
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 LEU 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 3.8 22.7 - - + +
250B LEU* 3.8 33.0 - - + -
285B LEU 3.7 9.2 - - - +
286B VAL* 2.9 14.7 + - + +
288B GLY* 1.3 76.5 - - - +
290B GLN* 1.3 65.0 + - - +
291B GLU 3.2 3.1 - - - -
292B GLN* 3.0 32.9 + - + +
293B LEU* 2.9 22.5 + - - +
308B ILE* 4.1 30.1 - - + -
311B ILE* 4.5 11.0 - - + -
339B MET* 4.4 1.3 - - + -
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Residues in contact with GLN 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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286B VAL 4.1 0.2 + - - -
287B LEU* 3.0 50.3 + - - +
288B GLY 3.2 0.2 - - - -
289B LEU* 1.3 77.3 - - - +
291B GLU* 1.3 57.6 + - - +
293B LEU* 3.3 9.8 + - + +
294B ARG* 3.0 53.8 + - - +
335B ALA* 4.2 6.5 + - - +
339B MET* 3.5 32.0 - - + +
342B PHE* 5.5 0.3 - - - -
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY 4.1 7.9 + - - +
289B LEU 3.2 0.8 - - - -
290B GLN* 1.3 73.8 - - - +
292B GLN* 1.3 67.2 + - - +
294B ARG* 3.3 24.0 + - - +
295B GLN* 3.0 31.8 + - + +
298B GLN* 5.5 3.6 + - - +
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Residues in contact with GLN 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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250B LEU* 3.0 30.5 + - - +
251B GLN* 4.8 5.3 + - - +
256B PHE* 3.9 16.9 - - - -
288B GLY 5.0 0.6 + - - +
289B LEU* 3.0 34.5 + - + +
291B GLU* 1.3 79.7 - - - +
293B LEU* 1.3 57.5 + - - +
295B GLN* 3.3 8.0 + - + +
296B ALA* 3.0 26.3 + - - +
304B THR* 4.0 11.0 - - + +
308B ILE* 3.7 13.2 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B LEU 2.9 12.0 + - - +
290B GLN* 3.5 10.5 - - + +
292B GLN* 1.3 75.0 - - - +
294B ARG* 1.3 64.6 + - - +
296B ALA* 3.3 4.7 + - - +
297B VAL* 3.1 25.4 + - + +
305B SER* 3.8 33.4 - - - +
308B ILE* 3.8 25.3 - - + +
339B MET* 4.3 20.0 - - + -
342B PHE* 3.5 30.7 - - + -
343B CYS* 3.8 25.6 - - - -
346B ILE* 4.5 1.1 - - + -
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Residues in contact with ARG 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 GLN* 3.0 42.6 + - - +
291B GLU* 3.6 24.1 + - - +
293B LEU* 1.3 72.5 - - - +
295B GLN* 1.3 64.5 + - - +
297B VAL* 3.3 4.1 + - + +
298B GLN* 2.9 50.2 + - + +
342B PHE* 4.3 37.6 - - + -
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Residues in contact with GLN 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 GLU* 3.0 26.6 + - - +
292B GLN* 3.6 8.1 - - - +
293B LEU 3.2 0.2 - - - -
294B ARG* 1.3 78.9 - - - +
296B ALA* 1.3 56.9 + - - +
298B GLN* 3.1 16.0 + - - +
299B ASN* 2.9 40.4 + - - +
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Residues in contact with ALA 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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292B GLN 3.0 14.0 + - - +
293B LEU* 3.3 9.6 + - - +
295B GLN* 1.3 72.5 - - - +
297B VAL* 1.3 60.9 + - - +
299B ASN* 4.5 2.7 - - - +
300B GLY* 2.8 24.6 + - - -
301B ASP* 2.9 33.9 + - + +
304B THR* 3.9 23.3 - - + -
305B SER* 4.1 8.3 - - - +
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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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293B LEU* 3.1 17.8 + - + +
294B ARG* 3.5 9.2 - - + +
296B ALA* 1.3 77.7 - - - +
298B GLN* 1.3 67.3 + - + +
300B GLY* 3.3 12.3 + - - +
305B SER* 4.7 4.9 - - - -
342B PHE* 3.9 22.2 - - + -
346B ILE* 3.8 27.6 - - + -
347B PRO* 3.6 34.5 - - + +
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Residues in contact with GLN 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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291B GLU* 5.5 2.9 + - - +
294B ARG* 2.9 49.3 + - + +
295B GLN* 3.3 15.8 - - - +
297B VAL* 1.3 81.5 - - + +
299B ASN* 1.3 68.0 + - - +
300B GLY 3.7 0.2 + - - -
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Residues in contact with ASN 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 GLN* 2.9 22.7 + - - +
296B ALA* 4.2 5.2 - - - +
298B GLN* 1.3 87.3 + - - +
300B GLY* 1.3 60.5 + - - +
301B ASP* 3.3 8.4 + - + +
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Residues in contact with GLY 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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296B ALA 2.8 7.2 + - - -
297B VAL* 3.3 10.7 + - - -
298B GLN 3.4 0.2 - - - -
299B ASN* 1.3 80.0 - - - +
301B ASP* 1.3 60.6 + - - +
302B MET* 3.0 24.1 + - - +
353B ASN 5.3 1.1 - - - +
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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
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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