Contacts of the helix formed by residues 292 - 296 (chain B) in PDB entry 2WTV
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 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LYS* 3.1 35.7 + - + +
260B GLU* 4.5 2.1 + - - -
281B ALA* 5.3 2.9 - - - +
285B ARG* 3.4 40.9 - - + +
286B ARG 3.8 6.3 - - - +
287B TPO 4.2 9.2 - - + +
291B GLY* 1.3 69.0 - - - -
293B LEU* 1.3 66.8 + - - +
294B ASP 4.3 6.7 - - - +
295B TYR* 3.1 19.1 + - + -
296B LEU* 3.5 9.4 + - - +
1392B ACT 2.8 22.6 + - - +
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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
----------------------------------------------------------
286B ARG* 3.1 48.6 + - + +
288B TPO 4.3 8.5 - - + -
291B GLY 3.3 4.5 + - - -
292B THR* 1.3 70.0 - - - +
294B ASP* 1.3 60.6 + - - +
295B TYR 2.9 6.4 + - - -
296B LEU* 3.0 31.7 + - + +
334B TYR* 3.5 34.8 - - + -
337B THR* 3.7 20.4 - - + -
338B TYR* 3.7 41.3 - - + +
341B ILE* 3.7 7.6 - - + +
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Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ARG* 4.9 10.8 - - - +
286B ARG* 2.9 33.2 + - - +
292B THR* 3.3 4.6 - - + +
293B LEU* 1.3 78.8 - - - +
295B TYR* 1.3 63.8 + - + +
296B LEU 3.5 0.4 - - - +
313B TRP* 5.2 0.5 + - - -
317B VAL* 3.6 19.4 - - - +
327B PRO* 3.6 28.3 - - + +
329B PHE* 3.6 16.2 - - - +
330B GLU* 3.2 37.6 + - - +
337B THR* 3.7 8.0 - - - +
341B ILE* 4.8 2.8 - - - +
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Residues in contact with TYR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE 4.9 0.7 - - - -
258B LYS* 4.1 26.7 - - + -
259B PRO* 3.2 15.8 - - + +
285B ARG* 3.9 14.6 - - - -
292B THR* 3.1 18.4 + - + +
293B LEU 3.0 1.0 - - - -
294B ASP* 1.3 87.4 - - + +
296B LEU* 1.3 62.5 + - - +
297B PRO* 3.3 8.7 - - - +
313B TRP* 4.0 11.1 - - - -
314B SER* 4.0 30.7 + - - +
317B VAL* 3.5 32.8 - - + +
318B LEU* 3.4 19.7 - - + +
321B GLU* 2.6 29.6 + - - -
327B PRO* 4.4 2.7 - - + -
1392B ACT 4.1 23.2 - - + +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TPO 4.3 11.9 - - + -
289B LEU 4.4 1.1 - - - +
290B CME 3.9 50.5 - - + +
292B THR 3.5 6.9 + - - +
293B LEU* 3.0 37.7 + - + +
294B ASP 3.5 0.4 - - - +
295B TYR* 1.3 75.7 - - - +
297B PRO* 1.3 69.3 - - + +
300B MET* 4.2 14.8 - - + -
301B ILE* 3.9 19.1 - - + -
313B TRP* 3.7 4.4 + - - -
338B TYR* 4.3 3.6 - - + -
341B ILE* 3.4 21.5 - - - +
1392B ACT 3.7 15.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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