Contacts of the helix formed by residues 244 - 252 (chain B) in PDB entry 2WO6
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 ASN 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B TYR* 1.3 85.1 - - - +
245B LEU* 1.3 59.4 + - - +
246B TYR* 2.8 21.5 + - - +
247B ASP* 2.9 26.3 + - - -
248B LEU* 3.1 21.1 + - - +
290B PRO 3.5 4.5 - - - +
291B GLU* 3.6 27.3 + - - +
293B ILE 3.1 17.5 - - - +
294B LEU* 3.6 18.0 - - + +
600B D15 5.8 1.4 + - - -
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Residues in contact with LEU 245 (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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244B ASN* 1.3 72.8 - - - +
246B TYR* 1.3 64.9 + - - +
248B LEU* 3.4 11.8 - - + +
249B LEU* 3.0 20.3 + - - +
265B PHE* 3.6 50.0 - - + -
269B MET* 6.2 0.2 - - + -
290B PRO* 3.2 12.4 + - + +
293B ILE* 3.1 44.7 + - + +
295B LEU* 4.1 12.3 - - + -
303B ILE* 4.0 14.8 - - + -
350B ILE* 5.4 2.0 - - + -
354B MET* 3.6 29.9 - - + +
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASN* 2.8 11.2 + - - +
245B LEU* 1.3 78.0 - - - +
247B ASP* 1.3 70.7 + - - +
249B LEU* 3.2 12.7 + - + +
250B ARG* 3.1 33.0 + - - +
254B PHE* 3.4 39.8 - + - -
290B PRO* 3.7 18.2 - - + +
291B GLU* 4.4 13.9 - - + -
353B GLU* 4.8 4.0 - - - -
5C ALA 5.9 0.3 + - - -
6C ARG* 3.7 55.8 - - + +
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Residues in contact with ASP 247 (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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243B TYR* 3.6 30.6 - - + +
244B ASN* 2.9 34.0 + - - +
246B TYR* 1.3 80.2 - - - +
248B LEU* 1.3 61.2 + - - +
250B ARG* 3.1 47.0 + - - +
251B ASN* 3.2 13.5 + - - +
600B D15 5.6 2.3 - - - -
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Residues in contact with LEU 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B TYR* 3.8 25.0 - - + +
244B ASN 3.1 8.8 + - - +
245B LEU* 3.4 21.5 - - + +
246B TYR 3.2 0.6 - - - -
247B ASP* 1.3 77.0 - - - +
249B LEU* 1.3 61.8 + - - +
251B ASN* 3.2 22.7 + - + +
252B THR* 3.7 8.2 + - + +
257B VAL* 3.4 29.4 - - + -
261B LEU* 4.2 7.4 - - + -
265B PHE* 3.4 36.1 - - + -
295B LEU* 4.5 9.2 - - + -
298B PRO 5.8 1.3 - - - +
354B MET* 4.0 3.6 - - + -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU 3.0 10.3 + - - +
246B TYR* 3.2 14.6 + - + +
248B LEU* 1.3 75.7 - - - +
250B ARG* 1.3 54.7 + - - +
252B THR* 2.7 28.9 + - - -
254B PHE* 2.9 26.5 + - + -
256B GLY* 3.7 19.3 - - - +
257B VAL* 3.8 5.8 - - + +
290B PRO* 5.7 1.1 - - + -
353B GLU* 3.5 33.9 - - + +
354B MET* 3.2 55.0 - - + +
357B GLY* 4.0 13.0 - - - +
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Residues in contact with ARG 250 (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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246B TYR* 3.1 25.5 + - - +
247B ASP* 3.1 38.0 + - - +
249B LEU* 1.3 75.8 - - - +
251B ASN* 1.3 60.6 + - - +
253B ASN* 3.1 14.0 + - - -
254B PHE* 3.9 28.5 - - + -
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Residues in contact with ASN 251 (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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243B TYR* 3.0 32.9 + - - -
247B ASP 3.2 9.2 + - - +
248B LEU* 3.5 14.5 - - + +
249B LEU 3.2 0.6 - - - -
250B ARG* 1.3 79.2 - - - +
252B THR* 1.3 59.0 + - + +
253B ASN 3.1 3.9 + - - -
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Residues in contact with THR 252 (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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248B LEU* 3.8 13.9 - - + +
249B LEU* 2.7 20.7 + - - -
251B ASN* 1.3 77.7 - - + +
253B ASN* 1.3 64.1 + - - +
255B ARG* 3.2 18.7 + - - +
256B GLY 3.1 43.0 + - - +
257B VAL* 4.2 11.4 - - + -
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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