Contacts of the helix formed by residues 338 - 346 (chain B) in PDB entry 3OEE
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 ALA 338 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B GLU* 3.9 14.8 - - - +
335B ASP* 3.4 20.8 + - + +
336B VAL 3.4 2.4 - - - -
337B SER* 1.3 83.2 - - - +
339B TYR* 1.3 67.3 + - - +
340B ILE 3.5 0.7 - - - +
341B PRO* 3.5 20.3 - - + +
342B THR* 3.0 19.1 + - - -
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Residues in contact with TYR 339 (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 ARG* 3.7 49.4 - - + +
294B GLU* 3.1 21.2 + - - +
296B TYR* 4.1 11.9 - + + -
297B PRO 4.4 6.9 + - - -
298B GLY* 4.4 8.8 + - - -
300B VAL* 3.6 26.6 - - + +
301B PHE* 5.1 2.4 + - - +
338B ALA* 1.3 73.3 - - - +
340B ILE* 1.3 72.8 + - + +
342B THR* 3.0 9.3 + - - -
343B ASN* 3.0 54.6 + - - -
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B SER* 5.0 4.9 - - - +
277B ALA* 4.3 8.1 - - + -
294B GLU* 4.9 2.4 + - - +
296B TYR* 3.7 55.6 - - + +
300B VAL* 4.0 17.7 - - + +
304B HIS* 4.0 20.9 - - + +
329B ILE* 3.8 22.2 - - + -
338B ALA* 4.6 0.2 - - - +
339B TYR* 1.3 83.0 - - + +
341B PRO* 1.3 74.3 - - + +
343B ASN* 3.2 7.5 + - + +
344B VAL* 3.1 22.7 + - - +
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Residues in contact with PRO 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.7 0.5 - - - +
170B ILE* 4.0 13.9 - - + -
329B ILE* 4.1 20.0 - - + -
330B GLU 5.4 1.3 - - - +
331B THR* 4.1 22.4 - - + -
335B ASP 4.1 1.6 - - - +
336B VAL 3.5 20.2 - - - +
338B ALA* 3.5 25.8 - - + +
340B ILE* 1.3 93.7 - - + +
342B THR* 1.3 62.2 + - - +
344B VAL* 3.3 2.3 + - - +
345B ILE* 3.0 29.5 + - - +
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Residues in contact with THR 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B VAL 3.2 20.9 - - - +
337B SER* 3.6 17.5 + - - +
338B ALA 3.0 16.6 + - - +
339B TYR* 3.0 12.3 + - - -
341B PRO* 1.3 72.8 - - - +
343B ASN* 1.3 69.0 + - - +
345B ILE* 3.9 10.2 - - + +
346B SER* 3.0 24.1 + - - -
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Residues in contact with ASN 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B VAL* 3.9 11.3 - - - +
301B PHE* 3.7 35.3 - - + +
304B HIS* 5.4 2.7 - - - +
339B TYR* 3.0 54.0 + - - +
340B ILE* 3.2 13.3 + - + +
342B THR* 1.3 77.7 + - - +
344B VAL* 1.3 59.6 + - + +
346B SER* 2.6 30.4 + - - -
347B ILE* 3.4 13.7 - - + +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.7 27.1 - - + -
273B LEU* 4.7 2.2 - - + -
304B HIS* 3.4 31.9 - - + +
308B LEU* 4.2 12.1 - - + -
327B PRO* 4.5 4.5 - - + -
329B ILE* 3.9 21.8 - - + -
340B ILE 3.1 16.0 + - - +
341B PRO 3.9 2.2 - - - +
343B ASN* 1.3 69.8 - - - +
345B ILE* 1.3 56.9 + - - +
346B SER 3.0 1.1 - - - -
347B ILE* 2.7 29.3 + - - +
348B THR* 2.9 29.2 + - + -
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Residues in contact with ILE 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.8 9.8 - - + +
170B ILE* 4.7 7.0 - - + -
336B VAL* 4.1 26.7 - - + +
341B PRO 3.0 30.0 + - - +
342B THR* 3.9 9.0 - - + +
344B VAL* 1.3 71.9 - - - +
346B SER* 1.3 59.6 + - - +
347B ILE 3.1 0.7 + - - -
348B THR* 3.8 15.6 + - - +
351B GLN* 3.5 41.0 + - + +
375B ARG* 3.5 22.1 + - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.7 16.8 - - - -
342B THR 3.0 13.2 + - - -
343B ASN* 2.6 25.0 + - - -
345B ILE* 1.3 76.1 - - - +
347B ILE* 1.3 59.7 + - - +
348B THR 4.9 0.7 - - - -
375B ARG* 5.4 3.1 - - - +
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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