Contacts of the helix formed by residues 291 - 300 (chain B) in PDB entry 2O05
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 PRO 291 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A THR* 5.3 1.1 - - - +
278A TYR* 3.5 44.2 - - + +
283A VAL* 4.0 4.3 - - + -
210B GLN* 3.5 33.0 - - - +
211B TRP* 5.0 3.6 - - - +
235B TYR* 4.4 8.3 - - + +
289B VAL 4.3 3.1 - - - +
290B LEU* 1.4 86.6 - - + +
292B GLU* 1.3 67.1 + - - +
293B PHE* 3.7 25.8 - - + -
294B ALA* 3.0 14.4 + - + -
295B ARG 3.0 6.6 + - - -
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Residues in contact with GLU 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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268A GLN* 3.1 13.8 + - - +
271A VAL* 3.7 16.6 - - + +
276A LEU 3.4 21.8 - - - +
277A LYS* 3.8 4.9 - - - -
278A TYR 2.9 27.6 + - - +
279A TYR 3.8 6.1 - - - +
280A ASN* 2.9 22.4 + - - +
290B LEU 3.6 1.2 + - - -
291B PRO* 1.3 70.9 - - - +
293B PHE* 1.3 58.4 + - - +
295B ARG* 2.9 43.4 + - - -
296B LYS* 2.9 36.5 + - + +
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Residues in contact with PHE 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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77A PHE* 3.7 24.7 - + + -
277A LYS* 2.9 40.6 + - + +
210B GLN* 3.2 31.4 - - + -
211B TRP* 4.0 31.6 - + - -
214B LEU* 3.6 19.8 - - + +
291B PRO* 3.1 29.3 + - + -
292B GLU* 1.3 74.8 - - - +
294B ALA* 1.3 62.9 + - + +
296B LYS* 3.8 8.7 - - - +
297B ALA* 3.2 25.3 + - - +
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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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210B GLN* 3.2 27.6 - - + +
214B LEU* 3.8 22.7 - - + -
290B LEU* 4.1 10.1 - - + -
291B PRO* 3.0 8.3 + - + +
293B PHE* 1.3 89.2 - - + +
295B ARG* 1.3 62.2 + - - +
296B LYS 3.3 0.2 - - - -
297B ALA* 3.8 0.3 - - - -
298B LEU* 2.9 36.6 + - + +
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Residues in contact with ARG 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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268A GLN* 3.6 20.0 + - - +
280A ASN* 4.2 9.2 - - - +
282A ASP* 5.8 3.4 - - - -
290B LEU* 4.0 20.2 - - + +
291B PRO 3.0 12.1 + - - +
292B GLU* 2.9 47.0 + - - +
294B ALA* 1.3 76.2 - - - +
296B LYS* 1.3 69.6 + - - +
299B ASN* 2.9 58.6 + - - +
300B ASP* 2.8 42.0 + - - -
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Residues in contact with LYS 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 GLU* 2.9 24.4 + - + +
293B PHE* 3.8 7.6 - - - +
295B ARG* 1.3 93.2 - - - +
297B ALA* 1.3 59.2 - - - +
300B ASP* 3.0 50.4 + - + +
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Residues in contact with ALA 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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214B LEU* 3.6 28.3 - - + -
218B LYS* 2.9 34.8 + - + +
293B PHE 3.2 16.7 + - - +
294B ALA 3.4 2.9 + - - +
296B LYS* 1.3 82.7 - - - +
298B LEU* 1.3 58.5 + - + +
300B ASP 4.5 5.4 - - - +
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Residues in contact with LEU 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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214B LEU* 4.0 17.5 - - + -
217B ILE* 3.9 32.1 - - + -
218B LYS* 4.0 23.8 - - + -
221B ARG* 4.3 30.8 + - + +
233B TYR* 4.2 14.6 - - + -
290B LEU* 3.4 27.4 - - + -
294B ALA 2.9 17.9 + - - +
297B ALA* 1.3 80.0 - - - +
299B ASN* 1.3 68.9 + - - +
300B ASP 5.0 0.7 - - - -
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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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221B ARG* 4.1 19.6 + - - +
290B LEU* 5.5 2.1 - - - +
295B ARG* 2.9 51.2 + - - +
298B LEU* 1.3 82.8 - - - +
300B ASP* 1.3 69.5 + - - +
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Residues in contact with ASP 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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268A GLN* 4.9 3.6 - - - +
218B LYS* 5.7 2.6 + - - -
295B ARG* 2.8 43.5 + - - -
296B LYS* 3.0 31.1 + - + +
297B ALA 4.5 5.5 - - - +
298B LEU 5.0 0.3 - - - -
299B ASN* 1.3 85.9 + - - +
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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