Contacts of the helix formed by residues 291 - 300 (chain A) in PDB entry 2O07
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.5 31.0 - - - +
211A TRP* 4.9 1.8 - - - +
235A TYR* 4.7 6.5 - - - +
289A VAL 4.5 2.0 - - - +
290A LEU* 1.3 84.9 - - + +
292A GLU* 1.3 67.4 + - - +
293A PHE* 3.6 23.8 - - + -
294A ALA* 2.9 14.1 + - + -
295A ARG 3.0 6.2 + - - -
237B THR* 4.6 6.1 - - - +
278B TYR* 3.5 48.0 - - + +
283B VAL* 4.0 4.4 - - + -
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU 3.5 1.2 + - - -
291A PRO* 1.3 71.3 - - - +
293A PHE* 1.3 57.6 + - - +
295A ARG* 2.8 41.0 + - - -
296A LYS* 2.9 42.7 + - + +
268B GLN* 3.3 14.5 + - - +
271B VAL* 3.7 17.7 - - + +
276B LEU 3.5 21.3 - - - +
277B LYS 3.7 9.2 - - - -
278B TYR 2.9 22.9 + - - +
279B TYR 4.0 3.6 - - - +
280B ASN* 2.8 30.2 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.3 33.0 - - + -
211A TRP* 3.9 33.4 - + - -
214A LEU* 3.5 17.7 - - + +
291A PRO* 3.1 23.8 + - + -
292A GLU* 1.3 74.1 - - - +
294A ALA* 1.3 62.5 + - + +
296A LYS* 3.8 7.5 - - - +
297A ALA* 3.1 27.0 + - - +
77B PHE* 3.7 25.6 - + + -
277B LYS* 2.8 40.7 + - + +
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.2 27.4 - - - +
214A LEU* 4.0 21.5 - - + -
290A LEU* 4.0 9.9 - - + -
291A PRO* 2.9 9.4 + - + +
293A PHE* 1.3 92.5 - - + +
295A ARG* 1.3 65.5 + - - +
297A ALA 3.3 0.7 + - - -
298A LEU* 2.9 30.5 + - - +
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A LEU* 4.0 20.4 - - + +
291A PRO 3.0 11.8 + - - +
292A GLU* 2.8 47.6 + - - +
294A ALA* 1.3 75.3 - - - +
296A LYS* 1.3 66.9 + - - +
299A ASN* 2.8 59.3 + - - +
300A ASP* 2.8 43.4 + - - -
268B GLN* 3.7 19.5 + - - +
280B ASN* 4.2 8.5 - - - +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 2.9 28.3 + - + +
293A PHE* 3.8 7.4 - - - +
295A ARG* 1.3 87.9 - - - +
297A ALA* 1.3 66.9 + - - +
300A ASP* 3.0 51.6 + - + +
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.8 26.9 - - + -
218A LYS* 3.5 36.4 + - + +
293A PHE 3.1 16.8 + - - +
294A ALA 3.3 1.7 + - - +
296A LYS* 1.3 81.9 - - - +
298A LEU* 1.3 61.6 + - + +
300A ASP 5.0 3.3 - - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 4.1 14.6 - - + -
217A ILE* 3.9 26.2 - - + -
218A LYS* 3.8 32.5 - - + +
221A ARG* 3.7 44.8 + - - +
225A GLN* 5.6 1.2 + - - -
233A TYR* 4.2 5.6 - - + -
290A LEU* 3.5 29.2 - - + -
294A ALA 2.9 16.1 + - - +
297A ALA* 1.3 80.5 - - - +
299A ASN* 1.3 68.4 + - - +
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Residues in contact with ASN 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ARG* 4.3 13.8 + - - +
290A LEU* 5.4 2.8 - - - +
295A ARG* 2.8 53.9 + - - +
296A LYS 3.4 0.2 + - - -
298A LEU* 1.3 91.9 - - - +
300A ASP* 1.3 63.8 + - - +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A LYS* 5.8 1.9 + - - -
295A ARG* 2.8 44.5 + - - -
296A LYS* 3.0 33.1 + - + +
297A ALA 5.0 3.1 - - - +
299A ASN* 1.3 83.0 + - - +
268B GLN* 5.0 4.5 + - - +
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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