Contacts of the helix formed by residues 245 - 252 (chain B) in PDB entry 2B9B
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 SER 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B GLN 3.6 3.9 + - - -
244B ILE* 1.3 76.6 - - - +
246B ALA* 1.3 66.8 + - - +
247B ALA* 2.9 10.8 - - - +
248B GLU* 2.9 45.4 + - - +
249B LEU* 3.1 12.0 + - - +
78C LYS* 4.7 11.5 - - - +
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Residues in contact with ALA 246 (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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233B PRO* 4.9 2.5 - - + +
236B VAL* 4.2 16.4 - - + -
237B GLU* 3.5 43.4 - - + +
244B ILE 3.9 1.4 + - - -
245B SER* 1.3 71.9 - - - +
247B ALA* 1.3 62.3 + - - +
249B LEU* 3.3 4.8 + - - +
250B LEU* 3.0 35.3 + - + +
75C THR* 4.3 10.5 - - + +
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Residues in contact with ALA 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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245B SER* 3.8 10.0 - - - +
246B ALA* 1.3 80.7 - - - +
248B GLU* 1.3 58.6 + - + +
250B LEU* 3.7 3.9 - - - +
251B SER* 2.9 32.6 + - - -
75C THR* 3.7 35.5 - - + +
78C LYS* 4.0 7.9 - - + -
79C LEU* 3.8 24.6 - - + +
204C THR* 3.9 2.4 + - - -
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Residues in contact with GLU 248 (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 GLN 4.8 1.9 - - - +
244B ILE* 3.5 26.5 - - + +
245B SER* 2.9 29.7 + - - +
247B ALA* 1.3 74.5 - - + +
249B LEU* 1.3 62.1 + - - +
251B SER* 3.6 8.3 - - - +
252B SER* 2.7 38.8 + - - +
254B LEU* 6.2 0.9 - - + -
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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
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221B ILE* 4.4 4.0 - - - +
236B VAL* 3.8 26.5 - - + +
237B GLU* 5.9 0.9 - - - -
240B PHE* 4.6 22.7 - - + +
242B THR* 4.6 2.5 - - - +
244B ILE* 3.6 30.7 - - + +
245B SER 3.1 13.4 + - - +
246B ALA* 3.8 8.3 - - - +
248B GLU* 1.3 76.7 - - - +
250B LEU* 1.3 59.7 + - - +
252B SER* 4.1 11.7 + - - +
254B LEU* 5.0 4.5 - - + -
255B LEU* 3.7 33.0 + - + +
275B LEU* 3.5 37.2 - - + -
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Residues in contact with LEU 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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221B ILE* 4.5 5.3 - - + +
225B ARG* 2.8 27.7 + - - -
232B LEU* 3.5 39.5 - - + -
233B PRO* 4.0 32.8 - - + -
236B VAL* 3.9 19.1 - - + -
246B ALA* 3.0 26.9 + - + +
247B ALA 3.7 0.9 - - - +
249B LEU* 1.3 80.2 - - - +
251B SER* 1.3 60.0 + - - +
252B SER 3.8 3.3 - - - +
255B LEU* 5.5 0.9 - - + -
75C THR* 4.6 12.8 - - + -
200C LEU* 4.6 4.7 - - + -
201C THR* 5.7 2.0 - - - +
204C THR* 3.6 22.7 - - + +
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Residues in contact with SER 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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225B ARG* 4.8 2.6 + - - -
247B ALA 2.9 18.6 + - - -
248B GLU* 3.5 9.4 + - - +
250B LEU* 1.3 75.4 - - - +
252B SER* 1.3 67.6 + - - +
79C LEU* 3.8 18.9 - - - +
204C THR* 3.4 22.1 + - - +
207C PHE 4.1 6.0 + - - -
208C HIS* 3.2 32.1 + - - +
209C ASN 5.2 0.7 + - - -
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Residues in contact with SER 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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221B ILE* 2.8 18.9 - - - +
225B ARG* 5.1 0.5 + - - -
248B GLU* 2.7 27.2 + - - -
249B LEU 4.1 2.2 + - - +
250B LEU 3.8 3.5 - - - +
251B SER* 1.3 84.6 + - - +
253B GLY* 1.3 59.9 + - - +
254B LEU* 3.5 23.2 + - - +
325B THR* 3.7 16.6 - - - -
208C HIS* 3.4 25.8 - - - -
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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