Contacts of the helix formed by residues 266 - 273 (chain B) in PDB entry 1B3U
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 PHE 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B VAL* 2.9 29.9 + - + -
263B ALA* 2.8 15.7 + - - +
264B ASP 3.5 0.4 - - - -
265B LYS* 1.3 77.7 - - - +
267B THR* 1.3 57.7 + - - +
269B LEU* 3.5 8.3 + - + +
270B GLN* 2.9 28.2 + - - +
282B LEU* 3.5 45.9 - - + +
285B ALA* 4.2 5.6 - - + -
286B PHE* 3.5 41.7 - + + -
289B LEU* 3.6 24.7 - - + -
304B LYS* 4.6 10.3 - - + +
308B PHE* 3.8 25.1 - + + -
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Residues in contact with THR 267 (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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265B LYS 3.2 0.4 - - - -
266B PHE* 1.3 75.8 - - - +
268B GLU* 1.3 74.3 + - + +
270B GLN* 3.2 12.9 + - - +
271B LYS* 3.1 41.2 + - + +
304B LYS* 3.7 17.3 - - - +
307B GLU* 3.5 45.7 + - - +
308B PHE* 4.6 1.6 + - - +
311B ASN* 4.1 14.8 - - - +
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Residues in contact with GLU 268 (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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228B VAL* 4.0 26.5 - - + +
232B GLN* 5.3 1.4 + - - -
264B ASP 4.0 5.7 - - - +
265B LYS* 3.0 40.4 - - + +
267B THR* 1.3 85.8 + - + +
269B LEU* 1.3 62.2 + - - +
271B LYS* 3.5 7.7 + - - +
272B ALA* 3.1 24.9 + - - +
304B LYS* 4.8 3.2 + - - -
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Residues in contact with LEU 269 (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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224B VAL* 4.4 9.2 - - + +
227B CYS* 4.3 8.5 - - - +
228B VAL* 3.5 32.8 - - + +
231B ALA* 6.4 0.9 - - + -
247B LEU* 4.3 32.3 - - + -
262B VAL* 3.8 35.4 - - + +
265B LYS* 3.0 23.7 + - + +
266B PHE* 3.6 10.1 - - + +
268B GLU* 1.3 75.8 - - - +
270B GLN* 1.3 57.5 + - - +
272B ALA* 3.8 3.8 - - + +
273B VAL* 2.7 40.2 + - - +
282B LEU* 4.2 9.6 - - + -
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Residues in contact with GLN 270 (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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266B PHE 2.9 14.7 + - - +
267B THR* 3.4 18.1 + - - +
269B LEU* 1.3 76.5 - - - +
271B LYS* 1.3 63.5 - - + +
274B GLY* 3.2 18.7 + - - -
275B PRO* 4.6 0.3 - - - +
278B THR* 3.5 22.3 + - + +
282B LEU* 3.6 13.4 - - + +
308B PHE* 3.1 60.6 + - + +
311B ASN* 3.5 33.2 - - + +
312B LEU* 4.0 6.1 - - - +
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Residues in contact with LYS 271 (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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232B GLN* 6.2 1.3 - - - +
267B THR* 3.1 33.0 + - + +
268B GLU* 3.9 6.5 - - - +
270B GLN* 1.3 79.5 - - + +
272B ALA* 1.3 62.7 + - - +
274B GLY* 3.6 8.8 + - - -
275B PRO* 5.6 0.3 - - - +
307B GLU* 5.9 0.4 - - - -
311B ASN* 4.9 16.6 - - + +
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Residues in contact with ALA 272 (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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228B VAL* 3.8 12.8 - - + +
231B ALA* 4.0 22.3 - - + +
232B GLN* 3.7 34.1 - - + +
236B GLN* 4.3 3.3 + - - -
239B LEU* 4.2 4.7 - - - +
268B GLU 3.1 18.9 + - - +
269B LEU* 3.8 5.4 - - + +
271B LYS* 1.3 80.0 - - - +
273B VAL* 1.3 62.8 + - - +
274B GLY* 3.4 0.5 + - - -
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Residues in contact with VAL 273 (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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231B ALA* 4.7 5.1 - - + +
236B GLN* 2.6 23.5 + - - -
239B LEU* 3.3 12.6 - - + +
243B VAL* 6.2 1.3 - - + -
244B MET* 3.8 18.6 - - + -
247B LEU* 5.3 6.7 - - + -
269B LEU* 2.7 25.2 + - + +
270B GLN 3.5 0.2 - - - +
272B ALA* 1.3 74.4 - - - +
274B GLY* 1.3 59.0 + - - +
277B ILE* 3.3 37.1 - - + +
278B THR* 3.4 30.3 - - + +
282B LEU* 3.7 12.8 - - + -
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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