Contacts of the helix formed by residues 244 - 251 (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 MET 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B LEU* 2.9 25.6 + - + +
240B GLU* 3.1 24.9 - - + +
243B VAL* 1.3 76.3 - - - +
245B PRO* 1.3 69.7 - - + +
247B LEU* 3.7 24.2 - - + +
248B ARG* 2.9 50.2 + - + +
273B VAL* 3.8 23.8 - - + -
277B ILE* 3.7 11.7 - - + -
281B ASP* 3.5 34.3 - - + +
282B LEU* 5.2 4.5 - - + -
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Residues in contact with PRO 245 (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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240B GLU 3.3 22.0 - - - +
241B ALA* 4.3 9.9 - - - +
242B LEU 4.3 4.5 - - - +
243B VAL 3.3 9.9 - - - +
244B MET* 1.3 91.1 - - + +
246B THR* 1.3 63.1 + - - +
248B ARG* 3.5 17.1 + - + +
249B GLN* 3.2 20.0 + - - +
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Residues in contact with THR 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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208B PHE* 3.8 30.4 - - + -
209B SER* 4.3 18.8 + - - +
212B ALA* 3.5 31.9 - - + -
242B LEU 4.4 6.9 + - - -
243B VAL 2.9 9.2 + - - -
245B PRO* 1.3 77.5 - - - +
247B LEU* 1.3 61.7 + - - +
249B GLN* 3.1 17.3 + - - +
250B ALA* 2.9 26.9 + - + +
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Residues in contact with LEU 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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224B VAL* 5.4 3.1 - - + -
227B CYS* 4.1 30.9 - - + -
243B VAL* 3.1 13.2 + - + +
244B MET* 3.1 33.6 + - + +
246B THR* 1.3 75.2 - - - +
248B ARG* 1.3 64.2 - - - +
250B ALA* 3.1 19.5 + - + -
251B ALA* 3.1 12.7 + - + +
262B VAL* 4.8 10.1 - - + -
269B LEU* 4.3 33.7 - - + -
273B VAL* 5.3 6.3 - - + -
282B LEU* 4.8 13.5 - - + -
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Residues in contact with ARG 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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240B GLU* 2.7 37.8 + - - -
244B MET* 2.9 46.8 + - + +
245B PRO* 3.7 17.6 - - - +
247B LEU* 1.3 75.9 - - + +
249B GLN* 1.3 62.0 + - - +
251B ALA* 3.3 7.6 + - - +
252B GLU* 2.9 42.7 + - - +
281B ASP* 3.5 27.8 + - + -
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Residues in contact with GLN 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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209B SER 5.1 1.2 - - - +
212B ALA* 3.9 21.5 - - - +
213B SER* 4.5 12.1 - - - -
245B PRO 3.2 12.3 + - - +
246B THR* 3.1 27.2 + - - +
248B ARG* 1.3 80.5 - - - +
250B ALA* 1.3 53.5 + - - -
252B GLU* 3.5 6.7 + - - +
253B ASP* 3.1 29.0 + - - +
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Residues in contact with ALA 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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212B ALA* 6.4 2.0 - - + -
224B VAL* 4.5 9.4 - - + -
246B THR* 2.9 12.9 + - + +
247B LEU* 3.1 16.4 + - + +
249B GLN* 1.3 76.3 - - - +
251B ALA* 1.3 63.8 + - - +
253B ASP* 3.2 22.9 + - - +
258B VAL* 3.6 17.8 - - + +
259B ARG* 3.9 4.7 - - - +
262B VAL* 3.9 17.6 - - + +
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Residues in contact with ALA 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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247B LEU* 3.1 12.2 + - + +
248B ARG* 3.3 11.9 + - - +
250B ALA* 1.3 77.1 - - - +
252B GLU* 1.3 61.7 + - + +
253B ASP 3.4 0.2 - - - -
259B ARG* 3.1 22.1 - - - +
262B VAL* 3.9 23.3 - - + +
285B ALA* 5.0 16.8 - - + +
289B LEU* 4.6 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