Contacts of the helix formed by residues 239 - 250 (chain B) in PDB entry 4U04
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 THR 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228B TYR* 3.9 8.5 - - - -
237B THR 4.5 5.6 - - - +
238B LEU* 1.3 77.5 - - - +
240B LEU* 1.3 59.5 + - - +
241B SER* 3.0 22.8 + - - -
242B GLU* 3.0 28.8 + - - +
243B ILE* 3.0 28.2 + - - +
256B LYS* 5.0 2.0 - - - +
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Residues in contact with LEU 240 (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 TYR* 3.4 44.6 - - + +
225B HIS* 3.7 13.2 - - + +
228B TYR* 3.8 28.9 - - + -
239B THR* 1.3 74.1 - - - +
241B SER* 1.3 58.3 + - - +
243B ILE* 3.4 3.9 + - + +
244B ARG* 3.0 61.6 + - - +
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Residues in contact with SER 241 (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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239B THR* 3.0 17.0 + - - -
240B LEU* 1.3 76.2 - - - +
242B GLU* 1.3 60.8 + - - +
244B ARG* 3.5 28.8 + - - +
245B HIS* 3.1 25.8 + - - +
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Residues in contact with GLU 242 (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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238B LEU* 3.4 15.3 - - + +
239B THR* 3.0 42.1 + - - +
241B SER* 1.3 75.1 - - - +
243B ILE* 1.3 59.0 + - - +
245B HIS* 3.1 6.6 + - - +
246B ILE* 3.0 33.9 + - - +
253B VAL* 3.6 33.1 - - + +
254B PRO 5.2 0.7 - - - +
256B LYS* 3.0 32.4 + - - +
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Residues in contact with ILE 243 (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 TYR* 4.3 22.2 - - + +
227B ILE* 4.3 5.8 - - + -
228B TYR* 3.6 42.0 - - + +
231B VAL* 4.4 4.7 - - + -
238B LEU* 4.1 12.8 - - + +
239B THR 3.0 22.8 + - - +
240B LEU* 3.6 4.5 - - - +
242B GLU* 1.3 73.6 - - - +
244B ARG* 1.3 57.9 + - - +
246B ILE* 3.3 7.5 + - - +
247B LEU* 3.1 49.6 + - + +
264B VAL* 3.8 31.2 - - + -
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Residues in contact with ARG 244 (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 TYR* 3.8 39.1 + - + +
240B LEU* 3.0 42.5 + - - +
241B SER* 3.6 31.3 + - - +
242B GLU 3.2 0.2 - - - -
243B ILE* 1.3 72.4 - - - +
245B HIS* 1.4 59.7 + - - +
247B LEU* 4.3 0.2 - - - +
248B GLU* 2.9 40.3 + - + +
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Residues in contact with HIS 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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241B SER 3.1 13.6 + - - +
242B GLU* 3.1 9.4 + - - +
244B ARG* 1.4 75.9 - - - +
246B ILE* 1.3 54.0 + - - +
248B GLU* 4.9 0.9 - - - -
249B THR* 2.5 69.5 + - + +
251B TYR* 3.6 15.1 + - + +
252B ALA 3.6 20.4 - - - -
253B VAL* 3.5 21.0 - - + +
254B PRO* 5.7 1.8 - - + -
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Residues in contact with ILE 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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258A LEU* 3.8 17.9 - - + -
238B LEU* 4.3 11.7 - - + -
242B GLU 3.0 17.2 + - - +
243B ILE* 3.3 9.6 + - - +
245B HIS* 1.3 75.5 - - - +
247B LEU* 1.3 58.1 + - - +
250B ARG* 2.9 31.9 + - - -
251B TYR 4.0 9.4 - - - +
253B VAL* 3.8 12.3 - - + -
261B GLN* 3.2 53.6 - - + +
264B VAL* 4.2 10.5 - - + -
265B ILE* 3.8 20.9 - - + +
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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 TYR* 3.5 41.1 - - + -
227B ILE* 3.7 23.3 - - + -
243B ILE* 3.1 22.6 + - + +
246B ILE* 1.3 77.5 - - + +
248B GLU* 1.3 58.8 + - - +
250B ARG* 2.9 40.5 + - - +
264B VAL* 4.0 18.8 - - + +
265B ILE* 4.4 7.4 - - + -
268B HIS* 3.4 37.5 - - + +
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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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224B TYR* 4.5 10.9 + - - +
244B ARG* 2.9 24.3 + - + +
245B HIS* 4.4 0.9 - - - +
247B LEU* 1.3 78.3 - - - +
249B THR* 1.3 66.3 + - + +
250B ARG* 4.5 3.6 + - - +
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Residues in contact with THR 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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245B HIS* 2.5 52.1 + - + +
248B GLU* 1.3 81.2 - - + +
250B ARG* 1.3 71.6 + - - +
251B TYR* 3.1 31.1 + - - +
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Residues in contact with ARG 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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257A SER* 3.8 6.2 - - - -
258A LEU* 3.2 28.5 + - - +
259A GLU 4.8 0.7 + - - -
246B ILE 2.9 23.9 + - - -
247B LEU* 2.9 37.1 + - - +
248B GLU 4.5 3.5 + - - +
249B THR* 1.3 80.0 + - - +
251B TYR* 1.4 60.3 + - + +
265B ILE* 5.0 19.8 - - - +
268B HIS* 3.4 38.4 + - - -
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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