Contacts of the helix formed by residues 239 - 250 (chain G) in PDB entry 4U0Z
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228G TYR* 4.1 4.5 - - - -
237G THR 4.4 6.1 - - - +
238G LEU* 1.3 74.2 - - - +
240G LEU* 1.3 58.3 + - - +
241G SER* 2.9 23.2 + - - -
242G GLU* 3.1 31.1 + - - +
243G ILE* 2.9 33.4 + - - +
256G LYS* 5.8 1.1 - - - -
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221G GLU* 5.5 3.6 - - + +
224G TYR* 3.3 43.7 - - + +
225G HIS* 3.9 8.7 - - + +
228G TYR* 3.7 33.4 - - + -
239G THR* 1.3 74.0 - - - +
241G SER* 1.4 57.8 + - - +
243G ILE* 3.5 5.3 + - + -
244G ARG* 3.0 35.0 + - + +
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Residues in contact with SER 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239G THR* 2.9 16.6 + - - -
240G LEU* 1.4 75.3 - - - +
242G GLU* 1.4 60.9 + - - +
244G ARG* 3.4 7.9 + - - +
245G HIS* 3.0 27.9 + - - +
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Residues in contact with GLU 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G LEU* 3.4 18.5 - - + +
239G THR* 3.1 44.0 + - - +
241G SER* 1.4 73.9 - - - +
243G ILE* 1.4 59.8 + - - +
245G HIS* 3.2 4.9 + - - +
246G ILE* 2.9 36.0 + - - +
253G VAL* 3.3 38.1 - - + +
254G PRO 4.9 1.6 - - - +
256G LYS* 3.4 22.1 - - - +
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Residues in contact with ILE 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G TYR* 4.1 17.0 - - + +
227G ILE* 4.1 10.1 - - + -
228G TYR* 3.6 41.1 - - + +
231G VAL* 4.4 6.1 - - + -
238G LEU* 4.2 16.6 - - + +
239G THR 2.9 21.4 + - - +
240G LEU* 3.8 6.1 - - + +
242G GLU* 1.4 73.5 - - - +
244G ARG* 1.4 57.4 + - - +
246G ILE* 3.5 7.2 + - - +
247G LEU* 3.1 49.0 + - + +
264G VAL* 3.8 28.0 - - + -
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Residues in contact with ARG 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G TYR* 3.9 32.0 - - + -
240G LEU* 3.0 23.1 + - + +
241G SER* 3.6 9.2 - - - +
243G ILE* 1.4 75.5 - - - +
245G HIS* 1.4 60.2 + - - +
247G LEU 4.0 0.5 + - - -
248G GLU* 3.1 51.0 + - - +
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Residues in contact with HIS 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G SER 3.0 14.3 + - - +
242G GLU* 3.4 10.1 - - - +
243G ILE 3.2 0.2 - - - -
244G ARG* 1.4 74.4 - - - +
246G ILE* 1.4 57.7 + - - +
248G GLU* 3.0 4.2 + - - -
249G THR* 2.9 75.1 + - + +
251G TYR* 3.6 23.8 + - + +
252G ALA 4.2 9.2 - - - -
253G VAL* 3.5 20.7 - - + +
254G PRO* 5.5 2.7 - - + -
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Residues in contact with ILE 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238G LEU* 3.9 17.5 - - + -
242G GLU 2.9 25.4 + - - +
243G ILE* 3.8 5.8 - - - +
245G HIS* 1.4 69.7 - - - +
247G LEU* 1.3 57.7 + - + +
250G ARG* 3.1 32.2 + - - -
251G TYR 4.0 15.0 - - - +
253G VAL* 3.8 19.1 - - + -
261G GLN* 3.6 49.6 - - + +
264G VAL* 3.9 21.3 - - + -
265G ILE* 4.4 14.0 - - + +
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Residues in contact with LEU 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223G TYR* 5.0 0.9 - - + -
224G TYR* 3.7 37.4 + - + +
227G ILE* 3.8 24.9 - - + -
243G ILE* 3.1 25.3 + - + +
246G ILE* 1.3 77.6 - - + +
248G GLU* 1.4 58.0 + - - +
250G ARG* 3.3 33.1 + - - +
264G VAL* 3.9 22.0 - - + +
265G ILE* 4.5 5.2 - - + -
268G HIS* 3.5 43.0 - - + +
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Residues in contact with GLU 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G TYR* 3.6 21.1 + - - +
244G ARG* 3.1 42.4 + - - +
245G HIS* 3.0 3.4 + - - +
247G LEU* 1.4 78.1 - - - +
249G THR* 1.3 67.5 + - + +
250G ARG* 4.7 4.3 + - - +
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Residues in contact with THR 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245G HIS* 2.9 59.2 + - + +
248G GLU* 1.3 78.8 - - + +
250G ARG* 1.4 66.3 + - - +
251G TYR* 3.0 43.7 + - + -
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Residues in contact with ARG 250 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246G ILE* 3.1 23.9 + - - -
247G LEU* 3.3 30.1 + - - +
248G GLU 4.7 4.4 + - - +
249G THR* 1.4 78.4 + - - +
251G TYR* 1.4 61.2 + - - +
265G ILE* 5.2 15.0 - - - +
268G HIS* 3.4 38.8 + - - -
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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