Contacts of the helix formed by residues 237 - 246 (chain B) in PDB entry 5W5T
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 ASP 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ASP* 3.3 18.2 - - - +
229B THR 4.5 0.9 - - - +
230B SER* 2.9 21.1 + - - +
231B SER* 2.3 42.5 + - - -
232B ARG 2.8 11.0 + - - -
233B ASP* 2.9 18.8 + - - +
235B GLY 3.7 0.2 - - - -
236B LYS* 1.3 79.1 - - - +
238B ILE* 1.3 68.4 + - - +
239B ILE 3.4 1.1 - - - -
240B PRO* 3.5 2.8 - - - +
241B TYR* 3.4 19.8 + - - +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.7 21.1 - - + -
212B PHE* 4.6 6.1 - - + -
220B ALA* 4.1 21.3 - - + +
221B LEU* 3.6 19.3 - - + -
224B ASP* 3.4 32.8 - - + +
233B ASP 3.0 8.4 + - - +
234B PHE* 3.8 28.0 - - + -
237B ASP* 1.3 75.3 - - - +
239B ILE* 1.3 64.4 + - + +
241B TYR* 3.2 18.4 + - - +
242B ILE* 3.4 25.6 + - + +
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 3.8 26.7 - - + -
159B ILE* 3.7 19.5 - - + -
175B MET* 4.2 12.3 - - + -
186B PHE* 5.1 3.8 - - + -
210B TYR* 3.7 39.5 - - + +
212B PHE* 4.5 10.1 - - + -
234B PHE* 2.9 30.4 + - + +
235B GLY* 4.4 4.0 - - - +
238B ILE* 1.3 72.5 - - + +
240B PRO* 1.3 70.6 - - + +
242B ILE* 3.1 6.4 + - + +
243B VAL* 3.1 31.0 + - + +
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Residues in contact with PRO 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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186B PHE* 3.9 20.6 - - + -
235B GLY 3.2 23.3 - - - +
236B LYS* 3.1 27.4 - - - +
237B ASP 3.5 4.7 - - - +
239B ILE* 1.3 90.6 - - + +
241B TYR* 1.3 60.7 + - - +
243B VAL* 3.9 8.6 - - + +
244B GLU* 3.4 25.5 + - - +
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Residues in contact with TYR 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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223B ARG* 3.2 47.4 + - - -
237B ASP 3.4 10.7 + - - +
238B ILE* 3.2 13.2 + - - +
239B ILE 3.1 0.4 - - - -
240B PRO* 1.3 79.9 - - - +
242B ILE* 1.3 63.3 + - + +
244B GLU* 4.0 0.8 - - - +
245B HIS* 2.9 57.2 + + + +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ASP* 3.7 20.4 - - + +
157B VAL* 3.4 34.5 - - + -
212B PHE* 4.0 15.0 - - + -
216B PHE* 3.7 29.6 - - + -
220B ALA* 5.4 3.8 - - + -
223B ARG* 5.5 3.8 - - - +
238B ILE* 3.4 23.1 + - + +
239B ILE* 3.1 8.3 + - + +
241B TYR* 1.3 79.1 - - + +
243B VAL* 1.3 63.3 + - - +
244B GLU 3.1 2.0 - - - -
245B HIS 4.6 0.4 - - - -
246B GLY* 2.6 38.0 + - - +
247B LYS 3.9 10.5 - - - +
248B ALA 4.3 0.2 - - - +
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Residues in contact with VAL 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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159B ILE* 5.0 0.7 - - + -
175B MET* 5.0 1.6 - - - -
183B ILE* 3.8 29.4 - - + +
184B ILE* 3.9 5.0 - - - +
185B ASP* 3.5 37.5 - - - +
186B PHE* 4.4 8.1 - - + +
239B ILE* 3.1 32.1 + - + +
240B PRO* 3.9 8.7 - - + +
242B ILE* 1.3 76.7 - - - +
244B GLU* 1.3 62.6 + - - +
246B GLY 3.8 6.1 - - - +
248B ALA* 3.8 24.0 + - + -
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Residues in contact with GLU 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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184B ILE 5.9 0.9 - - - -
240B PRO 3.4 14.6 + - - +
241B TYR* 4.0 1.8 - - - +
242B ILE 3.1 0.2 - - - -
243B VAL* 1.3 83.4 - - - +
245B HIS* 1.3 81.9 + - + +
246B GLY 3.3 7.5 + - - +
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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 TYR* 2.9 53.3 + + + +
242B ILE* 4.6 0.7 - - - -
244B GLU* 1.3 100.3 + - + +
246B GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 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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156B ASP* 3.3 10.3 - - - -
216B PHE* 6.2 0.2 - - - -
242B ILE* 2.6 28.8 + - - +
243B VAL 3.8 8.7 - - - +
244B GLU 3.3 3.5 - - - +
245B HIS* 1.3 75.0 - - - +
247B LYS* 1.3 60.5 + - - -
248B ALA 4.0 0.2 + - - -
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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