Contacts of the helix formed by residues 232 - 244 (chain B) in PDB entry 5LUB
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 TRP 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.0 23.3 - + + -
41A TYR* 4.6 25.6 - + + -
79A ASP* 5.2 0.7 - - - -
221A TYR* 3.7 7.5 + - - -
226A SER* 3.0 34.8 + - - -
217B TYR* 3.2 16.3 + - + +
218B ALA 3.6 15.9 + - - -
219B CYS* 3.4 25.4 - - + +
220B TYR* 4.5 23.6 - + - -
231B ASP* 1.3 69.2 - - - +
233B TYR* 1.3 59.3 + - - +
235B VAL* 4.0 1.5 - - + +
236B ASN* 2.8 61.3 + - - +
261B HIS 5.1 3.1 - - - -
262B THR* 4.4 9.9 - - + -
263B GLN 5.9 1.6 - - - -
264B THR* 3.3 35.9 - - + +
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B TYR* 4.9 1.1 - + - -
185B TYR* 3.3 20.9 - + - +
186B ILE 3.7 19.5 - - - -
187B GLU* 3.2 22.6 + - + +
207B THR* 3.2 46.2 + - + +
208B THR 4.0 2.7 - - - -
209B ALA* 3.4 34.8 - - + -
216B SER* 5.9 0.2 - - - -
217B TYR 5.1 0.2 + - - -
231B ASP 3.5 0.4 - - - -
232B TRP* 1.3 77.3 - - - +
234B SER* 1.3 66.3 + - - +
236B ASN* 3.7 2.3 - - - +
237B TRP* 3.1 41.6 + + + -
258B VAL* 3.6 23.0 - - + +
262B THR* 4.0 18.7 + - + +
267B VAL* 4.0 9.6 - - + -
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.4 22.3 + - - -
144B TYR* 2.8 27.5 + - - -
187B GLU* 2.8 33.3 + - - +
231B ASP 3.6 5.8 - - - -
233B TYR* 1.3 74.5 - - - +
235B VAL* 1.3 58.7 + - - +
237B TRP* 3.3 15.3 - - - +
238B MET* 3.0 35.4 + - - +
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Residues in contact with VAL 235 (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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48B ASP* 4.4 0.4 - - - +
88B ASN* 3.6 39.5 - - - +
219B CYS* 4.2 4.7 - - - -
220B TYR* 3.2 38.4 - - + +
230B GLY* 4.2 0.9 - - - -
231B ASP 2.8 32.6 + - - +
232B TRP* 4.0 4.5 - - + +
234B SER* 1.3 74.3 - - - +
236B ASN* 1.3 64.5 + - - +
238B MET* 4.4 4.5 - - - -
239B GLU* 2.9 43.9 + - + +
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Residues in contact with ASN 236 (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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41A TYR* 4.8 4.5 - - - -
232B TRP* 2.8 43.5 + - - +
233B TYR 3.7 4.5 - - - +
234B SER 3.2 0.2 - - - -
235B VAL* 1.3 80.2 - - - +
237B TRP* 1.3 60.9 + - - +
239B GLU* 4.2 4.7 - - - +
240B ASP* 3.2 23.6 + - - +
258B VAL* 3.8 18.3 - - + +
261B HIS* 3.5 39.5 + - + +
262B THR* 2.8 28.0 + - - +
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 4.2 14.8 - - + -
55B ILE* 4.3 7.6 - - + -
56B ILE* 5.8 1.8 - - + -
142B PHE* 4.1 15.5 - + - -
144B TYR* 3.6 45.5 - + - -
185B TYR* 3.5 35.4 - + + -
233B TYR* 3.1 31.0 + + + +
234B SER* 3.3 19.1 + - - +
236B ASN* 1.3 75.7 - - - +
238B MET* 1.3 82.6 + - + +
240B ASP* 3.4 2.3 - - - +
241B SER* 2.9 38.8 + - - -
254B GLN* 3.3 9.5 + - - +
258B VAL* 3.5 22.8 - - + +
284B GLN* 3.6 25.6 - - + -
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Residues in contact with MET 238 (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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48B ASP* 3.4 19.1 - - - +
51B HIS* 3.7 14.1 - - + -
52B ALA* 3.3 37.2 - - - -
55B ILE* 3.5 16.5 - - + +
88B ASN* 3.6 22.2 - - - +
144B TYR* 4.0 3.6 - - - +
234B SER* 3.0 42.4 + - - +
235B VAL* 4.2 2.0 - - - +
237B TRP* 1.3 101.0 - - + +
239B GLU* 1.3 60.8 + - - +
241B SER 3.3 0.5 + - - -
242B ASP* 3.0 34.5 + - - +
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Residues in contact with GLU 239 (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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51B HIS* 4.7 11.6 - - + -
88B ASN 4.6 0.3 - - - +
89B ARG* 3.8 22.6 - - - +
220B TYR* 2.8 34.4 + - - -
235B VAL* 2.9 33.1 + - + +
236B ASN* 4.4 5.2 - - - +
238B MET* 1.3 75.4 - - - +
240B ASP* 1.3 63.4 + - - +
242B ASP* 3.5 17.2 + - - +
243B VAL* 3.5 19.1 + - - +
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Residues in contact with ASP 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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236B ASN 3.2 21.1 + - - +
237B TRP* 3.4 5.8 - - - +
238B MET 3.2 0.2 - - - -
239B GLU* 1.3 74.3 - - - +
241B SER* 1.3 59.5 + - - +
243B VAL* 3.1 8.8 + - - +
244B GLU* 2.8 57.4 + - - +
249B GLU* 2.6 25.2 - - - +
254B GLN* 3.0 21.8 + - + +
257B LEU* 3.4 18.0 - - + +
258B VAL* 5.3 1.6 - - + -
261B HIS* 6.6 0.2 - - + -
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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
----------------------------------------------------------
55B ILE* 3.9 18.4 - - - -
58B ARG* 4.2 7.0 + - - -
237B TRP* 2.9 20.3 + - - -
238B MET* 3.3 6.2 + - - -
240B ASP* 1.3 72.4 - - - +
242B ASP* 1.3 61.7 + - - +
243B VAL 3.5 0.3 + - - -
244B GLU 4.0 4.3 - - - +
246B LEU* 3.6 29.8 - - - +
254B GLN* 3.0 20.7 + - - +
280B VAL* 4.5 1.7 - - - +
284B GLN* 2.7 28.6 + - - -
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Residues in contact with ASP 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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51B HIS* 2.7 30.7 + - - -
55B ILE* 3.4 10.4 - - - +
58B ARG* 2.7 41.4 + - - +
238B MET 3.0 16.1 + - - +
239B GLU* 3.6 13.8 - - - +
240B ASP 3.1 0.4 - - - -
241B SER* 1.3 76.9 - - - +
243B VAL* 1.3 63.4 + - + +
244B GLU 4.9 0.6 - - - +
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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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239B GLU 3.5 14.6 - - - +
240B ASP* 3.4 15.0 - - - +
242B ASP* 1.3 83.3 - - + +
244B GLU* 1.3 75.3 + - + +
245B ASP 4.0 0.2 + - - -
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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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240B ASP* 2.8 45.4 + - - +
241B SER 4.0 3.7 + - - +
242B ASP 3.7 1.1 - - - +
243B VAL* 1.3 86.0 - - + +
245B ASP* 1.3 63.9 + - - +
246B LEU* 3.3 18.5 + - + +
248B LYS* 6.1 0.5 - - - +
249B GLU* 3.2 41.2 - - - +
253B LYS* 3.5 20.7 + - - -
257B LEU* 3.3 13.7 - - - +
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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