Contacts of the helix formed by residues 235 - 246 (chain C) in PDB entry 2VZE
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 TYR 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C PHE* 3.3 32.7 - - + +
45C ASN* 4.2 7.0 - - - -
46C PHE* 5.1 2.1 + - - +
127C ILE* 3.8 31.0 + - + -
130C GLY* 3.2 34.8 + - - -
131C LEU 3.8 6.6 + - - -
210C THR* 3.5 28.5 - - + -
211C GLY 3.4 17.7 - - - +
212C SER* 3.5 0.8 + - - +
214C GLU* 3.1 30.7 + - + -
215C ALA 3.2 22.0 + - - -
216C SER* 3.3 23.6 - - - -
234C SER* 1.3 74.0 - - - +
236C SER* 1.3 56.8 + - - +
238C LEU* 4.7 0.8 - - - +
239C GLY* 3.2 21.0 + - - -
274C MET* 5.7 0.2 - - - +
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Residues in contact with SER 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C GLN* 4.8 6.4 + - - -
40C VAL* 4.3 16.7 - - - +
44C PHE* 4.4 2.9 - - - -
212C SER* 2.6 43.1 + - - +
213C GLN* 4.6 1.0 - - - +
234C SER* 3.2 4.0 + - - -
235C TYR* 1.3 75.6 - - - +
237C SER* 1.3 66.2 + - - +
238C LEU 3.2 2.2 - - - -
240C LEU* 3.1 21.8 + - - +
241C LYS 3.0 23.9 + - - -
420C ILE* 3.6 6.4 - - - +
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Residues in contact with SER 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C HIS* 3.0 17.8 + - - +
234C SER* 2.7 42.9 + - - -
236C SER* 1.3 75.7 + - - +
238C LEU* 1.3 60.4 + - - +
241C LYS* 3.2 18.3 - - - +
270C LEU* 5.1 1.4 - - - +
420C ILE* 4.7 0.2 - - - -
421C GLY* 3.4 24.5 - - - +
422C ILE 3.5 25.1 - - - -
423C PHE* 4.7 0.7 - - - -
424C SER* 5.7 0.2 - - - -
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Residues in contact with LEU 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PHE* 4.1 15.0 - - + -
216C SER* 4.8 4.5 - - - +
217C ALA* 3.9 21.5 - - + -
219C TYR* 4.9 1.6 - - + -
233C HIS* 3.8 40.8 - - + +
234C SER 3.4 10.8 + - - +
235C TYR* 4.7 0.4 - - - +
236C SER 3.2 0.2 - - - -
237C SER* 1.3 79.3 + - - +
239C GLY* 1.3 60.2 + - - +
240C LEU 3.7 0.2 - - - -
241C LYS* 3.6 2.6 - - - +
242C ALA* 2.9 30.8 + - - +
266C ILE* 4.1 16.4 - - + -
269C ILE* 4.4 13.2 - - + -
270C LEU* 4.0 23.1 - - + +
274C MET* 3.7 18.6 - - + +
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Residues in contact with GLY 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PHE* 3.5 15.6 - - - -
46C PHE* 3.8 13.1 - - - -
235C TYR 3.2 14.0 + - - -
238C LEU* 1.3 77.5 - - - +
240C LEU* 1.3 59.2 + - - +
242C ALA* 3.4 2.9 + - - +
243C LYS* 2.9 27.9 + - - +
274C MET* 3.7 17.8 - - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 4.4 7.0 - - + -
41C PRO* 3.9 30.1 - - + -
44C PHE* 3.3 33.0 - - + -
236C SER* 3.1 22.6 + - - +
239C GLY* 1.3 71.8 - - - +
241C LYS* 1.3 61.1 + - - +
243C LYS* 3.3 15.4 + - + -
244C MET* 2.9 49.6 + - + +
420C ILE* 3.7 26.2 - - + -
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Residues in contact with LYS 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C SER 3.0 8.3 + - - +
237C SER 3.2 22.9 - - - +
238C LEU 3.6 1.8 - - - +
240C LEU* 1.3 75.7 - - - +
242C ALA* 1.3 61.7 + - - +
244C MET* 3.2 8.5 + - + +
245C ASP* 2.6 54.7 + - - +
270C LEU* 5.6 6.3 - - + +
366C THR 4.8 0.6 + - - +
367C GLY* 5.3 1.5 - - - -
368C LEU* 3.1 34.6 + - - +
388C SER* 3.4 26.3 + - - -
390C TYR* 3.5 21.5 + - - -
420C ILE* 3.4 22.2 - - + +
421C GLY* 3.6 12.8 - - - +
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Residues in contact with ALA 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PHE* 4.8 1.3 - - + -
238C LEU 2.9 21.7 + - - +
239C GLY 3.6 4.9 - - - +
241C LYS* 1.3 73.7 - - - +
243C LYS* 1.3 59.1 + - - +
245C ASP* 3.7 5.5 - - - +
246C ALA* 2.9 31.4 + - - +
270C LEU* 4.7 10.5 - - + +
274C MET* 3.5 37.5 - - + +
275C GLU* 4.7 3.8 - - - +
278C ALA* 4.3 2.8 - - - +
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Residues in contact with LYS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PHE* 4.6 6.5 - - + -
46C PHE* 5.4 0.7 - - + -
49C ASP* 5.4 3.6 - - + +
50C VAL* 3.9 28.0 - - + -
239C GLY 2.9 17.8 + - - +
240C LEU* 3.3 23.3 + - + +
242C ALA* 1.3 76.2 - - - +
244C MET* 1.3 61.8 + - + +
246C ALA* 3.3 15.1 - - + +
278C ALA* 4.3 15.0 - - + +
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Residues in contact with MET 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C LEU* 2.9 32.3 + - + +
241C LYS* 3.5 6.7 - - + +
242C ALA 3.2 0.2 - - - -
243C LYS* 1.3 79.9 - - + +
245C ASP* 1.3 64.0 + - - +
246C ALA 3.6 2.1 + - - +
388C SER* 4.8 8.7 - - - -
389C CYS* 3.2 35.4 - - - -
420C ILE* 3.6 43.3 - - + +
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Residues in contact with ASP 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C LYS* 2.6 50.2 + - - +
242C ALA* 3.7 5.3 - - - +
244C MET* 1.3 76.4 - - - +
246C ALA* 1.3 67.6 + - - +
248C TRP* 2.9 43.8 + - + +
275C GLU* 5.4 0.2 - - - +
368C LEU* 3.8 15.7 - - + +
387C ALA* 5.4 0.2 - - - -
388C SER* 3.0 33.5 + - - -
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ALA 2.9 11.6 + - - +
243C LYS 3.3 17.0 - - - +
244C MET 3.3 3.6 - - - +
245C ASP* 1.3 75.0 - - - +
247C GLY* 1.3 58.5 + - - +
275C GLU* 3.2 10.5 - - - +
278C ALA* 3.5 25.4 - - + +
279C LEU* 4.1 18.0 - - + +
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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