Contacts of the helix formed by residues 233 - 246 (chain A) in PDB entry 5EJC
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 LYS 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU* 4.6 18.2 - - + -
180A TYR* 3.7 24.9 + - - -
231A SER* 3.5 8.4 - - - +
232A CYS* 1.3 81.1 - - - +
234A ILE* 1.3 64.8 + - - +
236A VAL* 3.0 23.0 + - + +
237A PHE* 3.4 11.8 - - + -
282A TRP* 4.4 7.9 - - + +
286A CYS* 3.2 31.4 - - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A VAL* 4.4 8.5 - - + +
226A LYS* 4.0 22.0 - - + -
227A VAL* 3.9 20.2 - - + -
231A SER* 3.3 25.7 + - - +
232A CYS 4.2 1.3 - - - +
233A LYS* 1.3 77.7 - - - +
235A LEU* 1.3 66.2 + - + +
237A PHE* 3.0 13.0 + - - -
238A VAL* 3.1 21.2 + - + +
278A ALA 4.1 11.7 - - - +
279A ILE* 4.2 16.4 - - + -
282A TRP* 3.6 48.1 - - + +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 5.9 0.7 - - + -
170A LEU* 4.4 18.4 - - + -
173A LEU* 4.3 1.6 - - + -
206A TRP 3.8 12.8 - - - +
207A PHE* 3.7 14.7 - - + -
210A CYS* 3.8 28.9 - - + -
211A PHE* 3.3 38.4 - - + -
223A VAL* 3.9 12.3 - - + -
224A TRP* 5.1 0.2 - - - +
227A VAL* 3.9 26.5 - - + -
232A CYS* 3.1 18.5 + - + +
234A ILE* 1.3 78.0 - - - +
236A VAL* 1.3 61.4 + - - +
238A VAL* 3.5 1.7 + - - -
239A ALA* 3.1 18.7 + - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.7 47.8 - - + +
176A ALA* 4.0 11.2 - - + +
177A PHE* 3.7 28.7 - - - +
180A TYR* 4.3 13.2 - - + -
207A PHE* 4.0 8.7 - - + -
233A LYS* 3.0 13.6 + - + +
235A LEU* 1.3 77.6 - - - +
237A PHE* 1.3 62.3 + - + +
239A ALA* 3.0 6.6 + - - +
240A VAL* 2.8 33.7 + - + +
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Residues in contact with PHE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A TYR* 3.6 43.5 - + + -
184A GLU* 6.4 0.7 - - + -
233A LYS* 3.4 20.9 - - - -
234A ILE 3.0 6.1 + - - +
236A VAL* 1.3 74.7 - - + +
238A VAL* 1.3 60.6 + - - +
240A VAL* 3.8 7.5 - - + +
241A GLU* 3.0 28.6 + - - +
278A ALA* 3.4 24.1 - - - +
281A LEU* 3.9 25.3 - - + +
282A TRP* 3.7 32.5 - + + -
285A HIS* 3.6 41.1 - + + -
286A CYS* 4.0 9.0 - - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A PHE* 3.5 26.5 - - + -
215A LEU* 4.1 19.7 - - + -
223A VAL* 4.0 32.5 - - + -
234A ILE* 3.1 19.8 + - + +
235A LEU* 3.6 7.4 - - - +
237A PHE* 1.3 74.5 - - - +
239A ALA* 1.3 63.6 + - - +
241A GLU* 3.2 3.1 + - - +
242A ILE* 3.0 26.9 + - + +
274A ILE* 4.3 6.9 - - + +
275A VAL* 5.5 2.2 - - + -
278A ALA* 3.6 18.2 - - + -
279A ILE* 6.3 0.4 - - + -
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.7 12.6 - - + -
206A TRP* 3.5 35.7 - - + -
207A PHE* 4.3 4.0 - - + -
211A PHE* 3.6 6.9 - - + -
235A LEU 3.1 10.5 + - - +
236A VAL 3.0 9.7 + - - +
238A VAL* 1.3 78.3 - - - +
240A VAL* 1.3 64.6 + - - +
242A ILE* 3.3 16.3 + - - +
243A LEU* 3.4 20.8 - - - +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.9 31.6 - - + +
180A TYR* 4.3 6.3 - - + +
181A LEU* 4.1 26.1 - - + +
184A GLU* 4.5 7.6 - - + -
236A VAL* 2.8 32.7 + - + +
237A PHE* 3.8 10.1 - - + +
239A ALA* 1.3 72.8 - - - +
241A GLU* 1.3 63.4 + - - +
243A LEU* 3.1 8.0 + - - +
244A LEU* 3.0 32.5 + - + +
281A LEU* 3.9 18.4 - - + -
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE 3.0 19.8 + - - +
238A VAL 3.2 4.5 + - - +
240A VAL* 1.3 73.0 - - - +
242A ILE* 1.3 59.5 + - - +
244A LEU* 3.7 22.7 - - - +
245A THR* 2.8 60.5 + - - +
274A ILE* 3.4 26.5 - - + +
277A LYS* 3.4 37.8 + - + +
278A ALA* 3.9 8.7 - - + +
281A LEU* 3.7 11.8 - - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A TRP* 4.5 10.8 - - + +
211A PHE* 3.7 34.1 - - + -
214A CYS* 4.5 3.1 - - - -
215A LEU* 4.9 3.6 - - + -
238A VAL* 3.0 20.7 + - + +
239A ALA* 3.4 9.6 - - - +
240A VAL 3.2 0.2 - - - -
241A GLU* 1.3 76.4 - - - +
243A LEU* 1.3 64.2 + - + +
245A THR* 3.4 2.8 + - - -
246A PHE* 3.1 41.9 + - + +
263A LEU* 4.1 22.7 - - + -
266A ILE* 4.5 24.0 - - + -
274A ILE* 4.1 18.1 - - + +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PHE* 3.8 22.9 - - + -
181A LEU* 3.8 11.9 - - + -
188A LEU* 3.7 18.8 - - + +
192A LEU* 3.6 36.8 - - + -
201A LEU* 5.2 2.2 - - + -
206A TRP* 4.1 15.5 - - + -
239A ALA 3.4 15.0 - - - +
240A VAL* 3.1 8.9 + - - +
242A ILE* 1.3 80.6 - - + +
244A LEU* 1.3 66.3 + - - +
246A PHE* 3.3 5.4 - - - +
247A LYS* 3.0 23.9 + - - -
250A VAL* 5.1 9.1 - - + +
263A LEU* 4.2 24.2 - - + -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 4.6 6.5 - - + -
184A GLU* 4.2 23.1 - - + +
185A ASP* 3.8 33.4 - - + +
188A LEU* 4.7 2.0 - - + -
240A VAL* 3.0 33.1 + - + +
241A GLU* 3.7 28.9 - - - +
243A LEU* 1.3 78.3 - - - +
245A THR* 1.3 63.8 + - - +
247A LYS* 3.3 18.6 + - + +
281A LEU* 4.1 8.7 - - + -
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLU* 2.8 37.8 + - - -
242A ILE 3.6 3.6 - - - -
244A LEU* 1.3 78.3 - - - +
246A PHE* 1.3 84.7 + - + +
247A LYS 3.5 2.1 + - - -
248A ILE* 5.2 1.0 + - - +
270A SER* 4.5 7.4 - - - -
273A ALA* 6.5 0.7 - - + -
274A ILE* 3.5 24.4 - - + +
277A LYS* 5.0 3.5 - - - +
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Residues in contact with PHE 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ILE* 3.1 31.0 + - + +
243A LEU* 3.3 4.5 - - - -
245A THR* 1.3 87.1 - - + +
247A LYS* 1.3 62.4 + - - +
248A ILE 3.5 1.8 - - - -
249A LYS* 3.6 10.0 + - + +
250A VAL* 3.1 26.3 + - + +
262A PHE* 3.9 32.3 - + + -
263A LEU* 6.1 0.4 - - + -
266A ILE* 4.3 14.1 - - + -
267A PRO* 3.9 35.9 - - + -
270A SER* 3.9 29.2 - - - -
274A ILE* 3.9 19.1 - - + -
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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