Contacts of the helix formed by residues 193 - 204 (chain B) in PDB entry 1EBF
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 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B PHE* 4.4 0.9 - - - -
191B ASP* 4.9 11.1 + - - +
192B VAL* 1.3 82.8 - - - +
194B PHE* 1.3 66.6 + - - +
195B SER* 4.0 2.5 - - - +
196B ASP* 3.0 31.3 + - - +
197B VAL* 3.2 10.8 + - - +
268B ASP* 3.5 24.2 - - + +
272B THR* 4.2 29.4 + - - +
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Residues in contact with PHE 194 (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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180B ILE* 3.7 23.8 - - + -
181B PHE* 4.6 13.7 - + - -
184B PHE* 3.7 40.5 - + + -
193B LYS* 1.3 71.1 - - - +
195B SER* 1.3 63.8 + - - +
197B VAL* 3.1 15.8 + - - +
198B VAL* 3.3 26.7 + - + +
215B LEU* 3.7 30.7 - - + -
246B LEU* 4.2 15.0 - - + -
264B LEU* 4.4 18.8 - - + -
268B ASP* 3.5 16.8 + - + +
271B LEU* 3.6 36.8 - - + -
272B THR* 5.3 0.4 + - - -
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Residues in contact with SER 195 (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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193B LYS* 4.3 3.1 - - - -
194B PHE* 1.3 75.3 - - - +
196B ASP* 1.3 59.7 + - - +
198B VAL* 2.7 29.2 - - - +
199B LYS* 3.3 24.7 + - - +
264B LEU* 4.1 6.3 - - - +
265B SER* 3.0 33.5 + - - -
268B ASP* 2.8 33.3 + - - -
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Residues in contact with ASP 196 (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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192B VAL* 4.0 11.4 - - + +
193B LYS* 3.0 34.6 + - - +
195B SER* 1.3 76.5 + - - +
197B VAL* 1.3 67.4 + - - +
199B LYS* 3.9 13.8 + - - +
200B VAL* 3.2 32.3 + - + +
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Residues in contact with VAL 197 (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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179B TYR* 4.9 3.2 - - + -
180B ILE* 3.4 43.7 - - + +
183B GLU* 3.6 19.7 - - + -
184B PHE* 4.0 26.2 - - + +
192B VAL* 3.8 16.2 - - + -
193B LYS 3.2 14.5 + - - +
194B PHE* 3.1 8.6 + - - +
196B ASP* 1.3 76.1 - - - +
198B VAL* 1.3 61.3 + - - +
200B VAL* 4.0 3.6 - - - +
201B ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 198 (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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180B ILE* 4.0 25.1 - - + -
194B PHE* 3.3 28.7 + - + +
195B SER 2.7 27.8 - - - +
197B VAL* 1.3 75.2 - - - +
199B LYS* 1.3 63.1 + - + +
201B ALA* 3.1 7.6 + - - +
202B LYS* 2.8 32.8 + - - +
207B THR* 5.1 1.2 - - - +
211B PRO* 5.3 7.9 - - + +
215B LEU* 4.6 9.9 - - + -
261B LEU* 4.0 13.7 - - + -
264B LEU* 3.5 26.5 - - + -
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Residues in contact with LYS 199 (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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195B SER* 3.3 33.4 + - - +
196B ASP* 3.5 15.2 + - - +
198B VAL* 1.3 81.8 - - - +
200B VAL* 1.3 60.1 + - + +
202B LYS* 3.3 9.3 - - - +
203B LYS* 3.1 35.0 + - - +
261B LEU* 3.0 50.3 + - + -
262B GLU* 3.9 15.4 + - - +
264B LEU* 5.5 0.4 - - - -
265B SER* 4.2 10.5 + - - -
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Residues in contact with VAL 200 (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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179B TYR* 5.2 5.4 - - + +
196B ASP* 3.2 19.1 + - + +
197B VAL* 4.0 3.6 - - - +
198B VAL 3.2 0.8 - - - -
199B LYS* 1.3 73.5 - - + +
201B ALA* 1.3 66.1 + - - +
202B LYS 3.0 2.0 - - - -
203B LYS* 3.2 11.4 + - + +
204B LEU* 3.0 44.4 + - + +
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Residues in contact with ALA 201 (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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176B THR* 5.5 0.7 - - + -
179B TYR* 4.0 24.9 - - + -
180B ILE* 4.4 11.9 - - + -
197B VAL 3.1 18.4 + - - +
198B VAL* 3.1 8.9 + - - +
200B VAL* 1.3 76.0 - - - +
202B LYS* 1.3 56.9 + - - +
204B LEU 3.7 0.3 + - - -
205B GLY 3.3 2.3 + - - -
206B TYR* 2.7 50.1 + - + +
207B THR* 3.6 9.0 + - - -
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Residues in contact with LYS 202 (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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198B VAL 2.8 15.3 + - - +
199B LYS* 3.3 9.4 - - - +
201B ALA* 1.3 76.8 - - - +
203B LYS* 1.3 67.0 + - + +
205B GLY* 3.0 18.7 + - - -
207B THR* 3.3 23.6 - - + +
208B GLU 4.5 0.7 - - - +
209B PRO* 2.5 41.0 + - + +
211B PRO* 4.3 7.2 - - + -
258B ASP* 6.0 3.4 - - - -
261B LEU* 3.8 24.0 - - + -
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Residues in contact with LYS 203 (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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199B LYS* 3.1 20.4 + - - +
200B VAL* 3.2 12.3 + - + +
202B LYS* 1.3 85.6 - - + +
204B LEU* 1.3 65.7 + - + +
205B GLY* 3.1 1.1 + - - -
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Residues in contact with LEU 204 (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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179B TYR* 4.4 7.4 - - - +
200B VAL* 3.0 39.7 + - + +
201B ALA 4.1 0.2 - - - +
203B LYS* 1.3 78.8 - - + +
205B GLY* 1.3 60.5 + - - +
206B TYR* 3.3 51.5 - - + +
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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