Contacts of the helix formed by residues 257 - 265 (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 ALA 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B ASP* 3.6 25.2 - - + +
212B ARG* 3.3 16.7 - - - +
255B LYS 3.0 8.1 + - - -
256B SER* 1.3 82.1 - - - +
258B ASP* 1.3 54.6 + - - +
259B GLU 2.7 2.9 + - - -
260B PHE* 2.6 35.5 + - - +
261B LEU* 3.9 1.4 + - - +
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Residues in contact with ASP 258 (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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202B LYS* 6.0 3.2 - - - -
256B SER 3.6 3.0 + - - +
257B ALA* 1.3 79.3 - - - +
259B GLU* 1.3 60.8 + - - +
260B PHE 3.2 0.4 + - - -
261B LEU* 3.7 24.0 + - - +
262B GLU* 3.8 10.4 + - - +
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Residues in contact with GLU 259 (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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255B LYS* 3.1 40.2 + - + -
256B SER* 3.5 26.4 - - - +
257B ALA 3.9 0.4 - - - +
258B ASP* 1.3 78.6 - - - +
260B PHE* 1.3 65.0 + - - +
262B GLU* 3.1 14.9 + - - +
263B LYS* 3.1 26.4 + - - +
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Residues in contact with PHE 260 (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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210B ASP* 4.9 1.1 - - - +
211B PRO* 4.9 3.4 - - + -
212B ARG* 3.4 39.9 - - + -
215B LEU* 3.6 27.1 - - + -
247B ILE* 3.3 33.2 - - + -
248B PRO* 3.7 20.9 - - + -
251B LEU 4.9 6.5 - - - -
252B GLU* 5.4 1.3 - - - -
255B LYS* 3.5 23.5 - - + +
257B ALA 2.6 21.6 + - - +
259B GLU* 1.3 71.6 - - - +
261B LEU* 1.3 74.3 + - + +
263B LYS* 2.9 4.8 + - - +
264B LEU* 2.9 40.1 + - + +
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Residues in contact with LEU 261 (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* 4.0 27.1 - - + -
199B LYS* 3.0 41.7 + - + +
202B LYS* 3.8 35.7 - - + -
211B PRO* 3.9 27.6 - - + -
257B ALA 3.9 1.9 + - - +
258B ASP* 3.7 20.5 + - - +
259B GLU 3.4 0.6 - - - -
260B PHE* 1.3 85.7 - - + +
262B GLU* 1.3 61.7 + - - +
263B LYS 3.4 0.2 + - - -
264B LEU* 3.4 15.6 + - + +
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Residues in contact with GLU 262 (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* 3.9 14.2 + - - +
258B ASP 3.8 8.3 + - - +
259B GLU* 3.1 18.6 + - - +
261B LEU* 1.3 79.4 - - - +
263B LYS* 1.3 58.9 + - - +
264B LEU 3.4 0.4 + - - -
265B SER* 3.9 11.4 + - - -
266B ASP* 5.2 1.6 - - - +
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Residues in contact with LYS 263 (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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251B LEU* 4.8 0.6 - - - +
255B LYS* 4.3 27.4 - - + +
259B GLU* 3.1 19.1 + - - +
260B PHE* 2.9 5.5 + - + +
262B GLU* 1.3 75.7 - - - +
264B LEU* 1.3 63.7 + - - +
265B SER 3.4 1.6 - - - -
266B ASP* 3.4 35.4 + - - +
267B TYR* 2.7 43.0 + - + +
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Residues in contact with LEU 264 (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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194B PHE* 4.4 20.0 - - + -
195B SER* 4.3 12.3 - - - +
198B VAL* 3.5 35.7 - - + -
215B LEU* 4.7 1.1 - - + -
246B LEU 5.3 0.2 - - - +
248B PRO* 3.4 38.1 - - + -
260B PHE* 2.9 36.7 + - + +
261B LEU* 3.7 12.3 - - + +
262B GLU 3.4 1.2 - - - -
263B LYS* 1.3 74.4 - - - +
265B SER* 1.3 53.6 + - - +
266B ASP 2.7 17.0 + - - -
267B TYR* 2.9 18.6 + - + -
268B ASP* 4.0 6.2 - - - +
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Residues in contact with SER 265 (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* 3.0 25.3 + - - -
199B LYS* 4.2 10.1 + - - -
261B LEU 4.4 1.4 + - - -
262B GLU* 3.9 14.2 + - - -
264B LEU* 1.3 76.0 - - - +
266B ASP* 1.3 66.9 + - - +
267B TYR 3.3 1.2 + - - -
268B ASP* 3.5 19.3 + - - +
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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