Contacts of the helix formed by residues 288 - 297 (chain E) in PDB entry 4DVQ
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 GLY 288 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E MET* 4.0 4.2 - - - +
202E LEU 4.6 0.4 - - - -
203E ALA 3.3 13.5 - - - -
204E LEU 4.3 2.7 - - - -
286E TYR* 3.3 25.4 - - - -
287E THR* 1.3 78.8 - - - +
289E ILE* 1.3 64.7 + - - -
290E VAL 3.5 2.0 - - - -
291E ALA* 3.5 5.3 + - - +
292E GLU* 3.3 25.5 + - - +
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Residues in contact with ILE 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ASP* 3.4 28.4 - - + +
148E VAL* 3.7 29.4 - - + +
157E PHE* 3.6 24.9 - - + -
203E ALA* 2.9 32.9 + - + +
204E LEU* 3.5 24.4 + - + -
286E TYR* 3.5 13.5 - - - +
288E GLY* 1.3 69.4 - - - -
290E VAL* 1.3 66.6 + - - +
292E GLU* 3.4 8.1 + - - +
293E LEU* 3.3 22.3 + - + +
311E LEU* 4.7 4.5 - - + -
455E LEU* 4.2 9.9 - - + -
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Residues in contact with VAL 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LEU* 2.9 39.2 + - + +
205E PHE* 4.0 15.0 - - + -
271E ILE* 4.0 27.4 - - + -
274E ILE* 4.1 4.3 - - + -
289E ILE* 1.3 69.7 - - - +
291E ALA* 1.3 64.0 + - - +
293E LEU* 3.2 14.4 + - + +
294E LEU* 3.0 30.3 + - + +
304E ILE* 4.5 9.4 - - + -
308E SER* 3.6 23.8 - - - +
311E LEU* 4.9 5.4 - - + -
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Residues in contact with ALA 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ARG* 4.4 0.9 - - - +
204E LEU 4.2 0.4 + - - -
274E ILE* 3.7 10.5 - - + +
278E LEU* 3.8 22.7 - - + -
287E THR* 3.5 30.7 - - - +
288E GLY 3.5 11.3 + - - +
289E ILE 3.3 0.4 - - - -
290E VAL* 1.3 75.5 - - - +
292E GLU* 1.3 66.5 + - - +
294E LEU* 3.1 1.7 + - - +
295E LEU* 2.8 38.9 + - + +
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Residues in contact with GLU 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ASP* 3.4 35.1 - - + +
156E ARG* 3.9 13.0 + - - -
285E HIS 5.3 1.2 - - - +
286E TYR* 3.3 37.3 - - + -
287E THR 5.0 1.0 + - - -
288E GLY 3.3 13.9 + - - +
289E ILE* 3.7 5.6 - - - +
290E VAL 3.3 0.4 - - - -
291E ALA* 1.3 77.0 - - - +
293E LEU* 1.3 63.6 + - - +
295E LEU* 4.0 14.8 - - - +
296E LYS* 3.1 40.3 + - - +
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Residues in contact with LEU 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E ARG 3.7 22.9 - - - +
144E LEU* 3.6 28.3 - - + -
147E ASP* 3.8 24.0 - - + +
148E VAL* 5.1 1.6 - - + -
289E ILE* 3.3 20.4 + - + +
290E VAL* 3.2 19.2 + - + +
291E ALA 3.2 0.8 - - - -
292E GLU* 1.3 78.6 - - - +
294E LEU* 1.3 56.2 + - - +
296E LYS* 4.2 4.0 - - + +
297E ALA* 3.1 19.4 + - - -
298E GLU 4.4 1.4 + - - -
299E LEU* 5.1 5.0 + - + -
304E ILE* 3.3 35.8 - - + +
307E ASN* 5.5 3.6 - - + -
308E SER* 6.0 1.3 - - - +
311E LEU* 4.9 7.2 - - + -
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Residues in contact with LEU 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ILE* 4.2 6.3 - - + -
274E ILE* 4.0 27.6 - - + -
275E TYR* 4.3 18.6 - - + -
278E LEU* 4.0 23.1 - - + -
290E VAL* 3.0 24.8 + - + +
291E ALA 3.1 0.2 + - - -
293E LEU* 1.3 73.5 - - - +
295E LEU* 1.3 68.4 + - - +
297E ALA* 3.3 13.7 + - - +
301E LEU* 3.8 23.6 - - + -
304E ILE* 3.5 33.7 - - + -
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Residues in contact with LEU 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278E LEU* 4.3 23.8 - - + -
282E ARG* 2.7 67.0 + - + +
283E PRO* 4.6 18.4 - - + +
285E HIS 5.9 2.2 - - - +
291E ALA* 2.8 30.7 + - + +
292E GLU* 4.0 19.5 - - - +
294E LEU* 1.3 79.0 - - - +
296E LYS* 1.3 64.4 + - + +
297E ALA* 3.2 1.4 + - - +
300G SER* 3.3 9.0 - - - -
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Residues in contact with LYS 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E PRO* 4.3 14.3 - - - +
147E ASP* 3.0 40.0 + - - +
292E GLU* 3.1 22.8 + - - +
293E LEU* 4.2 4.7 - - + +
295E LEU* 1.3 80.8 - - + +
297E ALA* 1.3 67.8 + - - +
298E GLU* 3.1 35.7 + - + +
300G SER* 4.4 8.3 - - - +
301G LEU* 5.4 2.7 + - - +
302G GLU* 4.4 10.0 + - - +
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Residues in contact with ALA 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E LEU 3.1 15.9 + - - -
294E LEU* 3.3 13.9 + - - +
295E LEU 3.1 3.9 - - - +
296E LYS* 1.3 77.8 - - - +
298E GLU* 1.3 60.7 + - - +
299E LEU 3.5 11.8 - - - +
304E ILE* 4.9 2.0 - - + -
126G LYS* 4.8 20.0 - - - +
300G SER* 5.2 3.6 - - - +
302G GLU* 4.3 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
------------------------------------------------------------
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