Contacts of the helix formed by residues 286 - 297 (chain E) in PDB entry 5TJ4
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 THR 286 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E GLU 4.2 2.2 - - - +
282E ASN* 3.2 32.5 + - - +
283E TYR 3.1 9.8 + - - +
284E LEU 2.9 4.8 + - - -
285E LEU* 1.3 80.4 - - - +
287E ASP* 1.3 66.3 - - - +
288E GLU* 3.0 9.3 + - - +
289E GLY 3.1 15.4 + - - -
290E LEU* 3.0 21.9 + - - +
304E LEU* 3.5 10.9 - - - +
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Residues in contact with ASP 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E THR* 1.3 71.8 - - - +
288E GLU* 1.3 60.6 + - - +
291E GLU* 3.2 26.0 + - - +
304E LEU* 4.1 1.0 - - - +
306E SER* 3.0 36.5 + - - +
307E TYR* 3.3 36.0 + - + +
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Residues in contact with GLU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E TYR 5.7 0.2 - - - +
286E THR* 3.1 8.6 + - - +
287E ASP* 1.3 79.6 - - - +
289E GLY* 1.3 61.2 + - - +
291E GLU* 3.6 4.3 + - - +
292E ALA* 3.3 20.6 + - - +
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Residues in contact with GLY 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E VAL* 3.5 20.5 - - - +
283E TYR 3.5 21.5 + - - -
284E LEU* 3.6 6.7 - - - -
286E THR* 3.0 7.7 + - - -
288E GLU* 1.3 77.9 - - - +
290E LEU* 1.3 63.8 + - - +
292E ALA* 3.1 14.4 + - - +
293E VAL* 3.2 11.3 + - - +
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Residues in contact with LEU 290 (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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108E ILE* 3.9 20.4 - - + +
284E LEU* 3.3 26.3 + - + +
285E LEU* 4.5 9.0 - - + -
286E THR 3.0 11.7 + - - +
289E GLY* 1.3 70.8 - - - +
291E GLU* 1.3 56.4 + - - +
293E VAL* 3.2 5.8 + - - +
294E ASN* 2.7 38.1 + - - +
299E LEU* 3.9 23.1 - - + +
302E VAL* 3.9 20.9 - - + -
304E LEU* 3.5 38.8 - - + +
307E TYR* 4.0 16.2 - - + -
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Residues in contact with GLU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E ASP 3.2 21.8 + - - +
288E GLU* 3.8 5.8 - - - +
290E LEU* 1.3 79.2 - - - +
292E ALA* 1.3 56.4 + - - +
294E ASN* 3.9 1.0 - - - +
295E LYS* 3.0 31.9 + - - +
307E TYR* 3.5 29.4 + - + +
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Residues in contact with ALA 292 (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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19E GLY* 3.7 24.9 - - - +
22E GLU* 4.8 9.9 - - + -
23E VAL* 3.9 8.3 - - + -
288E GLU 3.3 11.0 + - - +
289E GLY* 3.1 12.3 + - - +
291E GLU* 1.3 80.1 - - - +
293E VAL* 1.3 63.4 + - - +
295E LYS* 3.6 5.5 + - - +
296E ASP 3.5 11.6 + - - -
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Residues in contact with VAL 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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11E ILE* 5.8 5.2 - - + -
15E LYS* 6.2 0.2 - - + -
16E GLY* 3.6 24.6 - - - +
19E GLY* 4.1 6.7 - - - -
20E LEU* 4.0 24.5 - - + -
23E VAL* 4.2 2.0 - - + -
284E LEU* 3.8 23.6 - - + -
289E GLY 3.6 12.8 - - - +
290E LEU* 3.2 5.3 + - - +
292E ALA* 1.3 73.4 - - - +
294E ASN* 1.3 66.9 + - - +
296E ASP* 3.0 15.9 + - - +
297E LYS 3.2 12.3 + - - +
299E LEU* 3.7 28.9 - - + -
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Residues in contact with ASN 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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290E LEU 2.7 21.6 + - - +
291E GLU 3.9 2.9 - - - +
293E VAL* 1.3 74.9 - - - +
295E LYS* 1.3 62.6 + - - +
297E LYS 3.6 5.1 + - - -
298E PRO* 3.3 31.9 - - - +
299E LEU* 3.1 35.3 + - + +
300E GLY 4.3 6.8 + - - +
307E TYR* 3.7 16.8 + - + +
311E LEU* 3.6 28.1 - - - +
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Residues in contact with LYS 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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233E SER* 4.5 2.6 + - - -
291E GLU 3.0 19.1 + - - +
292E ALA* 3.8 6.3 - - - +
293E VAL 3.2 0.4 - - - -
294E ASN* 1.3 74.8 - - - +
296E ASP* 1.3 66.3 + - - +
298E PRO* 5.6 0.3 - - - +
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Residues in contact with ASP 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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15E LYS 4.8 0.4 - - - +
16E GLY* 3.2 13.8 - - - -
17E TYR 3.5 0.5 + - - -
18E ASN* 3.1 30.0 + - - +
19E GLY* 3.0 34.2 + - - +
233E SER* 2.6 28.3 + - - -
292E ALA 3.5 3.0 + - - +
293E VAL 3.0 10.1 + - - +
295E LYS* 1.3 79.7 - - - +
297E LYS* 1.3 56.6 + - - +
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Residues in contact with LYS 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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14E ASP 4.1 9.9 - - - +
15E LYS* 4.0 7.6 - - - +
16E GLY* 3.8 27.6 + - - +
230E TRP* 4.1 10.1 - - - +
233E SER* 4.0 4.9 - - - -
293E VAL 3.2 10.7 + - - +
294E ASN* 3.5 2.5 - - - -
296E ASP* 1.3 84.0 - - - +
298E PRO* 1.3 76.2 - - + +
299E LEU* 3.6 5.5 + - - +
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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