Contacts of the helix formed by residues 289 - 296 (chain E) in PDB entry 3LUE
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 ILE 289 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C GLU 4.9 0.7 - - - +
60C SER* 1.2 85.0 - - - +
61C LYS* 2.9 45.1 - - + +
64C ILE* 4.1 0.2 - - + -
166E TYR* 3.8 5.8 - - + -
171E LEU* 3.7 25.6 - - + -
285E CYS* 4.4 6.1 - - + -
286E ASP* 2.8 29.8 + - + +
288E ASP* 1.4 68.5 - - - +
290E ARG* 1.3 54.6 + - - +
291E LYS 3.2 2.9 - - - -
292E ASP* 2.6 37.4 + - + +
293E LEU* 3.0 17.6 + - + +
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Residues in contact with ARG 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C THR* 2.6 39.4 + - - -
202C THR* 1.5 55.9 + - + +
205C GLU* 3.4 15.5 + - - +
244C ASP* 5.6 7.4 - - + +
268D GLY 5.8 0.8 + - - -
270D GLU* 4.8 1.8 + - - -
282E ILE* 3.3 31.3 + - + +
283E MET* 2.8 43.5 + - - +
284E LYS 4.6 0.2 - - - -
285E CYS* 2.8 14.1 + - + -
286E ASP 3.5 0.8 + - - -
287E VAL 3.9 4.0 + - - +
288E ASP 3.7 0.6 - - - -
289E ILE* 1.3 75.1 - - - +
291E LYS* 1.3 65.6 + - - +
293E LEU* 2.9 12.6 + - - +
294E TYR* 2.9 35.4 + - + -
325E MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ALA* 3.0 19.5 - - + +
205C GLU* 4.0 5.0 + - - +
208C ILE* 5.0 3.6 - - - -
243C PRO* 3.4 44.4 - - + +
287E VAL 2.5 30.9 + - - -
288E ASP* 3.5 19.1 - - - +
289E ILE* 4.5 0.2 - - - -
290E ARG* 1.3 83.1 - - - +
292E ASP* 1.3 71.0 + - - +
294E TYR* 3.9 7.8 + - - +
295E ALA* 3.5 19.8 + - - +
325E MET* 4.8 4.7 - - - -
326E LYS 5.2 1.2 - - - +
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Residues in contact with ASP 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 4.7 15.0 - - - +
60C SER* 4.6 1.2 - - - -
149E THR* 4.4 24.6 - - + +
150E GLY* 5.0 1.1 - - - -
288E ASP 4.1 5.9 - - - +
289E ILE* 2.6 32.2 + - + +
291E LYS* 1.3 79.4 - - - +
293E LEU* 1.3 63.5 + - + +
295E ALA* 3.3 2.7 + - - +
296E ASN* 2.8 37.6 + - - +
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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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61C LYS* 5.4 0.4 - - - -
149E THR* 5.1 4.0 - - + -
150E GLY* 3.0 37.7 - - - +
151E ILE* 3.4 10.8 - - + +
164E PRO* 3.8 11.2 - - + -
165E ILE 4.1 8.1 - - - +
171E LEU* 5.9 0.2 - - + -
282E ILE* 4.0 25.4 - - + -
285E CYS* 3.6 37.9 - - + -
289E ILE* 3.0 19.7 + - + +
290E ARG* 2.9 12.4 + - - +
292E ASP* 1.3 76.4 - - - +
294E TYR* 1.4 59.8 + - - +
296E ASN 3.3 12.0 + - - +
297E THR* 3.2 15.4 + - - -
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Residues in contact with TYR 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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244C ASP* 3.7 15.6 + - - -
279E PHE* 3.7 27.0 - + - -
282E ILE* 3.4 43.7 - - + +
283E MET* 4.6 2.1 - - - -
290E ARG* 2.9 38.1 + - + +
291E LYS* 4.3 4.5 - - - +
292E ASP 3.4 0.2 - - - -
293E LEU* 1.4 73.1 - - - +
295E ALA* 1.3 58.2 + - - +
296E ASN 3.2 1.2 + - - -
297E THR* 3.8 7.1 + - - -
317E ILE* 4.0 15.9 - - + -
321E ALA* 3.7 20.2 - - + -
322E PRO* 3.9 2.9 - - + +
325E MET* 4.1 24.0 - - + -
326E LYS 3.9 13.2 - - - +
327E ILE* 3.4 23.1 - - + +
328E LYS 3.1 22.7 + - - +
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Residues in contact with ALA 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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147E ARG* 5.6 0.2 + - - -
291E LYS 3.5 12.3 + - - +
292E ASP* 3.3 5.4 + - - +
294E TYR* 1.3 77.9 - - - +
296E ASN* 1.3 77.5 + - - +
326E LYS* 4.0 24.8 + - + +
328E LYS* 3.1 35.3 - - + +
330E ILE* 3.7 2.3 - - - +
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Residues in contact with ASN 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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44C MET* 3.5 19.5 - - + +
147E ARG* 2.8 35.4 + - - +
149E THR* 3.9 9.0 + - - -
150E GLY* 3.4 0.3 - - - -
151E ILE 2.9 25.1 + - - +
292E ASP* 2.8 31.6 + - - +
293E LEU 3.3 5.6 - - - +
294E TYR 3.2 0.6 - - - -
295E ALA* 1.3 93.2 - - - +
297E THR* 1.3 60.6 + - - +
298E VAL* 3.7 1.8 - - - -
330E ILE* 3.7 7.4 - - - -
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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