Contacts of the helix formed by residues 289 - 296 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G GLU 4.9 0.4 - - - +
60G SER* 1.2 82.5 - - - +
61G LYS* 2.9 46.7 - - + +
166I TYR* 3.8 5.4 - - + -
171I LEU* 3.7 25.6 - - + -
285I CYS* 4.4 6.3 - - + -
286I ASP* 2.8 29.2 + - + +
288I ASP* 1.4 67.6 - - - +
290I ARG* 1.3 55.4 + - - +
291I LYS 3.2 2.9 - - - -
292I ASP* 2.6 37.6 + - + +
293I LEU* 3.0 17.6 + - + +
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Residues in contact with ARG 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201G THR* 2.6 39.2 + - - -
202G THR* 1.5 56.3 + - + +
205G GLU* 3.4 15.3 + - - +
244G ASP* 5.6 7.2 - - + +
270H GLU* 4.8 1.8 + - - -
282I ILE* 3.3 30.6 + - + +
283I MET* 2.8 43.5 + - - +
284I LYS 4.6 0.4 - - - -
285I CYS* 2.8 13.9 + - + -
286I ASP 3.5 0.8 + - - -
287I VAL 3.9 4.5 + - - +
288I ASP 3.7 0.4 - - - -
289I ILE* 1.3 75.3 - - - +
291I LYS* 1.3 64.8 + - - +
293I LEU* 2.9 12.5 + - - +
294I TYR* 2.9 35.4 + - + -
325I MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G ALA* 3.0 19.1 - - + +
205G GLU* 4.0 5.2 + - - +
208G ILE* 5.0 3.6 - - - -
243G PRO* 3.4 44.4 - - + +
244G ASP 5.7 0.2 - - - +
287I VAL 2.5 30.9 + - - -
288I ASP* 3.5 19.4 - - - +
289I ILE 3.0 0.4 + - - -
290I ARG* 1.3 84.1 - - - +
292I ASP* 1.3 71.2 + - - +
294I TYR* 3.9 8.1 + - - +
295I ALA* 3.5 19.8 + - - +
325I MET* 4.8 4.7 - - - -
326I LYS 5.2 1.2 - - - +
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Residues in contact with ASP 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G GLU* 4.7 15.8 - - - +
60G SER* 4.6 1.4 - - - -
149I THR* 4.4 24.2 - - + +
150I GLY* 5.0 1.1 - - - -
288I ASP 4.1 5.5 - - - +
289I ILE* 2.6 32.3 + - - +
291I LYS* 1.3 78.7 - - - +
293I LEU* 1.3 62.1 + - - +
295I ALA* 3.3 2.7 + - - +
296I ASN* 2.8 38.0 + - - +
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Residues in contact with LEU 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G LYS* 5.4 0.4 - - - -
149I THR* 5.1 4.7 - - + -
150I GLY* 3.0 37.5 - - - +
151I ILE* 3.4 10.6 - - + +
164I PRO* 3.8 11.9 - - + -
165I ILE 4.1 8.1 - - - +
171I LEU* 5.9 0.2 - - + -
282I ILE* 4.0 24.7 - - + -
285I CYS* 3.6 38.1 - - + -
289I ILE* 3.0 18.8 + - + +
290I ARG* 2.9 13.1 + - - +
292I ASP* 1.3 74.7 - - - +
294I TYR* 1.4 59.5 + - - +
296I ASN 3.3 11.8 + - - +
297I THR* 3.2 15.1 + - - -
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Residues in contact with TYR 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ASP* 3.7 15.6 + - - -
279I PHE* 3.7 26.8 - + - -
282I ILE* 3.4 42.0 - - + +
283I MET* 4.6 2.1 - - - -
290I ARG* 2.9 38.3 + - + +
291I LYS* 4.3 4.5 - - - +
293I LEU* 1.4 72.7 - - - +
295I ALA* 1.3 57.8 + - - +
296I ASN 3.2 1.2 + - - -
297I THR* 3.8 7.6 + - - -
317I ILE* 4.0 16.2 - - + -
321I ALA* 3.7 20.9 - - + -
322I PRO* 3.9 2.7 - - + +
325I MET* 4.1 24.0 - - + -
326I LYS 3.9 13.7 - - - +
327I ILE* 3.4 23.5 - - + +
328I LYS 3.1 22.3 + - - +
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Residues in contact with ALA 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I ARG* 5.6 0.2 + - - -
291I LYS 3.5 11.6 + - - +
292I ASP* 3.3 5.2 + - - +
294I TYR* 1.3 77.9 - - - +
296I ASN* 1.3 77.6 + - - +
326I LYS* 4.0 25.1 + - + +
328I LYS* 3.1 35.6 - - + +
330I ILE* 3.7 2.1 - - - +
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Residues in contact with ASN 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G MET* 3.5 20.0 - - + +
147I ARG* 2.8 35.3 + - - +
149I THR* 3.9 8.8 + - - -
150I GLY* 3.4 0.5 - - - -
151I ILE 2.9 25.3 + - - +
292I ASP* 2.8 32.1 + - - +
293I LEU 3.3 5.2 - - - +
294I TYR 3.2 0.6 - - - -
295I ALA* 1.3 92.8 - - - +
297I THR* 1.3 60.5 + - - +
298I VAL* 3.7 2.0 - - - -
330I 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
------------------------------------------------------------
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