Contacts of the helix formed by residues 289 - 296 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E GLU 4.9 0.7 - - - +
60E SER* 1.2 84.0 - - - +
61E LYS* 2.9 45.8 - - + +
64E ILE* 4.1 0.2 - - + -
166G TYR* 3.8 4.5 - - + -
171G LEU* 3.7 26.2 - - + -
285G CYS* 4.4 6.5 - - + -
286G ASP* 2.8 28.7 + - + +
288G ASP* 1.4 68.5 - - - +
290G ARG* 1.3 55.4 + - - +
291G LYS 3.2 2.7 - - - -
292G ASP* 2.6 37.9 + - + +
293G LEU* 3.0 16.4 + - + +
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Residues in contact with ARG 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201E THR* 2.6 39.4 + - - -
202E THR* 1.5 55.7 + - + +
205E GLU* 3.4 15.3 + - - +
244E ASP* 5.6 6.7 - - + -
270F GLU* 4.8 2.0 + - - -
282G ILE* 3.3 31.3 + - + +
283G MET* 2.8 43.2 + - - +
284G LYS 4.6 0.2 - - - -
285G CYS* 2.8 14.1 + - + +
286G ASP 3.5 1.2 + - - +
287G VAL 4.0 4.0 - - - +
288G ASP 3.7 1.0 - - - -
289G ILE* 1.3 75.3 - - - +
291G LYS* 1.3 65.9 + - - +
293G LEU* 2.9 12.1 + - - +
294G TYR* 2.9 34.3 + - + -
325G MET* 6.2 0.2 - - - -
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Residues in contact with LYS 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E ALA* 3.0 20.7 - - + +
205E GLU* 4.0 5.2 + - - +
208E ILE* 5.0 3.8 - - - -
243E PRO* 3.4 44.6 - - + +
287G VAL 2.5 31.3 + - - -
288G ASP* 3.5 19.4 - - - +
289G ILE 3.0 0.4 + - - -
290G ARG* 1.3 81.2 - - - +
292G ASP* 1.3 70.7 + - - +
294G TYR* 3.9 8.3 + - - +
295G ALA* 3.5 19.8 + - - +
325G MET* 4.8 4.5 - - - -
326G LYS 5.2 1.0 - - - +
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Residues in contact with ASP 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLU* 4.7 14.7 - - - +
60E SER* 4.6 1.4 - - - -
149G THR* 4.4 25.7 - - + +
150G GLY* 5.0 1.3 - - - -
288G ASP 4.1 5.4 - - - +
289G ILE* 2.6 31.8 + - - +
291G LYS* 1.3 79.5 - - - +
293G LEU* 1.3 62.7 + - + +
295G ALA* 3.3 2.3 + - - +
296G ASN* 2.8 39.0 + - - +
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Residues in contact with LEU 293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LYS* 5.2 0.2 - - - +
149G THR* 5.1 4.9 - - + -
150G GLY* 3.0 38.8 - - - +
151G ILE* 3.4 9.6 - - + +
164G PRO* 3.8 12.1 - - + -
165G ILE 4.1 7.0 - - - +
282G ILE* 4.0 25.1 - - + -
285G CYS* 3.6 38.4 - - + -
289G ILE* 3.6 18.8 - - + +
290G ARG* 2.9 12.6 + - - +
292G ASP* 1.3 76.8 - - - +
294G TYR* 1.4 59.8 + - - +
296G ASN 3.3 12.1 + - - +
297G THR* 3.2 15.2 + - - -
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Residues in contact with TYR 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ASP* 3.7 15.6 + - - -
279G PHE* 3.7 26.7 - + - -
282G ILE* 3.4 42.7 - - + +
283G MET* 4.6 1.7 - - - -
290G ARG* 2.9 39.2 + - + +
291G LYS* 4.3 4.0 - - - +
293G LEU* 1.4 73.1 - - - +
295G ALA* 1.3 57.0 + - - +
296G ASN 3.2 1.0 + - - -
297G THR* 3.8 7.1 + - - -
317G ILE* 4.0 16.2 - - + -
321G ALA* 3.7 21.5 - - + -
322G PRO* 3.9 3.1 - - + +
325G MET* 4.1 23.3 - - + -
326G LYS 3.9 12.6 - - - +
327G ILE* 3.4 23.2 - - + +
328G LYS 3.1 23.0 + - - +
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Residues in contact with ALA 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147G ARG* 5.6 0.2 + - - -
291G LYS 3.5 11.5 + - - +
292G ASP* 3.3 6.2 + - - +
294G TYR* 1.3 77.5 - - - +
296G ASN* 1.3 75.9 + - - +
326G LYS* 4.0 24.4 + - + +
328G LYS* 3.1 37.0 - - - +
330G ILE* 3.7 1.9 - - - +
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Residues in contact with ASN 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E MET* 3.5 19.7 - - + +
147G ARG* 2.8 35.1 + - - +
149G THR* 3.9 9.3 + - - -
150G GLY* 3.4 0.2 - - - -
151G ILE 2.9 25.6 + - - +
292G ASP* 2.8 31.7 + - - +
293G LEU 3.3 5.3 - - - +
294G TYR 3.2 0.2 - - - -
295G ALA* 1.3 93.5 - - - +
297G THR* 1.3 61.0 + - - +
298G VAL* 3.7 1.3 - - - -
330G ILE* 3.7 7.6 - - - -
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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