Contacts of the helix formed by residues 273 - 283 (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 GLY 273 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178G LEU* 4.9 0.2 - - - -
261G LEU 3.1 15.0 - - - -
262G PHE 3.4 19.0 + - - -
264G PRO* 3.7 9.3 - - - +
272G CYS* 1.3 76.6 - - - +
274G ILE* 1.3 60.4 + - - -
275G HIS* 2.8 15.8 + - - -
276G GLU* 2.9 17.0 + - - +
277G THR* 3.3 10.7 + - - -
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Residues in contact with ILE 274 (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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153G MET* 3.5 30.3 - - + -
155G SER* 5.7 0.2 - - - +
160G THR* 3.4 25.6 - - + +
162G THR* 4.9 0.6 - - + +
178G LEU* 3.3 29.8 - - + -
180G LEU* 5.4 0.4 - - + +
261G LEU* 2.9 30.8 + - + +
262G PHE* 3.6 32.3 - - + -
273G GLY* 1.3 71.4 - - - -
275G HIS* 1.3 59.1 + - - +
276G GLU 3.4 0.2 - - - -
277G THR* 4.0 7.0 - - + -
278G THR* 3.1 27.5 + - - -
309G ILE* 5.5 3.1 - - + -
313G MET* 4.0 15.2 - - + +
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Residues in contact with HIS 275 (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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262G PHE* 3.1 55.7 + + + -
263G GLN* 5.9 0.2 - - + -
273G GLY* 2.8 7.0 + - - -
274G ILE* 1.3 75.4 - - - +
276G GLU* 1.3 90.8 + - + +
278G THR* 4.1 0.7 + - - -
279G PHE* 3.6 18.5 + - - +
312G ARG* 5.6 0.2 - - - -
313G MET* 4.1 12.1 - - - -
316G GLU* 3.7 43.0 + - + -
317G ILE* 4.1 9.6 - - + +
320G LEU* 3.9 16.4 - - + +
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Residues in contact with GLU 276 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G CYS* 3.9 30.2 - - + +
273G GLY 2.9 7.4 + - - +
275G HIS* 1.3 107.4 + - + +
277G THR* 1.3 58.6 + - - +
278G THR 3.5 0.2 - - - -
279G PHE* 3.4 6.4 + - - +
280G ASN* 2.9 41.4 + - - +
320G LEU* 3.5 25.2 - - + +
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Residues in contact with THR 277 (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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160G THR* 6.2 0.9 - - + -
161G HIS* 6.0 0.4 - - - -
162G THR* 3.4 24.5 - - + +
176G LEU* 3.7 23.6 - - + +
177G ARG 5.6 0.9 - - - -
178G LEU* 3.8 29.5 - - + +
272G CYS* 3.9 12.3 - - - +
273G GLY 3.3 13.7 + - - -
274G ILE* 4.1 5.8 - - + -
276G GLU* 1.3 72.3 - - - +
278G THR* 1.4 64.9 + - - +
280G ASN* 2.9 17.8 + - - +
281G SER* 3.1 14.6 + - - -
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Residues in contact with THR 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ILE* 4.0 14.3 - - + +
153G MET* 3.5 11.3 - - + +
162G THR* 3.4 24.1 - - - +
274G ILE 3.1 17.6 + - - -
275G HIS 4.1 4.9 - - - -
277G THR* 1.4 74.4 - - - +
279G PHE* 1.3 62.8 + - - +
281G SER* 3.1 10.9 + - - -
282G ILE* 3.2 25.6 + - + +
297G THR* 3.9 19.5 - - + +
313G MET* 3.9 2.5 - - + +
317G ILE* 3.6 26.9 - - + -
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Residues in contact with PHE 279 (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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275G HIS 3.6 13.4 + - - +
276G GLU* 3.4 10.0 + - - +
277G THR 3.2 0.6 - - - -
278G THR* 1.3 78.1 - - - +
280G ASN* 1.3 77.1 + - - +
282G ILE* 3.9 9.0 - - - +
283G MET* 3.0 54.0 + - + +
294G TYR* 3.7 27.8 - + + -
317G ILE* 5.4 6.0 - - + +
320G LEU* 3.4 56.3 - - + -
321G ALA* 4.4 2.0 - - - -
322G PRO* 5.1 2.5 - - + -
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Residues in contact with ASN 280 (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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176G LEU* 3.7 16.7 - - + +
272G CYS* 4.7 13.7 - - - -
276G GLU* 2.9 32.6 + - - +
277G THR* 2.9 3.3 + - - +
279G PHE* 1.3 92.8 - - - +
281G SER* 1.3 64.0 + - - +
283G MET* 3.8 9.6 + - - +
284G LYS* 3.6 21.6 + - + +
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Residues in contact with SER 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ILE* 3.7 22.9 - - - -
162G THR* 3.0 23.6 + - - -
164G PRO* 3.8 5.4 - - - -
174G ALA* 2.7 28.9 + - - +
176G LEU* 3.1 10.5 - - - +
277G THR 3.1 3.8 + - - -
278G THR 3.1 2.7 + - - -
280G ASN* 1.3 74.2 - - - +
282G ILE* 1.3 66.1 + - - +
284G LYS* 2.8 20.4 + - - +
285G CYS* 3.4 12.9 - - - -
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Residues in contact with ILE 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G ILE* 4.3 14.1 - - + +
278G THR* 3.2 25.5 + - + +
279G PHE* 3.9 5.2 - - - +
281G SER* 1.3 76.9 - - - +
283G MET* 1.3 67.3 + - + +
284G LYS 3.2 1.2 + - - -
285G CYS* 3.3 16.4 + - - +
290G ARG* 3.3 26.7 + - + +
293G LEU* 4.0 22.9 - - + +
294G TYR* 3.4 68.2 - - + +
297G THR* 5.1 1.3 - - - +
317G ILE* 5.8 1.1 - - + -
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Residues in contact with MET 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E SER* 6.1 3.4 - - - -
201E THR* 4.2 8.2 + - - +
244E ASP* 4.5 15.9 - - - +
268F GLY 5.1 2.3 - - - +
279G PHE* 3.0 46.5 + - + +
280G ASN* 4.0 7.9 - - - +
281G SER 3.1 1.6 + - - -
282G ILE* 1.3 81.4 - - + +
284G LYS* 1.3 57.6 - - + +
285G CYS 3.4 0.4 - - - -
290G ARG* 2.8 44.9 + - - +
294G TYR* 4.6 5.4 - - - -
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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