Contacts of the helix formed by residues 273 - 283 (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 GLY 273 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178E LEU* 4.9 0.2 - - - -
261E LEU 3.1 14.6 - - - -
262E PHE 3.4 18.6 + - - -
264E PRO* 3.7 8.4 - - - +
272E CYS* 1.3 76.8 - - - +
274E ILE* 1.3 61.1 + - - -
275E HIS* 2.8 16.7 + - - -
276E GLU* 2.9 16.6 + - - +
277E THR* 3.3 11.2 + - - -
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Residues in contact with ILE 274 (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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153E MET* 3.5 29.8 - - + +
155E SER* 5.7 0.4 - - - +
160E THR* 3.4 24.0 - - + +
162E THR* 5.6 0.7 - - + -
178E LEU* 3.3 31.0 - - + -
180E LEU 5.4 0.2 - - - +
261E LEU* 2.9 32.2 + - + +
262E PHE* 3.6 31.9 - - + -
273E GLY* 1.3 69.7 - - - -
275E HIS* 1.3 61.5 + - - +
277E THR* 4.0 6.8 - - + -
278E THR* 3.1 28.1 + - - -
309E ILE* 5.5 3.1 - - + -
313E MET* 4.0 14.7 - - + +
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Residues in contact with HIS 275 (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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262E PHE* 3.1 54.4 + + + -
263E GLN* 5.9 0.2 - - + -
273E GLY* 2.8 6.8 + - - -
274E ILE* 1.3 75.4 - - - +
276E GLU* 1.3 89.3 + - + +
278E THR* 4.1 1.0 + - - -
279E PHE* 3.6 19.1 + - - +
312E ARG* 5.6 0.4 - - - -
313E MET* 4.1 12.3 - - - -
316E GLU* 3.7 42.0 - - + -
317E ILE* 4.1 9.1 - - + +
320E LEU* 3.9 16.3 - - + +
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Residues in contact with GLU 276 (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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272E CYS* 3.9 29.8 - - + +
273E GLY 3.5 8.2 + - - +
275E HIS* 1.3 107.2 + - + +
277E THR* 1.3 59.6 + - - +
279E PHE* 3.4 6.3 + - - +
280E ASN* 2.9 40.5 + - - +
320E LEU* 3.5 25.0 - - + +
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Residues in contact with THR 277 (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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160E THR* 6.2 0.7 - - + -
161E HIS* 6.0 0.4 - - - -
162E THR* 3.4 25.4 - - + +
176E LEU* 3.7 22.4 - - + +
177E ARG 5.3 1.3 - - - +
178E LEU* 3.8 28.7 - - + +
272E CYS* 3.9 12.1 - - - +
273E GLY 3.5 12.4 + - - -
274E ILE* 4.1 6.3 - - + -
276E GLU* 1.3 72.9 - - - +
278E THR* 1.4 66.1 + - - +
280E ASN* 2.9 17.6 + - - +
281E SER* 3.1 14.4 + - - -
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Residues in contact with THR 278 (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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151E ILE* 4.0 14.0 - - + +
153E MET* 3.5 12.2 - - + +
162E THR* 3.4 23.4 - - - +
274E ILE 3.1 16.8 + - - -
275E HIS 4.1 5.4 - - - -
277E THR* 1.4 73.3 - - - +
279E PHE* 1.3 62.2 + - - +
281E SER* 3.1 10.4 + - - -
282E ILE* 3.2 26.8 + - + +
297E THR* 3.9 19.5 - - + +
313E MET* 3.9 2.5 - - + +
317E ILE* 3.6 26.5 - - + -
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Residues in contact with PHE 279 (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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275E HIS 3.6 12.6 + - - +
276E GLU* 3.4 9.6 + - - +
277E THR 3.2 0.8 - - - -
278E THR* 1.3 80.0 - - - +
280E ASN* 1.3 76.0 + - - +
282E ILE* 3.8 9.4 - - - +
283E MET* 3.0 52.3 + - + +
294E TYR* 3.7 27.6 - + + -
317E ILE* 5.4 6.4 - - + +
320E LEU* 3.4 57.9 - - + -
321E ALA* 4.4 1.6 - - + -
322E PRO* 5.1 2.5 - - + -
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Residues in contact with ASN 280 (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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176E LEU* 3.7 17.4 - - + +
272E CYS* 4.7 13.7 - - - -
276E GLU* 2.9 33.2 + - - +
277E THR* 2.9 3.4 + - - -
279E PHE* 1.3 92.2 - - - +
281E SER* 1.3 64.3 + - - +
283E MET* 3.8 9.9 + - - +
284E LYS* 3.6 21.5 + - - +
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Residues in contact with SER 281 (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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151E ILE* 3.7 22.7 - - - -
162E THR* 3.0 24.0 + - - -
164E PRO* 3.8 5.2 - - - -
174E ALA* 2.7 29.0 + - - +
176E LEU* 3.1 10.7 - - - +
277E THR 3.1 5.1 + - - -
278E THR 3.7 2.5 - - - -
280E ASN* 1.3 73.1 - - - +
282E ILE* 1.3 65.6 + - - +
284E LYS* 2.8 19.9 + - - +
285E CYS* 3.4 12.8 - - - -
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Residues in contact with ILE 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ILE* 4.3 14.3 - - + +
278E THR* 3.2 26.6 + - + +
279E PHE* 3.8 5.2 - - - +
281E SER* 1.3 77.6 - - - +
283E MET* 1.3 67.9 + - + +
284E LYS 3.2 0.7 + - - -
285E CYS* 3.3 15.6 + - - +
290E ARG* 3.3 25.8 + - + +
293E LEU* 4.0 22.0 - - + +
294E TYR* 3.4 68.0 - - + +
297E THR* 5.1 1.6 - - - +
317E ILE* 5.8 1.3 - - + -
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Residues in contact with MET 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C SER* 6.1 3.4 - - - -
201C THR* 4.2 9.3 + - - +
244C ASP* 4.5 15.7 - - - +
268D GLY 5.1 2.4 - - - +
279E PHE* 3.0 47.4 + - + +
280E ASN* 4.0 8.5 - - - +
281E SER 3.1 1.8 + - - -
282E ILE* 1.3 79.8 - - + +
284E LYS* 1.3 57.3 + - + +
285E CYS 3.4 0.4 - - - -
290E ARG* 2.8 44.3 + - - +
294E TYR* 4.6 5.6 - - - -
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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