Contacts of the helix formed by residues 273 - 283 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178H LEU* 4.4 0.7 - - - -
261H LEU 3.1 14.6 - - - -
262H PHE 3.4 18.5 + - - -
264H PRO* 3.7 8.6 - - - +
272H CYS* 1.3 77.8 - - - +
274H ILE* 1.3 61.3 + - - -
275H HIS* 2.8 16.7 + - - -
276H GLU* 2.9 16.7 + - - +
277H THR* 3.3 10.6 + - - -
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Residues in contact with ILE 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H MET* 3.5 31.1 - - + +
155H SER* 5.7 0.2 - - - +
160H THR* 3.4 25.4 - - + +
162H THR* 4.9 0.6 - - + +
178H LEU* 3.3 29.4 - - + -
180H LEU* 5.4 0.4 - - + +
261H LEU* 2.9 31.6 + - + +
262H PHE* 3.6 31.6 - - + -
273H GLY* 1.3 70.0 - - - -
275H HIS* 1.3 60.9 + - - +
276H GLU 3.4 0.2 - - - -
277H THR* 4.0 7.2 - - + -
278H THR* 3.1 28.1 + - - -
309H ILE* 5.5 3.4 - - + -
313H MET* 4.0 15.2 - - + +
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Residues in contact with HIS 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H PHE* 3.1 55.1 + + + -
263H GLN* 5.9 0.4 - - + -
273H GLY* 2.8 7.6 + - - -
274H ILE* 1.3 75.6 - - - +
276H GLU* 1.3 90.0 + - + +
278H THR* 4.1 0.7 + - - -
279H PHE* 3.6 18.9 + - - +
312H ARG* 5.6 0.4 - - - -
313H MET* 4.1 12.1 - - - -
316H GLU* 3.7 42.6 + - + -
317H ILE* 4.1 9.5 - - + +
320H LEU* 3.9 16.4 - - + +
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Residues in contact with GLU 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H CYS* 3.9 29.1 - - + +
273H GLY 2.9 8.3 + - - +
275H HIS* 1.3 106.5 + - + +
277H THR* 1.3 59.6 + - - +
279H PHE* 3.4 6.4 + - - +
280H ASN* 2.9 41.4 + - - +
320H LEU* 3.5 25.3 - - + +
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Residues in contact with THR 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H THR* 6.2 0.4 - - + -
161H HIS* 6.0 0.4 - - - -
162H THR* 3.4 24.5 - - + +
176H LEU* 3.7 23.0 - - + +
177H ARG 5.6 0.9 - - - -
178H LEU* 3.8 29.4 - - + +
272H CYS* 3.9 12.1 - - - +
273H GLY 3.3 12.5 + - - -
274H ILE* 4.1 7.2 - - + -
276H GLU* 1.3 73.4 - - - +
278H THR* 1.4 64.5 + - - +
280H ASN* 2.9 16.9 + - - +
281H SER* 3.1 14.7 + - - -
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Residues in contact with THR 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H ILE* 4.0 14.0 - - + +
153H MET* 3.5 11.9 - - + +
162H THR* 3.4 24.1 - - - +
274H ILE 3.1 17.2 + - - -
275H HIS 4.1 4.9 - - - -
277H THR* 1.4 73.6 - - - +
279H PHE* 1.3 63.6 + - - +
281H SER* 3.1 10.6 + - - -
282H ILE* 3.2 25.8 + - + +
297H THR* 3.9 19.3 - - + +
313H MET* 3.9 2.6 - - + +
317H ILE* 3.6 26.5 - - + -
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Residues in contact with PHE 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244F ASP* 5.4 0.2 - - - -
275H HIS 3.6 13.2 + - - +
276H GLU* 3.4 10.2 + - - +
277H THR 3.2 0.2 - - - -
278H THR* 1.3 79.2 - - - +
280H ASN* 1.3 78.0 + - - +
282H ILE* 3.8 8.9 - - - +
283H MET* 3.0 52.5 + - + +
294H TYR* 3.7 27.8 - + + -
317H ILE* 5.4 6.5 - - + +
320H LEU* 3.4 57.2 - - + -
321H ALA* 4.4 1.1 - - - -
322H PRO* 5.1 2.2 - - + -
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Residues in contact with ASN 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H LEU* 3.7 17.6 - - + +
272H CYS* 4.7 13.2 - - - -
276H GLU* 2.9 34.0 + - - +
277H THR* 2.9 3.5 + - - +
279H PHE* 1.3 93.0 - - - +
281H SER* 1.3 63.2 + - - +
283H MET* 3.8 10.0 + - - +
284H LYS* 3.6 22.9 + - + +
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Residues in contact with SER 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H ILE* 3.7 23.3 - - - -
162H THR* 3.0 23.6 + - - -
164H PRO* 3.8 5.2 - - - -
174H ALA* 2.7 29.4 + - - +
176H LEU* 3.1 10.6 - - - +
277H THR 3.1 4.9 + - - -
278H THR 3.1 2.0 + - - -
280H ASN* 1.3 73.4 - - - +
282H ILE* 1.3 67.2 + - - +
284H LYS* 2.8 20.5 + - - +
285H CYS* 3.4 12.0 - - - -
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Residues in contact with ILE 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H ILE* 4.3 14.1 - - + +
278H THR* 3.2 26.0 + - + +
279H PHE* 3.8 5.8 - - - +
281H SER* 1.3 77.3 - - - +
283H MET* 1.3 67.4 + - + +
284H LYS 3.2 0.9 + - - -
285H CYS* 3.3 16.4 + - - +
290H ARG* 3.3 25.1 + - + +
293H LEU* 4.0 22.7 - - + +
294H TYR* 3.4 69.1 - - + +
297H THR* 5.1 1.1 - - - +
317H ILE* 5.8 0.9 - - + -
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Residues in contact with MET 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F SER* 6.1 3.4 - - - -
201F THR* 4.2 9.0 + - - +
244F ASP* 4.5 15.7 - - - +
268G GLY 5.1 2.6 - - - +
279H PHE* 3.0 47.1 + - + +
280H ASN* 4.0 7.9 - - - +
281H SER 3.1 1.2 + - - -
282H ILE* 1.3 80.3 - - + +
284H LYS* 1.3 57.4 + - + +
285H CYS 3.4 0.4 - - - -
290H ARG* 2.8 44.8 + - - +
294H 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