Contacts of the helix formed by residues 273 - 283 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D LEU* 4.4 0.7 - - - -
261D LEU 3.1 14.4 - - - -
262D PHE 3.4 17.9 + - - -
264D PRO* 3.7 8.9 - - - +
272D CYS* 1.3 77.6 - - - +
274D ILE* 1.3 61.2 + - - -
275D HIS* 2.8 16.3 + - - -
276D GLU* 2.9 17.0 + - - +
277D THR* 3.3 10.4 + - - -
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D MET* 3.5 30.9 - - + +
155D SER* 5.7 0.2 - - - +
160D THR* 3.4 25.6 - - + +
162D THR* 4.9 0.4 - - + +
178D LEU* 3.3 29.4 - - + -
180D LEU 5.4 0.2 - - - +
261D LEU* 2.9 33.2 + - + +
262D PHE* 3.6 31.6 - - + -
273D GLY* 1.3 70.4 - - - -
275D HIS* 1.3 61.7 + - - +
276D GLU 3.4 0.2 - - - -
277D THR* 3.8 7.4 + - + -
278D THR* 3.1 27.7 + - - -
309D ILE* 5.5 3.4 - - + -
313D MET* 4.0 15.7 - - + +
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Residues in contact with HIS 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D PHE* 3.1 54.8 + + + -
263D GLN* 5.9 0.4 - - + -
273D GLY* 2.8 7.0 + - - -
274D ILE* 1.3 76.0 - - - +
276D GLU* 1.3 89.6 + - + +
278D THR* 4.1 0.7 + - - -
279D PHE* 3.6 19.1 + - - +
312D ARG* 5.6 0.7 - - - -
313D MET* 4.1 12.6 - - - -
316D GLU* 3.7 43.3 + - + -
317D ILE* 4.1 9.8 - - + +
320D LEU* 3.9 16.0 - - + +
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D CYS* 3.9 30.0 - - + +
273D GLY 2.9 8.0 + - - +
275D HIS* 1.3 107.0 + - + +
277D THR* 1.3 60.3 + - - +
279D PHE* 3.4 6.2 + - - +
280D ASN* 2.9 40.7 + - - +
320D LEU* 3.5 25.6 - - + +
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Residues in contact with THR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D THR* 6.2 0.7 - - + -
161D HIS* 6.0 0.4 - - - -
162D THR* 3.4 24.2 - - + +
176D LEU* 3.7 22.6 - - + +
177D ARG 5.6 0.9 - - - -
178D LEU* 3.8 29.3 - - + +
272D CYS* 3.9 12.1 - - - +
273D GLY 3.3 13.1 + - - -
274D ILE* 4.1 6.7 - - + -
276D GLU* 1.3 72.3 - - - +
278D THR* 1.4 65.3 + - - +
280D ASN* 2.9 17.8 + - - +
281D SER* 3.1 14.2 + - - -
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Residues in contact with THR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ILE* 4.0 14.2 - - + +
153D MET* 3.5 11.5 - - + +
162D THR* 3.4 24.2 - - - +
274D ILE 3.1 17.8 + - - -
275D HIS 4.1 5.4 - - - -
276D GLU 3.5 0.2 - - - -
277D THR* 1.4 73.5 - - - +
279D PHE* 1.3 63.2 + - - +
281D SER* 3.1 10.0 + - - -
282D ILE* 3.2 25.7 + - + +
297D THR* 3.9 19.1 - - + +
313D MET* 3.9 2.5 - - + +
317D ILE* 3.6 26.9 - - + -
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Residues in contact with PHE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D HIS 3.6 13.6 + - - +
276D GLU* 3.4 9.5 + - - +
278D THR* 1.3 77.9 - - - +
280D ASN* 1.3 77.4 + - - +
281D SER 3.3 0.2 - - - -
282D ILE* 3.8 9.2 - - - +
283D MET* 3.0 52.4 + - + +
294D TYR* 3.7 27.1 - + + -
317D ILE* 5.4 6.2 - - + +
320D LEU* 3.4 57.9 - - + -
321D ALA* 4.4 1.3 - - - -
322D PRO* 5.1 2.7 - - + -
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Residues in contact with ASN 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 3.7 18.3 - - + +
272D CYS* 4.7 13.2 - - - -
276D GLU* 2.9 33.5 + - - +
277D THR* 2.9 3.1 + - - -
279D PHE* 1.3 93.0 - - - +
281D SER* 1.3 62.4 + - - +
283D MET* 3.8 9.9 + - - +
284D LYS* 3.6 22.8 + - + +
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ILE* 3.7 22.4 - - - -
162D THR* 3.0 23.4 + - - -
164D PRO* 3.8 5.4 - - - -
174D ALA* 2.7 29.7 + - - +
176D LEU* 3.1 10.2 - - - +
277D THR 3.1 4.7 + - - -
278D THR 3.1 2.4 + - - -
280D ASN* 1.3 73.6 - - - +
282D ILE* 1.3 65.8 + - - +
284D LYS* 2.8 20.2 + - - +
285D CYS* 3.4 12.8 - - - -
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Residues in contact with ILE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 4.3 14.0 - - + +
278D THR* 3.2 25.8 + - + +
279D PHE* 3.8 5.2 - - - +
281D SER* 1.3 77.4 - - - +
283D MET* 1.3 66.8 + - + +
284D LYS 3.2 1.2 + - - -
285D CYS* 3.3 15.9 + - - +
290D ARG* 3.3 25.3 + - + +
293D LEU* 4.0 22.7 - - + +
294D TYR* 3.4 69.3 - - + +
297D THR* 5.1 1.6 - - - +
317D ILE* 5.8 0.9 - - + -
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Residues in contact with MET 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B SER* 6.1 3.4 - - - -
201B THR* 4.2 8.8 + - - +
244B ASP* 4.5 16.4 - - - +
268C GLY 5.1 2.6 - - - +
279D PHE* 3.0 47.4 + - + +
280D ASN* 4.0 7.9 - - - +
281D SER 3.1 1.2 + - - -
282D ILE* 1.3 80.7 - - + +
284D LYS* 1.3 57.5 + - + +
285D CYS 3.4 0.2 - - - -
290D ARG* 2.8 44.6 + - - +
294D TYR* 4.6 5.2 - - - -
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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