Contacts of the helix formed by residues 308 - 321 (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 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D VAL* 3.8 16.6 - - - -
221D LEU* 5.7 0.2 - - - +
306D TYR 3.5 0.2 + - - -
307D PRO* 1.4 71.2 - - - +
309D ILE* 1.4 62.4 + - - +
310D ALA 3.4 2.9 + - - -
311D ASP* 3.5 17.5 + - - +
312D ARG* 2.9 26.2 + - - +
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Residues in contact with ILE 309 (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* 5.3 9.4 - - + -
219D VAL* 4.0 15.0 - - + +
261D LEU* 4.4 17.5 - - + -
262D PHE* 4.3 19.1 - - + -
274D ILE* 5.5 1.3 - - + -
299D LEU* 3.8 16.6 - - + -
303D THR 4.1 19.7 - - - +
304D THR* 3.2 29.6 - - + +
306D TYR* 3.1 24.1 + - + +
307D PRO 3.5 1.0 + - - -
308D GLY* 1.4 76.2 - - - +
310D ALA* 1.3 61.8 + - - +
312D ARG* 4.5 0.4 - - - +
313D MET* 2.8 38.6 + - + +
335D ARG* 4.3 4.9 - - - +
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Residues in contact with ALA 310 (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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299D LEU* 4.4 2.9 - - - -
309D ILE* 1.3 82.6 - - + +
311D ASP* 1.3 60.3 + - - +
313D MET* 3.6 2.1 - - - +
314D GLN* 2.9 30.3 + - - +
329D ILE* 3.6 22.7 - - + +
331D ALA* 4.3 19.1 - - + -
335D ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (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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221D LEU* 4.0 20.3 - - + +
308D GLY* 3.5 18.3 + - - +
310D ALA* 1.3 80.3 - - - +
312D ARG* 1.3 58.4 + - - +
314D GLN* 3.5 8.0 + - - +
315D LYS* 2.9 29.1 + - - +
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Residues in contact with ARG 312 (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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219D VAL* 3.9 14.2 - - + +
220D ALA 2.6 37.1 + - - +
221D LEU* 3.7 25.7 + - + +
223D PHE* 4.7 5.4 - - - +
259D GLU* 2.8 28.9 + - - -
262D PHE* 3.5 39.9 - - + +
263D GLN* 4.8 5.1 - - - +
275D HIS* 5.6 0.4 - - - -
308D GLY 2.9 17.9 + - - +
309D ILE* 4.1 1.6 - - - +
311D ASP* 1.3 74.1 - - - +
313D MET* 1.3 64.1 + - - +
315D LYS* 4.0 6.6 - - - +
316D GLU* 2.7 65.8 + - - +
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Residues in contact with MET 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D MET* 3.8 39.7 - - + -
262D PHE* 4.0 14.4 - - + -
274D ILE* 4.0 17.5 - - + +
275D HIS* 4.1 12.6 - - - -
278D THR* 3.9 13.0 - - + +
297D THR* 5.2 0.7 - - + -
299D LEU* 3.9 16.4 - - + -
309D ILE* 2.8 27.6 + - + +
310D ALA* 3.6 5.4 - - - +
312D ARG* 1.3 74.2 - - - +
314D GLN* 1.3 61.7 + - - +
316D GLU* 3.0 4.7 + - - +
317D ILE* 2.9 43.4 + - + +
329D ILE* 4.3 15.5 - - + -
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Residues in contact with GLN 314 (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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310D ALA 2.9 18.6 + - - +
311D ASP* 3.5 8.3 - - - +
313D MET* 1.3 74.6 - - - +
315D LYS* 1.3 63.5 + - - +
317D ILE* 3.0 0.5 + - - +
318D THR* 2.7 52.2 + - - +
327D ILE* 3.0 33.5 + - - +
328D LYS* 4.6 0.2 - - - +
329D ILE* 3.9 24.0 - - + +
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Residues in contact with LYS 315 (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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221D LEU* 2.9 44.8 + - + +
222D ASP* 4.6 14.7 + - - +
311D ASP 2.9 21.4 + - - +
312D ARG* 3.8 6.5 - - - +
314D GLN* 1.3 72.1 - - + +
316D GLU* 1.3 91.1 + - + +
318D THR* 3.7 7.0 - - - -
319D ALA* 3.3 19.9 + - - +
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Residues in contact with GLU 316 (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* 4.7 2.0 - - + -
275D HIS* 3.7 37.5 + - + -
312D ARG* 2.7 59.7 + - + +
313D MET 3.0 5.1 + - - +
315D LYS* 1.3 98.0 + - - +
317D ILE* 1.3 64.8 + - - +
319D ALA* 3.4 16.8 + - - +
320D LEU* 3.2 22.1 + - - +
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Residues in contact with ILE 317 (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* 4.1 16.4 - - - +
278D THR* 3.6 30.3 - - + -
279D PHE* 5.4 5.8 - - + +
282D ILE* 5.8 0.9 - - + -
294D TYR* 4.0 18.4 - - + -
297D THR* 4.2 7.2 - - + +
313D MET* 2.9 36.6 + - - +
314D GLN 3.9 1.8 - - - +
316D GLU* 1.3 76.2 - - - +
318D THR* 1.3 58.8 + - - +
319D ALA 3.2 0.3 + - - -
320D LEU* 3.3 6.4 + - + +
321D ALA* 2.9 28.6 + - - +
327D ILE* 3.6 29.2 - - + -
329D ILE* 4.1 15.3 - - + -
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Residues in contact with THR 318 (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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314D GLN* 2.7 40.9 + - - +
315D LYS* 3.7 8.7 - - - -
317D ILE* 1.3 78.2 - - - +
319D ALA* 1.3 59.9 + - - +
321D ALA* 3.9 10.2 - - - +
327D ILE* 3.6 19.3 - - + +
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Residues in contact with ALA 319 (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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315D LYS 3.3 14.0 + - - +
316D GLU* 3.7 15.5 - - - +
317D ILE 3.2 1.2 - - - -
318D THR* 1.3 77.9 - - - +
320D LEU* 1.3 63.8 + - + +
321D ALA 3.6 2.9 + - - +
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Residues in contact with LEU 320 (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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246B GLN* 6.0 0.2 - - - +
275D HIS* 3.9 38.1 - - + +
276D GLU* 3.5 23.3 - - - +
279D PHE* 3.4 49.1 - - + -
316D GLU 3.2 20.8 + - - +
317D ILE* 3.3 6.2 + - - +
319D ALA* 1.3 77.2 - - + +
321D ALA* 1.3 63.9 + - - +
322D PRO* 3.8 1.6 - - - +
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Residues in contact with ALA 321 (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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244B ASP 3.8 5.8 - - - +
279D PHE* 4.4 0.2 - - - -
294D TYR* 3.7 19.3 - - + -
317D ILE 2.9 17.5 + - - +
318D THR 3.9 10.7 - - - +
319D ALA 3.4 3.0 - - - +
320D LEU* 1.3 79.8 - - - +
322D PRO* 1.4 76.0 - - + +
323D SER* 3.5 3.6 + - - -
325D MET* 4.2 0.7 - - + -
327D ILE* 3.4 24.0 - - + -
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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