Contacts of the helix formed by residues 308 - 321 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B VAL* 3.8 17.0 - - - +
307B PRO* 1.4 69.3 - - - +
309B ILE* 1.4 63.6 + - - +
310B ALA 3.4 2.6 + - - -
311B ASP* 3.5 17.8 + - - +
312B ARG* 2.9 26.0 + - - +
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B MET* 5.3 9.4 - - + -
219B VAL* 4.1 14.6 - - + -
261B LEU* 4.4 17.5 - - + -
262B PHE* 4.3 19.1 - - + -
274B ILE* 5.5 1.1 - - + -
299B LEU* 3.8 16.8 - - + -
303B THR 4.1 20.0 - - - +
304B THR* 3.2 30.1 - - - +
306B TYR* 3.1 23.5 + - + +
307B PRO 3.5 1.0 + - - -
308B GLY* 1.4 75.5 - - - +
310B ALA* 1.3 60.4 + - - +
312B ARG* 4.6 0.2 - - - -
313B MET* 2.8 38.9 + - + +
335B ARG* 4.3 5.4 - - - +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 4.4 3.1 - - - -
308B GLY 3.4 0.6 - - - -
309B ILE* 1.3 84.2 - - + +
311B ASP* 1.3 59.3 + - - +
313B MET* 3.6 1.9 - - - +
314B GLN* 2.9 30.2 + - - +
329B ILE* 3.6 23.9 - - + +
331B ALA* 4.3 19.3 - - + -
335B ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU* 4.0 18.9 - - + +
308B GLY* 3.5 17.3 + - - +
310B ALA* 1.3 79.9 - - - +
312B ARG* 1.3 59.8 + - - +
314B GLN* 3.5 8.5 + - - +
315B LYS* 2.9 29.6 + - - +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B VAL* 3.9 14.4 - - + +
220B ALA 2.6 36.5 + - - +
221B LEU* 3.7 24.9 + - + +
223B PHE* 4.7 5.2 - - - +
259B GLU* 2.8 29.9 + - - -
262B PHE* 3.5 39.5 - - + +
263B GLN* 4.8 5.5 - - - +
275B HIS* 5.6 0.6 - - - -
308B GLY 2.9 19.2 + - - +
309B ILE* 4.1 1.8 - - - +
311B ASP* 1.3 73.8 - - - +
313B MET* 1.3 64.0 + - - +
315B LYS* 3.8 7.6 - - - +
316B GLU* 2.7 64.3 + - - +
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 3.8 39.7 - - + -
262B PHE* 4.0 14.8 - - + -
274B ILE* 4.0 16.4 - - + +
275B HIS* 4.1 11.9 - - - -
278B THR* 3.9 12.6 - - + +
297B THR* 5.2 0.9 - - + -
299B LEU* 3.9 16.4 - - + -
309B ILE* 2.8 28.4 + - + +
310B ALA* 3.6 4.9 - - - +
312B ARG* 1.3 75.2 - - - +
314B GLN* 1.3 62.3 + - - +
316B GLU* 3.0 5.1 + - - +
317B ILE* 2.9 44.0 + - + +
329B ILE* 4.3 14.6 - - + -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ALA 2.9 17.5 + - - +
311B ASP* 3.5 8.7 - - - +
313B MET* 1.3 73.7 - - - +
315B LYS* 1.3 63.1 + - - +
317B ILE* 3.0 0.9 + - - +
318B THR* 2.7 52.0 + - - +
327B ILE* 3.0 34.6 + - - +
328B LYS* 4.6 0.2 - - - +
329B ILE* 3.9 23.7 - - + +
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Residues in contact with LYS 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B LEU* 2.9 44.7 + - + +
222B ASP* 4.6 14.7 + - - +
311B ASP 2.9 20.8 + - - +
312B ARG* 3.8 7.1 - - - +
314B GLN* 1.3 73.6 - - - +
316B GLU* 1.3 90.5 + - + +
318B THR* 3.7 7.2 - - - +
319B ALA* 3.3 20.6 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B PHE* 4.7 1.3 - - + -
275B HIS* 3.7 39.9 + - + -
312B ARG* 2.7 60.1 + - + +
313B MET 3.0 4.2 + - - +
315B LYS* 1.3 96.5 + - - +
317B ILE* 1.3 65.5 + - - +
319B ALA* 3.4 16.4 + - - +
320B LEU* 3.2 21.3 + - - +
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Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B HIS* 4.1 16.4 - - - +
278B THR* 3.6 29.6 - - + -
279B PHE* 5.4 6.1 - - + +
282B ILE* 5.8 0.7 - - + -
294B TYR* 4.0 18.6 - - + -
297B THR* 4.2 7.0 - - + +
313B MET* 2.9 36.6 + - - +
314B GLN 3.9 1.6 - - - +
316B GLU* 1.3 76.2 - - - +
318B THR* 1.3 59.3 + - - +
319B ALA 3.2 0.3 + - - -
320B LEU* 3.3 6.4 + - + +
321B ALA* 2.9 27.9 + - - +
327B ILE* 3.6 28.3 - - + -
329B ILE* 4.1 15.0 - - + -
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B GLN* 2.7 40.7 + - - +
315B LYS* 3.7 8.1 - - - -
317B ILE* 1.3 78.0 - - - +
319B ALA* 1.3 60.8 + - - +
321B ALA* 3.9 10.4 - - - +
327B ILE* 3.6 19.1 - - + +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B LYS* 3.3 14.1 + - + +
316B GLU* 3.7 15.3 - - - +
317B ILE 3.2 1.0 - - - -
318B THR* 1.3 78.1 - - - +
320B LEU* 1.3 62.4 + - + +
321B ALA 4.2 2.4 - - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B HIS* 3.9 38.6 - - + +
276B GLU* 3.5 22.2 - - - +
279B PHE* 3.4 47.8 - - + -
316B GLU 3.2 21.0 + - - +
317B ILE* 3.3 6.4 + - - +
319B ALA* 1.3 76.3 - - + +
321B ALA* 1.3 62.4 + - - +
322B PRO* 3.8 1.7 - - - +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PHE* 4.4 0.6 - - - -
294B TYR* 3.7 18.8 - - + -
317B ILE 2.9 18.5 + - - +
318B THR 3.9 10.1 - - - +
319B ALA 3.4 3.4 - - - +
320B LEU* 1.3 78.9 - - - +
322B PRO* 1.4 81.2 - - + +
323B SER* 3.5 3.1 + - - -
325B MET* 4.2 3.1 - - + -
327B ILE* 3.4 24.5 - - + -
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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