Contacts of the helix formed by residues 308 - 321 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219F VAL* 3.8 17.9 - - - +
307F PRO* 1.4 70.0 - - - +
309F ILE* 1.4 62.6 + - - +
310F ALA 3.4 2.4 + - - -
311F ASP* 3.5 17.9 + - - +
312F ARG* 2.9 25.5 + - - +
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Residues in contact with ILE 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F MET* 5.3 9.0 - - + -
219F VAL* 4.0 15.9 - - + +
261F LEU* 4.4 17.3 - - + -
262F PHE* 4.3 19.1 - - + -
274F ILE* 5.5 1.1 - - + -
299F LEU* 3.8 16.6 - - + -
303F THR 4.1 19.5 - - - +
304F THR* 3.2 29.8 - - - +
306F TYR* 3.1 23.0 + - + +
307F PRO 3.5 1.2 + - - -
308F GLY* 1.4 75.5 - - - +
310F ALA* 1.3 60.1 + - - +
312F ARG* 4.6 0.2 - - - -
313F MET* 2.8 39.7 + - + +
335F ARG* 4.3 5.4 - - - +
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Residues in contact with ALA 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU* 4.4 2.7 - - - -
308F GLY 3.4 0.6 - - - -
309F ILE* 1.3 83.6 - - + +
311F ASP* 1.3 59.6 + - - +
313F MET* 3.3 1.9 + - - +
314F GLN* 2.9 30.0 + - - +
329F ILE* 3.6 24.1 - - + +
331F ALA* 4.3 19.3 - - + -
335F ARG* 6.0 0.2 - - - +
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Residues in contact with ASP 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F LEU* 4.0 19.5 - - + +
308F GLY* 3.5 17.9 + - - +
310F ALA* 1.3 80.1 - - - +
312F ARG* 1.3 59.2 + - - +
314F GLN* 3.5 8.6 - - - +
315F LYS* 2.9 30.0 + - - +
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Residues in contact with ARG 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F VAL* 3.9 14.8 - - + +
220F ALA 2.6 37.3 + - - +
221F LEU* 3.7 25.3 + - + +
223F PHE* 4.7 5.2 - - - +
259F GLU* 2.8 29.7 + - - -
262F PHE* 3.5 39.8 - - + +
263F GLN* 4.8 5.3 - - - +
275F HIS* 5.6 0.6 - - - -
308F GLY 2.9 17.3 + - - +
309F ILE 4.1 1.8 - - - +
311F ASP* 1.3 75.9 - - - +
313F MET* 1.3 62.5 + - - +
315F LYS* 4.0 7.3 - - - +
316F GLU* 2.7 65.1 + - - +
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Residues in contact with MET 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F MET* 3.8 39.5 - - + -
262F PHE* 4.0 15.3 - - + -
274F ILE* 4.0 16.8 - - + +
275F HIS* 4.1 11.9 - - - -
278F THR* 3.9 13.0 - - + +
297F THR* 5.2 0.9 - - + -
299F LEU* 3.9 16.4 - - + -
309F ILE* 2.8 28.9 + - + +
310F ALA* 3.6 4.9 - - - +
312F ARG* 1.3 74.3 - - - +
314F GLN* 1.3 62.9 + - - +
316F GLU* 3.0 5.6 + - - +
317F ILE* 2.9 43.7 + - + +
329F ILE* 4.3 14.6 - - + -
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Residues in contact with GLN 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F ALA 2.9 18.0 + - - +
311F ASP* 3.5 9.0 - - - +
313F MET* 1.3 73.4 - - - +
315F LYS* 1.3 63.5 + - - +
317F ILE* 3.0 0.9 + - - +
318F THR* 2.7 52.7 + - - +
327F ILE* 3.0 34.1 + - - +
328F LYS* 4.6 0.4 - - - +
329F ILE* 3.9 24.2 - - + +
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Residues in contact with LYS 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221F LEU* 2.9 43.8 + - + +
222F ASP* 4.6 14.8 + - - +
311F ASP 2.9 20.8 + - - +
312F ARG* 3.8 7.3 - - - +
314F GLN* 1.3 73.1 - - - +
316F GLU* 1.3 89.3 + - + +
318F THR* 3.7 7.4 - - - +
319F ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F PHE* 4.7 1.3 - - + -
275F HIS* 3.7 39.7 + - + -
312F ARG* 2.7 59.6 + - + +
313F MET 3.0 4.2 + - - +
315F LYS* 1.3 97.1 + - - +
317F ILE* 1.3 64.7 + - - +
319F ALA* 3.4 15.5 + - - +
320F LEU* 3.2 21.9 + - - +
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Residues in contact with ILE 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F HIS* 4.1 15.9 - - - +
278F THR* 3.6 29.8 - - + -
279F PHE* 5.4 5.6 - - + +
282F ILE* 5.8 0.4 - - + -
294F TYR* 4.0 18.6 - - + -
297F THR* 4.2 6.7 - - + +
313F MET* 2.9 36.8 + - - +
314F GLN 3.9 1.6 - - - +
316F GLU* 1.3 75.8 - - - +
318F THR* 1.3 58.9 + - - +
319F ALA 3.2 0.3 + - - -
320F LEU* 3.3 6.7 + - + +
321F ALA* 2.9 27.9 + - - +
327F ILE* 3.6 28.5 - - + -
329F ILE* 4.1 15.3 - - + -
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Residues in contact with THR 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F GLN* 2.7 41.0 + - - +
315F LYS* 3.7 7.9 - - - -
317F ILE* 1.3 77.6 - - - +
319F ALA* 1.3 60.7 + - - +
321F ALA* 3.9 11.0 - - - +
327F ILE* 3.6 18.4 - - + +
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Residues in contact with ALA 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F LYS* 3.3 13.6 + - + +
316F GLU* 3.7 15.3 - - - +
317F ILE 3.2 1.2 - - - -
318F THR* 1.3 77.7 - - - +
320F LEU* 1.3 63.4 + - + +
321F ALA 4.2 2.6 - - - +
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Residues in contact with LEU 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D GLN* 6.0 0.3 - - - +
275F HIS* 3.9 38.1 - - + +
276F GLU* 3.5 22.0 - - - +
279F PHE* 3.4 48.1 - - + -
316F GLU 3.2 21.3 + - - +
317F ILE* 3.3 5.8 + - - +
319F ALA* 1.3 76.5 - - + +
321F ALA* 1.3 63.4 + - - +
322F PRO* 3.8 1.6 - - - +
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Residues in contact with ALA 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D ASP 3.8 5.4 - - - +
279F PHE* 4.4 0.6 - - - -
294F TYR* 3.7 19.5 - - + -
317F ILE 2.9 18.7 + - - +
318F THR 3.9 9.9 - - - +
319F ALA 3.4 3.6 - - - +
320F LEU* 1.3 78.1 - - - +
322F PRO* 1.4 78.7 - - + +
323F SER* 3.5 2.9 + - - -
325F MET* 4.2 0.7 - - + -
327F ILE* 3.4 23.6 - - + -
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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