Contacts of the helix formed by residues 308 - 321 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E VAL* 3.8 16.8 - - - -
220E ALA 5.9 0.2 - - - -
307E PRO* 1.4 70.8 - - - +
309E ILE* 1.4 62.7 + - - +
310E ALA 3.4 2.9 + - - -
311E ASP* 3.5 17.2 + - - +
312E ARG* 2.9 25.8 + - - +
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Residues in contact with ILE 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E MET* 5.3 9.4 - - + -
219E VAL* 4.0 15.7 - - + +
261E LEU* 4.4 17.7 - - + -
262E PHE* 4.3 19.1 - - + -
274E ILE* 5.5 1.1 - - + -
299E LEU* 3.8 16.8 - - + -
303E THR 4.1 20.0 - - - +
304E THR* 3.2 29.8 - - - +
306E TYR* 3.1 22.9 + - + +
307E PRO 3.5 1.2 + - - -
308E GLY* 1.4 75.9 - - - +
310E ALA* 1.3 61.1 + - - +
312E ARG* 4.6 0.4 - - - -
313E MET* 2.8 38.4 + - + +
335E ARG* 4.3 4.7 - - - +
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299E LEU* 4.4 2.5 - - - -
308E GLY 3.4 0.4 - - - -
309E ILE* 1.3 83.8 - - - +
311E ASP* 1.3 60.0 + - - +
313E MET* 3.6 1.6 - - - +
314E GLN* 2.9 29.8 + - - +
329E ILE* 3.6 24.5 - - + +
331E ALA* 4.3 19.1 - - + -
335E ARG* 6.0 0.4 - - - +
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Residues in contact with ASP 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E LEU* 4.0 20.0 - - + +
308E GLY* 3.5 17.0 + - - +
310E ALA* 1.3 80.2 - - - +
312E ARG* 1.3 58.1 - - - +
314E GLN* 3.5 8.7 + - - +
315E LYS* 2.9 29.5 + - - +
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Residues in contact with ARG 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219E VAL* 3.9 14.9 - - + +
220E ALA 2.6 36.7 + - - +
221E LEU* 3.7 26.6 + - + +
223E PHE* 4.7 5.4 - - - +
259E GLU* 2.8 29.7 + - - -
262E PHE* 3.5 40.0 - - + +
263E GLN* 4.8 5.7 - - - +
275E HIS* 5.6 0.6 - - - -
308E GLY 2.9 17.9 + - - +
309E ILE 4.1 1.6 - - - +
311E ASP* 1.3 74.4 - - - +
313E MET* 1.3 63.4 + - - +
315E LYS* 4.0 6.8 - - - +
316E GLU* 2.7 65.3 + - - +
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Residues in contact with MET 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E MET* 3.8 40.4 - - + -
262E PHE* 4.0 14.6 - - + -
274E ILE* 4.0 16.6 - - + +
275E HIS* 4.1 12.1 - - - -
278E THR* 3.9 12.8 - - + +
297E THR* 5.2 0.9 - - + -
299E LEU* 3.9 16.4 - - + -
309E ILE* 2.8 27.4 + - + +
310E ALA* 3.6 5.4 - - - +
312E ARG* 1.3 74.8 - - - +
314E GLN* 1.3 63.1 + - - +
316E GLU* 3.0 5.4 + - - +
317E ILE* 2.9 43.2 + - + +
329E ILE* 4.3 15.3 - - + -
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Residues in contact with GLN 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E ALA 2.9 18.4 + - - +
311E ASP* 3.5 9.2 - - - +
313E MET* 1.3 73.8 - - - +
315E LYS* 1.3 62.9 + - + +
317E ILE 3.0 0.2 + - - -
318E THR* 2.7 53.2 + - - +
327E ILE* 3.0 33.1 + - - +
329E ILE* 3.9 25.2 - - + +
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Residues in contact with LYS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E LEU* 2.9 45.6 + - + +
222E ASP* 4.6 13.9 + - - +
311E ASP 2.9 20.8 + - - +
312E ARG* 3.8 6.0 - - - +
314E GLN* 1.3 73.5 - - - +
316E GLU* 1.3 89.6 + - + +
318E THR* 3.7 7.2 - - - -
319E ALA* 3.3 20.3 + - - +
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Residues in contact with GLU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E PHE* 4.7 1.3 - - + -
275E HIS* 3.7 38.8 + - + -
312E ARG* 2.7 60.6 + - + +
313E MET 3.0 4.1 + - - +
314E GLN 2.9 0.2 + - - -
315E LYS* 1.3 98.9 + - - +
317E ILE* 1.3 64.9 + - - +
319E ALA* 3.4 16.0 + - - +
320E LEU* 3.2 21.3 + - - +
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E HIS* 4.1 16.6 - - - +
278E THR* 3.6 31.0 - - + -
279E PHE* 5.4 6.3 - - + +
282E ILE* 5.8 0.7 - - + -
294E TYR* 4.0 18.6 - - + -
297E THR* 4.2 6.7 - - + +
313E MET* 2.9 36.2 + - - +
314E GLN 3.9 2.0 - - - +
316E GLU* 1.3 77.0 - - - +
318E THR* 1.3 58.7 + - - +
319E ALA 3.2 0.3 + - - -
320E LEU* 3.3 6.3 + - + +
321E ALA* 2.9 28.2 + - - +
327E ILE* 3.6 28.7 - - + -
329E ILE* 4.1 15.5 - - + -
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Residues in contact with THR 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314E GLN* 2.7 41.5 + - - +
315E LYS* 3.7 7.9 - - - -
317E ILE* 1.3 77.6 - - - +
319E ALA* 1.3 58.6 + - - +
321E ALA* 3.9 10.6 - - - +
327E ILE* 3.6 18.3 - - + +
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Residues in contact with ALA 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E LYS* 3.3 13.6 + - + +
316E GLU* 3.7 15.5 - - - +
317E ILE 3.2 1.2 - - - -
318E THR* 1.3 78.3 - - - +
320E LEU* 1.3 63.6 + - + +
321E ALA 3.6 2.6 + - - +
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Residues in contact with LEU 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E HIS* 3.9 37.7 - - + +
276E GLU* 3.5 22.7 - - - +
279E PHE* 3.4 48.3 - - + -
316E GLU 3.2 20.8 + - - +
317E ILE* 3.3 5.8 + - - +
319E ALA* 1.3 77.2 - - + +
321E ALA* 1.3 62.7 + - - +
322E PRO* 3.8 1.7 - - - +
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Residues in contact with ALA 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ASP 3.8 5.4 - - - +
279E PHE* 4.3 0.6 - - - -
294E TYR* 3.7 18.8 - - + -
317E ILE 2.9 17.9 + - - +
318E THR 3.9 10.2 - - - +
319E ALA 3.4 3.0 - - - +
320E LEU* 1.3 78.7 - - - +
322E PRO* 1.4 79.1 - - + +
323E SER* 3.5 3.5 + - - -
325E MET* 4.2 0.7 - - + -
327E 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