Contacts of the helix formed by residues 301 - 315 (chain E) in PDB entry 5DO9
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 ASP 301 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283E ILE* 4.0 6.1 - - - +
295E TYR* 4.3 1.9 + - - -
298E PRO* 3.2 32.4 + - + +
299E GLN 3.2 8.7 - - - +
300E ARG* 1.3 78.3 - - - +
302E ALA* 1.3 58.4 + - - +
303E GLN* 3.3 8.8 + - - +
304E ALA* 2.9 24.9 + - + +
305E ALA* 3.1 27.5 + - - +
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Residues in contact with ALA 302 (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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279E LEU* 3.5 19.1 - - + +
280E GLU* 3.7 33.4 - - - +
283E ILE* 4.0 23.6 - - + +
284E MET* 5.5 2.8 - - + +
300E ARG 4.3 0.4 + - - -
301E ASP* 1.3 70.6 + - - +
303E GLN* 1.3 61.2 + - - +
305E ALA* 3.5 2.6 - - - +
306E ARG* 2.9 35.2 + - - +
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Residues in contact with GLN 303 (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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301E ASP* 3.3 6.4 + - - +
302E ALA* 1.3 78.1 - - - +
304E ALA* 1.3 65.5 + - - +
306E ARG* 3.7 28.6 - - - +
307E GLU* 3.2 36.3 + - + +
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Residues in contact with ALA 304 (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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295E TYR* 3.2 22.0 - - + +
297E GLY* 5.1 0.7 - - - -
298E PRO* 3.9 12.6 - - + -
301E ASP* 2.9 28.1 + - - +
303E GLN* 1.3 77.1 - - - +
305E ALA* 1.3 62.1 + - - +
307E GLU* 3.4 6.5 + - - +
308E PHE* 3.1 23.0 + - - +
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Residues in contact with ALA 305 (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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279E LEU* 4.6 8.3 - - + -
283E ILE* 4.0 21.1 - - + -
288E LEU* 3.9 21.7 - - + +
295E TYR* 3.7 8.2 + - + +
301E ASP 3.1 17.6 + - - +
302E ALA* 3.5 6.3 - - - +
303E GLN 3.2 0.2 - - - -
304E ALA* 1.3 74.1 - - - +
306E ARG* 1.3 60.5 + - - +
308E PHE* 3.4 3.3 + - - +
309E ILE* 3.0 34.9 + - + +
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Residues in contact with ARG 306 (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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232E LEU* 3.8 25.4 - - + -
273E LEU* 4.3 0.5 - - - +
276E LYS* 4.1 23.0 - - - +
279E LEU* 3.9 10.5 - - + +
280E GLU* 4.4 12.9 + - - -
302E ALA* 2.9 25.0 + - - +
303E GLN* 3.7 28.2 - - - +
305E ALA* 1.3 74.6 - - - +
307E GLU* 1.3 60.9 + - - +
309E ILE* 3.8 1.9 - - - +
310E LEU* 2.9 28.8 + - - +
328E PHE* 3.5 60.8 - - + +
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Residues in contact with GLU 307 (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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303E GLN* 3.2 30.9 + - + +
304E ALA* 3.7 7.0 - - - +
306E ARG* 1.3 75.1 + - - +
308E PHE* 1.3 66.6 + - - +
310E LEU* 3.4 14.3 + - - +
311E LYS* 3.0 24.3 + - - +
328E PHE* 3.5 28.0 - - - -
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Residues in contact with PHE 308 (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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288E LEU* 3.9 16.8 - - + -
292E PHE* 4.3 11.0 - - + -
294E GLU* 4.0 18.2 - - + -
295E TYR* 3.5 58.8 - + + -
296E ASP* 5.2 2.7 - - - -
304E ALA 3.1 8.2 + - - +
305E ALA 3.6 5.6 - - - +
306E ARG 3.3 0.2 - - - -
307E GLU* 1.3 80.4 - - - +
309E ILE* 1.3 66.6 - - - +
311E LYS* 3.2 18.1 + - + +
312E MET* 2.9 56.7 + - + +
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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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232E LEU* 3.9 41.3 - - + +
235E TYR* 5.1 3.4 - - + -
248E MET* 4.0 22.4 - - + -
273E LEU* 4.6 6.7 - - + -
279E LEU* 5.2 3.4 - - + -
288E LEU* 4.2 20.6 - - + -
305E ALA* 3.0 28.0 + - + +
306E ARG* 3.8 4.5 - - - +
308E PHE* 1.3 73.8 - - - +
310E LEU* 1.3 66.5 + - - +
312E MET* 3.0 31.4 + - + +
313E PHE* 3.1 34.1 + - + -
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Residues in contact with LEU 310 (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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271E LEU* 4.0 11.9 - - + -
273E LEU* 3.8 20.8 - - + +
306E ARG 2.9 17.8 + - - +
307E GLU* 3.4 17.5 - - - +
309E ILE* 1.3 75.8 - - - +
311E LYS* 1.3 62.9 + - - +
313E PHE* 3.0 15.0 + - - +
314E VAL* 3.0 25.8 + - + +
326E SER* 3.7 35.9 - - - +
328E PHE* 4.0 20.9 - - + -
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Residues in contact with LYS 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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307E GLU 3.0 17.5 + - - +
308E PHE* 3.5 17.5 - - + +
309E ILE 3.2 0.2 - - - -
310E LEU* 1.3 77.2 - - - +
312E MET* 1.3 57.7 + - - +
314E VAL* 3.5 7.4 + - + +
315E ASP* 2.9 59.7 + - - +
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Residues in contact with MET 312 (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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248E MET* 4.2 13.9 - - + -
252E LYS* 3.3 36.6 - - + +
292E PHE* 3.6 30.3 - - + -
294E GLU* 6.2 0.2 - - - +
308E PHE* 2.9 45.0 + - + +
309E ILE* 3.0 27.6 + - + +
311E LYS* 1.3 74.8 - - - +
313E PHE* 1.3 66.2 + - + +
315E ASP* 3.4 12.0 + - - +
316E LEU* 3.3 21.0 + - - +
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Residues in contact with PHE 313 (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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230E VAL* 3.7 30.5 - - + -
248E MET* 4.3 8.5 - - + -
251E SER* 3.6 38.1 - - - -
252E LYS* 3.7 24.9 - - + -
255E PHE* 3.8 36.4 - + + -
271E LEU* 3.8 20.6 - - + -
273E LEU* 4.8 4.5 - - + -
309E ILE* 3.1 31.9 + - + -
310E LEU 3.0 8.3 + - - +
312E MET* 1.3 81.4 - - + +
314E VAL* 1.3 66.0 + - - +
316E LEU* 3.1 28.6 + - + +
317E ASN* 4.7 1.4 + - - -
324E ILE* 4.7 0.5 - - - +
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Residues in contact with VAL 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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271E LEU* 5.4 0.7 - - + -
310E LEU* 3.0 35.0 + - + +
311E LYS* 4.0 7.0 - - - +
313E PHE* 1.3 76.1 - - + +
315E ASP* 1.3 68.0 + - - +
316E LEU 3.3 1.2 + - - -
317E ASN* 4.1 10.0 + - - +
318E PRO* 5.6 0.3 - - - +
324E ILE* 4.2 32.7 - - + +
326E SER* 6.2 0.2 - - - -
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Residues in contact with ASP 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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311E LYS* 2.9 55.9 + - - +
312E MET* 3.4 7.5 + - - +
313E PHE 3.1 1.0 - - - -
314E VAL* 1.3 82.9 - - - +
316E LEU* 1.3 62.1 + - - +
317E ASN 3.4 1.6 + - - -
318E PRO* 3.5 20.2 - - - +
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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