Contacts of the helix formed by residues 284 - 293 (chain I) in PDB entry 4E2I
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 284 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349H ARG* 4.3 2.1 + - - -
516H LYS* 3.2 24.9 - - - +
517H ARG* 3.5 17.4 + - - +
282I CYS* 3.2 5.6 - - - -
283I ASP* 1.3 81.9 - - - +
285I VAL* 1.3 73.9 + - - +
286I LEU* 2.9 7.8 + - - +
287I LEU* 2.7 45.5 + - + -
288I LEU* 3.1 19.6 - - - +
341I VAL* 3.1 15.2 - - - +
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Residues in contact with VAL 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514H LEU* 5.7 4.5 - - + -
516H LYS* 5.4 11.4 - - + +
283I ASP 5.6 0.2 - - - +
284I ASP* 1.3 78.9 + - - +
286I LEU* 1.3 68.3 + - + +
287I LEU 3.2 1.1 - - - -
288I LEU* 3.3 4.2 + - - +
289I LEU* 3.0 22.5 + - + +
334I LYS* 4.1 31.2 - - + +
337I CYS* 4.3 3.7 - - + +
338I GLN* 3.3 48.7 - - + +
341I VAL* 3.7 15.3 - - + -
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Residues in contact with LEU 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ASP* 3.8 42.2 - - + +
345H LEU* 4.0 26.5 - - + -
346H ALA* 3.4 15.6 - - - +
349H ARG* 3.1 43.3 - - + +
511H LYS* 4.8 1.3 - - + +
516H LYS* 4.0 20.6 - - + +
284I ASP* 2.9 4.0 + - - +
285I VAL* 1.3 78.3 - - + +
287I LEU* 1.3 62.3 + - - +
289I LEU* 3.3 9.9 + - + +
290I GLY* 3.0 19.4 + - - -
334I LYS* 4.6 12.3 - - + +
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Residues in contact with LEU 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H ARG* 3.5 26.5 - - + +
350H VAL* 4.2 6.2 - - - +
353H LEU* 3.6 30.1 - - + -
517H ARG* 3.7 14.1 - - - +
282I CYS* 3.8 18.2 - - - -
284I ASP* 2.7 31.1 + - + +
286I LEU* 1.3 70.6 - - - +
288I LEU* 1.3 64.8 + - - +
289I LEU 3.2 0.2 + - - -
290I GLY* 3.3 1.2 + - - -
291I MET* 3.1 45.1 + - + +
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Residues in contact with LEU 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273I VAL* 5.1 4.9 - - + +
276I TYR* 4.1 22.2 - - + -
277I ALA* 3.8 21.8 - - + -
280I THR* 4.6 0.2 - - - +
282I CYS* 3.5 28.9 - - + +
284I ASP 3.1 15.6 + - - +
285I VAL 3.3 3.7 + - - +
287I LEU* 1.3 79.2 - - - +
289I LEU* 1.3 61.4 + - - +
291I MET* 4.1 3.7 - - + +
292I TYR* 3.3 22.9 + - + +
337I CYS* 3.4 22.6 - - + +
340I ALA* 3.4 32.8 - - + -
341I VAL* 3.9 9.0 - - + +
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Residues in contact with LEU 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H GLN* 5.6 0.4 - - + +
342H ASP* 4.0 35.2 - - + +
343H THR* 4.5 4.0 - - - +
346H ALA* 4.0 4.0 - - + -
285I VAL* 3.0 14.0 + - + +
286I LEU* 3.4 14.8 - - + +
287I LEU 3.1 0.2 - - - -
288I LEU* 1.3 76.3 - - - +
290I GLY* 1.3 66.8 + - - +
292I TYR* 3.3 3.6 + - - +
293I LEU* 3.0 40.4 + - + +
327I PHE* 3.7 17.3 - - + -
333I GLN* 3.2 37.9 - - + +
334I LYS* 4.6 13.7 - - + +
337I CYS* 3.6 9.2 - - + -
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Residues in contact with GLY 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346H ALA* 3.8 15.0 - - - +
347H LYS* 5.1 1.3 - - - -
350H VAL* 3.7 21.1 - - - -
286I LEU 3.0 8.5 + - - -
287I LEU 3.3 0.2 + - - -
289I LEU* 1.3 78.6 - - - +
291I MET* 1.3 64.0 + - - +
293I LEU* 3.1 19.9 + - - +
294I GLU* 3.5 14.2 - - - +
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Residues in contact with MET 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350H VAL* 3.5 15.3 - - + +
354H GLN* 3.4 33.2 - - + +
276I TYR* 3.8 21.8 - - + +
282I CYS* 5.9 1.3 - - - -
287I LEU* 3.1 33.9 + - + +
288I LEU* 4.1 4.9 - - - +
290I GLY* 1.3 75.8 - - - +
292I TYR* 1.3 60.2 + - - +
294I GLU* 3.5 19.0 + - - +
295I PHE* 3.1 22.5 - - + -
310I GLN* 5.3 3.8 - - + +
312I SER* 3.1 32.5 - - - +
313I HIS* 5.5 1.6 - - + -
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Residues in contact with TYR 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272I LEU* 4.1 0.2 - - - +
273I VAL* 3.5 33.5 + - + +
276I TYR* 3.6 27.8 - + + -
288I LEU* 3.3 16.0 + - + +
289I LEU 3.3 4.4 + - - +
290I GLY 3.2 0.6 - - - -
291I MET* 1.3 74.9 - - - +
293I LEU* 1.3 58.0 + - - +
294I GLU 3.1 9.2 + - - -
295I PHE* 3.3 25.9 + + - +
320I HIS* 3.4 49.1 + + + +
323I ASN* 2.8 31.4 + - - +
324I ALA* 3.9 13.8 - - + +
327I PHE* 3.7 31.3 - + + -
337I CYS* 4.7 3.4 - - - -
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Residues in contact with LEU 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H MET* 5.7 3.8 - - + -
343H THR* 3.7 28.9 - - + -
346H ALA* 4.9 0.7 - - + -
289I LEU* 3.0 44.6 + - + +
290I GLY* 3.1 12.9 + - - +
292I TYR* 1.3 75.9 - - - +
294I GLU* 1.3 58.0 + - - +
295I PHE 3.3 0.9 - - - -
296I GLN* 3.2 44.3 - - - +
297I TYR* 3.7 9.5 + - - -
327I PHE* 3.5 27.1 - - + -
333I GLN* 3.8 18.6 - - - +
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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