Contacts of the helix formed by residues 284 - 293 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349G ARG* 4.5 0.8 + - - -
516G LYS* 3.0 29.0 - - - +
517G ARG* 3.9 13.9 + - - -
282H CYS* 3.2 2.0 - - - -
283H ASP* 1.3 83.0 - - - +
285H VAL* 1.3 72.9 + - - +
286H LEU* 2.9 7.6 + - - +
287H LEU* 2.7 50.1 + - + -
288H LEU* 3.1 19.9 - - - +
341H VAL* 3.1 15.2 - - - +
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Residues in contact with VAL 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514G LEU* 5.2 9.9 - - + -
515G ASN 5.6 4.7 - - - +
516G LYS* 5.2 8.5 - - + +
284H ASP* 1.3 77.6 + - - +
286H LEU* 1.3 66.9 + - + +
287H LEU 3.2 1.3 + - - -
288H LEU* 3.3 4.0 + - - +
289H LEU* 3.0 22.6 + - + +
334H LYS* 4.1 31.6 - - + +
337H CYS* 4.3 4.5 - - + +
338H GLN* 3.2 48.9 - - + +
341H VAL* 3.7 15.3 - - + -
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Residues in contact with LEU 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342G ASP* 3.7 40.8 - - + +
345G LEU* 4.3 24.9 - - + -
346G ALA* 3.6 14.6 - - - +
349G ARG* 3.2 39.9 - - + +
511G LYS* 4.8 2.5 - - + +
516G LYS* 3.6 24.8 - - + +
284H ASP* 2.9 5.1 + - - +
285H VAL* 1.3 78.3 - - + +
287H LEU* 1.3 63.4 + - - +
289H LEU* 3.3 12.0 + - + +
290H GLY 3.0 18.4 + - - -
334H LYS* 4.6 13.2 - - + -
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Residues in contact with LEU 287 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349G ARG* 3.6 28.8 - - + +
350G VAL* 4.6 4.6 - - + +
353G LEU* 3.8 28.7 - - + -
517G ARG* 3.6 14.1 - - - +
282H CYS* 3.8 17.7 - - - -
284H ASP* 2.7 31.0 + - + +
286H LEU* 1.3 70.8 - - - +
288H LEU* 1.3 65.8 + - - +
289H LEU 3.2 0.2 + - - -
290H GLY* 3.3 1.6 + - - -
291H MET* 3.1 44.5 + - + +
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Residues in contact with LEU 288 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273H VAL* 5.1 4.5 - - + +
276H TYR* 4.1 22.0 - - + -
277H ALA* 3.8 21.1 - - + -
280H THR* 4.6 0.2 - - - +
282H CYS* 3.5 29.6 - - + +
284H ASP 3.1 15.6 + - - +
285H VAL 3.3 3.9 + - - +
287H LEU* 1.3 78.8 - - - +
289H LEU* 1.3 62.0 + - - +
291H MET* 4.1 3.3 - - + +
292H TYR* 3.3 22.2 + - - +
337H CYS* 3.4 34.4 - - + +
340H ALA* 3.4 22.0 - - + -
341H VAL* 3.9 9.0 - - + +
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Residues in contact with LEU 289 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339G GLN* 5.6 0.7 - - + +
342G ASP* 4.1 36.3 - - + +
343G THR* 4.7 1.3 - - - +
346G ALA* 4.4 2.5 - - + -
285H VAL* 3.0 13.3 + - + +
286H LEU* 3.4 15.7 - - + +
288H LEU* 1.3 76.1 - - - +
290H GLY* 1.3 66.1 + - - +
292H TYR* 3.3 3.5 + - - +
293H LEU* 3.0 39.9 + - + +
327H PHE* 3.7 16.4 - - + -
333H GLN* 3.2 40.6 - - + +
334H LYS* 4.5 13.2 - - + +
337H CYS* 3.6 10.0 - - + -
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Residues in contact with GLY 290 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346G ALA* 3.7 20.6 - - - +
347G LYS* 5.1 0.9 - - - -
350G VAL* 3.9 16.1 - - - +
286H LEU 3.0 8.3 + - - -
287H LEU 3.9 1.6 - - - -
289H LEU* 1.3 80.0 - - - +
291H MET* 1.3 62.8 + - - +
293H LEU* 3.1 19.2 + - - +
294H GLU* 3.5 14.6 - - - +
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Residues in contact with MET 291 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350G VAL* 3.7 28.9 - - - +
353G LEU* 6.3 0.7 - - - -
354G GLN* 4.0 15.5 - - + +
276H TYR* 3.9 21.3 - - + +
287H LEU* 3.1 34.8 + - + +
288H LEU* 4.1 5.4 - - + +
290H GLY* 1.3 77.2 - - - +
292H TYR* 1.3 60.4 + - - +
294H GLU* 3.5 19.2 + - - +
295H PHE* 3.1 22.7 - - + -
310H GLN* 5.3 3.6 - - + +
312H SER* 3.1 32.5 - - - +
313H HIS* 5.5 2.5 - - + -
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Residues in contact with TYR 292 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272H LEU* 4.1 2.4 - - - +
273H VAL* 3.6 32.7 - - + +
276H TYR* 3.6 26.9 - + + -
288H LEU 3.3 16.6 + - - +
289H LEU 3.3 4.6 + - - +
290H GLY 3.2 0.4 - - - -
291H MET* 1.3 75.7 - - - +
293H LEU* 1.3 56.6 + - - +
294H GLU 3.1 10.0 + - - -
295H PHE* 3.3 25.1 + + - +
320H HIS* 3.4 49.2 + + + +
323H ASN* 2.8 31.9 + - - +
324H ALA* 3.9 14.2 - - + +
327H PHE* 3.7 33.2 - + + -
337H CYS* 4.7 3.1 - - - -
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Residues in contact with LEU 293 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278G MET* 6.1 0.2 - - + -
343G THR* 3.8 30.3 - - + +
346G ALA* 4.8 0.9 - - + -
289H LEU* 3.0 45.2 + - + +
290H GLY* 3.1 12.9 + - - +
292H TYR* 1.3 76.1 - - - +
294H GLU* 1.3 58.2 + - - +
295H PHE 3.3 0.9 - - - -
296H GLN* 3.2 43.2 - - - +
297H TYR* 3.7 9.5 + - - -
327H PHE* 3.5 27.1 - - + -
333H GLN* 3.8 20.0 - - - +
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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