Contacts of the helix formed by residues 284 - 293 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349E ARG* 4.5 0.8 + - - -
516E LYS* 2.8 30.0 - - - +
517E ARG* 3.9 14.6 + - - +
282F CYS* 3.2 5.3 - - - +
283F ASP* 1.3 80.8 - - - +
285F VAL* 1.3 74.3 + - - +
286F LEU* 2.9 7.6 + - - +
287F LEU* 2.7 46.1 + - + -
288F LEU* 3.1 19.8 - - - +
341F VAL* 3.1 15.4 - - - +
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Residues in contact with VAL 285 (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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514E LEU* 5.2 9.6 - - + -
515E ASN 5.4 6.7 - - - +
516E LYS* 5.1 8.5 - - + +
283F ASP 5.6 0.2 - - - +
284F ASP* 1.3 77.6 + - - +
286F LEU* 1.3 69.1 + - + +
287F LEU 3.2 1.1 - - - -
288F LEU* 3.3 4.0 + - - +
289F LEU* 3.0 21.7 + - + +
334F LYS* 4.2 31.0 - - + +
337F CYS* 4.3 4.5 - - + +
338F GLN* 3.3 48.9 - - + +
341F VAL* 3.7 15.9 - - + -
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Residues in contact with LEU 286 (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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342E ASP* 3.8 39.5 - - + +
345E LEU* 4.4 24.9 - - + -
346E ALA* 3.8 13.0 - - - +
349E ARG* 3.1 41.3 - - + +
511E LYS* 4.7 2.5 - - + +
516E LYS* 3.6 28.9 - - + +
284F ASP* 2.9 4.9 + - - +
285F VAL* 1.3 78.4 - - + +
287F LEU* 1.3 61.5 + - - +
289F LEU* 3.3 11.7 + - + +
290F GLY* 3.0 19.1 + - - -
334F LYS* 4.6 11.0 - - + -
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Residues in contact with LEU 287 (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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349E ARG* 3.5 25.0 - - + +
350E VAL* 4.6 2.1 - - + +
353E LEU* 3.6 28.9 - - + -
517E ARG* 3.4 19.5 - - - +
282F CYS* 3.8 18.6 - - - -
284F ASP* 2.7 31.1 + - + +
286F LEU* 1.3 70.8 - - - +
288F LEU* 1.3 64.3 + - - +
289F LEU 3.2 0.2 + - - -
290F GLY* 3.3 1.8 + - - -
291F MET* 3.1 44.3 + - + +
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Residues in contact with LEU 288 (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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273F VAL* 5.1 4.3 - - + +
276F TYR* 4.1 22.0 - - + -
277F ALA* 3.8 22.2 - - + -
280F THR* 4.6 0.2 - - - +
282F CYS* 3.5 29.0 - - + +
284F ASP 3.1 16.0 + - - +
285F VAL 3.3 3.9 + - - +
287F LEU* 1.3 78.3 - - - +
289F LEU* 1.3 61.8 + - - +
291F MET* 4.1 4.1 - - + +
292F TYR* 3.3 22.9 + - - +
337F CYS* 3.4 22.9 - - + +
340F ALA* 3.4 32.8 - - + -
341F VAL* 3.9 9.4 - - + +
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Residues in contact with LEU 289 (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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339E GLN* 5.8 1.1 - - + +
342E ASP* 4.2 34.3 - - + +
343E THR* 4.8 1.3 - - - +
346E ALA* 4.3 3.1 - - + -
285F VAL* 3.0 13.8 + - + +
286F LEU* 3.4 16.6 - - + +
288F LEU* 1.3 75.9 - - - +
290F GLY* 1.3 66.7 + - - +
292F TYR* 3.3 4.0 + - - +
293F LEU* 3.0 39.3 + - + +
327F PHE* 3.7 17.3 - - + -
333F GLN* 3.2 39.9 - - + +
334F LYS* 4.6 14.8 - - + +
337F CYS* 3.6 9.2 - - + -
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Residues in contact with GLY 290 (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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346E ALA* 3.8 18.4 - - - +
347E LYS* 5.7 0.4 - - - -
350E VAL* 3.7 20.1 - - - +
286F LEU 3.0 7.9 + - - -
287F LEU 3.3 0.6 + - - -
289F LEU* 1.3 80.2 - - - +
291F MET* 1.3 63.1 + - - +
293F LEU* 3.1 19.2 + - - +
294F GLU* 3.5 14.4 - - - +
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Residues in contact with MET 291 (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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350E VAL* 3.7 28.6 - - + +
353E LEU* 5.9 2.9 - - - -
354E GLN* 4.0 15.7 - - + +
276F TYR* 3.8 22.4 - - + +
282F CYS* 5.9 0.9 - - - -
287F LEU* 3.1 34.9 + - + +
288F LEU* 4.1 5.4 - - + +
290F GLY* 1.3 75.8 - - - +
292F TYR* 1.3 61.4 + - - +
294F GLU* 3.5 18.2 + - - +
295F PHE* 3.1 21.9 - - + -
310F GLN* 5.3 3.4 - - + +
312F SER* 3.1 32.5 - - - +
313F HIS* 5.5 2.2 - - + -
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Residues in contact with TYR 292 (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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272F LEU* 4.1 0.3 - - - +
273F VAL* 3.5 32.8 + - + +
276F TYR* 3.6 27.5 - + + -
288F LEU* 3.3 16.6 + - + +
289F LEU 3.3 4.2 + - - +
290F GLY 3.2 0.4 - - - -
291F MET* 1.3 75.1 - - - +
293F LEU* 1.3 57.7 + - - +
294F GLU 3.1 9.6 + - - -
295F PHE* 3.3 24.8 + + - +
296F GLN* 5.3 0.2 - - - +
320F HIS* 3.4 48.8 + + + +
323F ASN* 2.8 31.3 + - - +
324F ALA* 3.9 13.7 - - + +
327F PHE* 3.7 33.6 - + + -
337F CYS* 4.7 2.9 - - - -
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Residues in contact with LEU 293 (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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278E MET* 6.2 1.3 - - + -
343E THR* 3.9 27.4 - - + -
346E ALA* 4.7 2.7 - - + -
289F LEU* 3.0 44.8 + - + +
290F GLY* 3.1 13.2 + - - +
292F TYR* 1.3 75.7 - - - +
294F GLU* 1.3 58.1 + - - +
295F PHE 3.3 0.9 - - - -
296F GLN* 3.2 44.6 - - - +
297F TYR* 3.7 9.4 + - - -
327F PHE* 3.5 27.8 - - + -
328F ALA* 4.9 0.2 - - - -
333F GLN* 3.8 19.1 - - - +
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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