Contacts of the helix formed by residues 284 - 293 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349B ARG* 4.6 0.8 + - - -
516B LYS* 3.1 27.8 - - - +
517B ARG* 3.9 13.9 + - - -
282C CYS* 3.2 2.2 - - - -
283C ASP* 1.3 81.4 - - - +
285C VAL* 1.3 72.7 + - - +
286C LEU* 2.9 7.8 + - - +
287C LEU* 2.7 50.6 + - + -
288C LEU* 3.1 19.7 - - - +
341C VAL* 3.1 15.4 - - - +
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B LEU* 5.3 9.6 - - + -
515B ASN 5.7 4.5 - - - +
516B LYS* 5.3 8.3 - - + +
283C ASP 5.6 0.2 - - - +
284C ASP* 1.3 78.2 + - - +
286C LEU* 1.3 68.4 + - + +
287C LEU 3.2 0.9 - - - -
288C LEU* 3.3 4.0 + - - +
289C LEU* 3.0 22.6 + - - +
334C LYS* 4.1 31.6 - - + +
337C CYS* 4.3 3.9 - - + +
338C GLN* 3.3 47.8 - - + +
341C VAL* 3.7 15.7 - - + -
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ASP* 3.7 41.1 - - + +
345B LEU* 4.4 24.5 - - + -
346B ALA* 3.7 14.6 - - - +
349B ARG* 3.3 39.2 - - + +
511B LYS* 4.9 1.8 - - + +
516B LYS* 3.6 24.9 - - + +
284C ASP* 2.9 5.3 + - - +
285C VAL* 1.3 78.4 - - + +
287C LEU* 1.3 62.6 + - - +
289C LEU* 3.3 11.6 + - + +
290C GLY* 3.0 19.1 + - - -
334C LYS* 4.6 14.4 - - + -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 3.7 27.9 - - + +
350B VAL* 4.7 4.4 - - + +
353B LEU* 3.9 27.8 - - + -
517B ARG* 3.7 13.9 - - - +
282C CYS* 3.8 17.9 - - - -
284C ASP* 2.7 31.3 + - + +
286C LEU* 1.3 70.7 - - - +
288C LEU* 1.3 65.3 + - - +
289C LEU 3.2 0.2 + - - -
290C GLY* 3.3 2.0 + - - -
291C MET* 3.1 45.2 + - + +
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Residues in contact with LEU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C VAL* 5.1 4.0 - - + +
276C TYR* 4.1 22.0 - - + -
277C ALA* 3.8 21.8 - - + -
280C THR* 4.6 0.2 - - - +
282C CYS* 3.5 29.9 - - + +
284C ASP 3.1 15.6 + - - +
285C VAL 3.3 3.5 + - - +
287C LEU* 1.3 79.9 - - - +
289C LEU* 1.3 61.4 + - - +
291C MET* 4.1 3.2 - - - +
292C TYR* 3.3 22.9 + - - +
337C CYS* 3.4 34.8 - - + +
340C ALA* 3.4 21.5 - - + -
341C VAL* 3.9 9.0 - - + +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B GLN* 5.7 1.6 - - + +
342B ASP* 4.3 33.4 - - + +
343B THR* 4.8 1.8 - - - +
346B ALA* 4.6 1.1 - - + -
285C VAL* 3.0 14.0 + - + +
286C LEU* 3.4 16.2 - - + +
287C LEU 3.1 0.2 - - - -
288C LEU* 1.3 75.4 - - - +
290C GLY* 1.3 65.3 + - - +
292C TYR* 3.3 3.8 + - - +
293C LEU* 3.0 41.8 + - + +
327C PHE* 3.7 15.7 - - + -
333C GLN* 3.2 39.9 - - + +
334C LYS* 4.6 14.4 - - + +
337C CYS* 3.6 8.3 - - + -
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ALA* 3.8 20.8 - - - +
350B VAL* 4.0 16.2 - - - -
286C LEU 3.0 8.8 + - - -
287C LEU 3.3 2.2 + - - -
289C LEU* 1.3 78.7 - - - +
291C MET* 1.3 62.3 + - - +
293C LEU* 3.1 19.2 + - - +
294C GLU* 3.5 14.7 - - - +
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Residues in contact with MET 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B VAL* 3.7 28.9 - - + +
353B LEU* 6.3 0.7 - - - -
354B GLN* 4.0 14.6 - - + +
276C TYR* 3.8 22.0 - - + +
282C CYS* 5.9 1.1 - - - -
287C LEU* 3.1 34.3 + - + +
288C LEU* 4.1 5.8 - - - +
290C GLY* 1.3 75.8 - - - +
292C TYR* 1.3 60.5 + - - +
294C GLU* 3.5 20.3 + - - +
295C PHE* 3.1 22.6 - - + -
310C GLN* 5.3 4.9 - - + +
312C SER* 3.1 32.8 - - - +
313C HIS* 5.5 2.5 - - + -
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Residues in contact with TYR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C LEU* 4.1 1.9 - - - +
273C VAL* 3.5 30.4 - - + +
276C TYR* 3.6 27.8 - + + -
288C LEU 3.3 15.5 + - - +
289C LEU 3.3 3.5 + - - +
290C GLY 3.2 0.6 - - - -
291C MET* 1.3 74.8 - - - +
293C LEU* 1.3 58.3 + - - +
294C GLU 3.1 10.3 + - - -
295C PHE* 3.3 25.1 + + - +
296C GLN* 5.3 0.2 - - - +
320C HIS* 3.4 50.0 + + + +
323C ASN* 2.8 31.7 + - - +
324C ALA* 3.9 13.0 - - - +
327C PHE* 3.7 34.0 - + + -
337C CYS* 4.7 3.4 - - - -
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.9 28.9 - - + -
346B ALA* 5.0 0.7 - - + -
289C LEU* 3.0 43.9 + - + +
290C GLY* 3.1 12.9 + - - +
292C TYR* 1.3 76.1 - - - +
294C GLU* 1.3 59.2 + - - +
295C PHE 3.3 0.7 - - - -
296C GLN* 3.2 44.1 - - - +
297C TYR* 3.7 9.4 + - - -
327C PHE* 3.5 28.0 - - + -
333C GLN* 3.8 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