Contacts of the helix formed by residues 284 - 293 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349J ARG* 4.2 1.2 + - - -
516J LYS* 3.0 29.1 - - - +
517J ARG* 3.6 17.2 + - - +
282K CYS* 3.2 1.8 - - - -
283K ASP* 1.3 80.2 - - - +
285K VAL* 1.3 74.3 + - - +
286K LEU* 2.9 8.0 + - - +
287K LEU* 2.7 50.8 + - + -
288K LEU* 3.1 20.1 - - - +
341K VAL* 3.1 15.1 - - - +
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Residues in contact with VAL 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514J LEU* 5.4 6.3 - - + -
515J ASN 5.6 4.3 - - - +
516J LYS* 5.1 13.4 - - + +
283K ASP 5.6 0.2 - - - +
284K ASP* 1.3 78.2 + - - +
286K LEU* 1.3 68.9 + - + +
287K LEU 3.2 0.9 - - - -
288K LEU* 3.3 3.5 + - - +
289K LEU* 3.0 22.6 + - + +
334K LYS* 4.2 31.9 - - + +
337K CYS* 4.3 3.7 - - + +
338K GLN* 3.3 47.8 - - + +
341K VAL* 3.7 15.3 - - + -
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Residues in contact with LEU 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342J ASP* 3.8 44.0 - - + +
345J LEU* 4.0 28.0 - - + -
346J ALA* 3.4 16.7 - - - +
349J ARG* 3.1 41.3 - - + +
511J LYS* 4.6 2.5 - - + +
516J LYS* 3.9 21.7 - - + +
284K ASP* 2.9 4.6 + - - +
285K VAL* 1.3 78.8 - - - +
287K LEU* 1.3 61.5 + - - +
289K LEU* 3.3 8.9 + - + +
290K GLY* 3.0 19.2 + - - -
334K LYS* 4.6 11.2 - - + -
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Residues in contact with LEU 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349J ARG* 3.4 29.0 - - + +
350J VAL* 4.2 5.5 - - - +
353J LEU* 3.6 30.1 - - + -
517J ARG* 3.5 15.7 - - - +
282K CYS* 3.8 18.6 - - - -
284K ASP* 2.7 30.2 + - + +
286K LEU* 1.3 71.5 - - - +
288K LEU* 1.3 63.9 + - - +
290K GLY* 3.3 1.6 + - - -
291K MET* 3.1 44.0 + - + +
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Residues in contact with LEU 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273K VAL* 5.1 4.7 - - + +
276K TYR* 4.1 21.8 - - + -
277K ALA* 3.8 22.0 - - + +
280K THR* 4.6 0.4 - - - +
282K CYS* 3.5 28.7 - - + +
284K ASP 3.1 16.1 + - - +
285K VAL 3.3 3.9 + - - +
287K LEU* 1.3 78.8 - - - +
289K LEU* 1.3 61.2 + - - +
291K MET* 4.1 3.4 - - + +
292K TYR* 3.3 22.9 + - - +
337K CYS* 3.4 23.1 - - + +
340K ALA* 3.4 33.0 - - + -
341K VAL* 3.9 8.7 - - + +
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Residues in contact with LEU 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339J GLN* 5.5 0.4 - - + +
342J ASP* 3.8 38.8 - - + +
343J THR* 4.3 6.3 - - - +
346J ALA* 4.0 2.2 - - + -
285K VAL* 3.0 13.8 + - + +
286K LEU* 3.4 13.5 - - + +
287K LEU 3.1 0.2 - - - -
288K LEU* 1.3 75.1 - - - +
290K GLY* 1.3 66.9 + - - +
292K TYR* 3.3 3.8 + - - +
293K LEU* 3.0 37.5 + - + +
327K PHE* 3.7 17.5 - - + -
333K GLN* 3.2 37.7 - - + +
334K LYS* 4.6 13.0 - - + +
337K CYS* 3.6 8.9 - - + -
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Residues in contact with GLY 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346J ALA* 3.6 16.9 - - - +
347J LYS* 4.9 1.3 - - - -
350J VAL* 3.6 22.4 - - - +
286K LEU 3.0 7.9 + - - -
287K LEU 3.3 0.2 + - - -
289K LEU* 1.3 78.5 - - - +
291K MET* 1.3 62.0 + - - +
293K LEU* 3.0 20.0 + - - +
294K GLU* 3.5 14.6 - - - +
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Residues in contact with MET 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350J VAL* 3.4 29.3 - - + +
353J LEU* 6.2 1.3 - - - -
354J GLN* 3.6 17.9 - - + +
276K TYR* 3.9 21.8 - - + +
282K CYS* 5.9 1.3 - - - -
287K LEU* 3.1 35.2 + - + +
288K LEU* 4.1 5.6 - - + +
290K GLY* 1.3 74.9 - - - +
292K TYR* 1.3 59.8 + - - +
294K GLU* 3.5 18.6 + - - +
295K PHE* 3.1 22.3 - - + -
310K GLN* 5.3 3.1 - - + +
312K SER* 3.1 32.1 - - - +
313K HIS* 5.5 1.8 - - + -
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Residues in contact with TYR 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272K LEU* 4.1 0.2 - - - +
273K VAL* 3.5 33.6 + - + +
276K TYR* 3.6 26.4 - + + -
288K LEU* 3.3 16.6 + - + +
289K LEU 3.3 4.6 + - - +
290K GLY 3.2 0.6 - - - -
291K MET* 1.3 74.5 - - - +
293K LEU* 1.3 57.6 + - - +
294K GLU 3.1 9.3 + - - -
295K PHE* 3.3 23.8 + + - -
320K HIS* 3.4 49.5 + + + +
323K ASN* 2.8 32.0 + - - +
324K ALA* 3.9 15.9 - - + +
327K PHE* 3.7 31.7 - + + -
337K CYS* 4.7 3.1 - - - -
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Residues in contact with LEU 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278J MET* 5.7 4.5 - - + -
343J THR* 3.5 32.8 - - + -
346J ALA* 4.8 0.7 - - + -
289K LEU* 3.0 44.1 + - + +
290K GLY* 3.0 12.9 + - - +
292K TYR* 1.3 75.9 - - - +
294K GLU* 1.3 57.2 + - - +
295K PHE 3.3 0.7 - - - -
296K GLN* 3.2 44.3 - - - +
297K TYR* 3.7 9.9 + - - -
327K PHE* 3.5 27.8 - - + -
333K GLN* 3.8 17.9 - - - +
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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