Contacts of the helix formed by residues 269 - 281 (chain J) 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 SER 269 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267J GLN 3.9 2.7 + - - -
268J VAL* 1.3 73.0 - - - +
270J TRP* 1.3 61.6 + - - +
271J LYS* 3.7 6.9 + - - +
272J LEU* 3.3 43.2 + - - +
273J VAL* 3.3 9.4 + - - +
323J ASN* 2.6 33.0 + - - -
336J ILE* 4.6 1.0 - - - +
329K ASP* 5.7 0.2 + - - -
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Residues in contact with TRP 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J VAL* 3.6 19.9 - - + +
269J SER* 1.3 72.9 + - - +
271J LYS* 1.3 58.1 + - - +
272J LEU 3.2 2.0 - - - -
273J VAL* 3.2 3.3 + - - +
274J THR* 2.8 38.0 + - - +
332J ASN* 5.1 7.6 - - + -
335J THR* 3.6 33.7 - - + -
336J ILE* 3.6 48.1 - - + +
339J GLN* 3.1 37.2 - - + +
328K ALA 5.3 1.6 - - - +
329K ASP* 5.7 3.1 - - - -
330K SER 4.5 7.6 - - - +
331K LYS* 2.8 73.5 - - + +
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Residues in contact with LYS 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J SER* 3.6 6.2 + - - +
270J TRP* 1.3 80.5 - - - +
272J LEU* 1.3 58.3 + - + +
274J THR* 3.7 7.4 - - - -
275J GLU* 2.9 39.2 + - - +
296K GLN* 4.2 14.1 - - - +
297K TYR* 6.3 0.4 - - - -
325K ALA 6.0 0.2 - - - -
328K ALA* 3.9 37.3 + - + +
329K ASP* 3.3 34.6 - - - +
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Residues in contact with LEU 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J SER* 3.3 21.9 + - - +
270J TRP 3.2 0.6 - - - -
271J LYS* 1.3 77.0 - - + +
273J VAL* 1.3 60.5 + - - +
275J GLU* 3.1 20.1 + - - +
276J TYR* 3.0 24.6 + - - +
292J TYR* 4.1 0.4 - - - +
319J LYS* 4.9 8.1 - - + +
320J HIS* 3.2 28.5 - - + +
322J ALA* 5.8 3.4 - - + -
323J ASN* 3.5 35.2 - - + +
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Residues in contact with VAL 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269J SER 3.3 9.6 - - - +
270J TRP 3.2 5.3 + - - +
272J LEU* 1.3 75.8 - - - +
274J THR* 1.3 58.6 + - - +
276J TYR* 3.4 4.5 + - - +
277J ALA* 3.0 26.0 + - - +
288J LEU* 5.1 4.6 - - + +
292J TYR* 3.5 30.5 - - + -
323J ASN* 3.2 26.0 - - - +
327J PHE* 4.7 2.5 - - + -
336J ILE* 3.6 33.0 - - + +
337J CYS* 4.2 24.0 - - - -
340J ALA* 4.4 3.4 - - + -
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Residues in contact with THR 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270J TRP* 2.8 22.7 + - - +
271J LYS* 3.7 8.7 - - - -
273J VAL* 1.3 73.3 - - - +
275J GLU* 1.3 59.8 + - - +
277J ALA* 3.2 2.1 + - - +
278J MET* 2.9 32.0 + - + +
336J ILE 5.3 1.2 + - - -
339J GLN* 4.2 12.3 + - - -
340J ALA* 3.9 18.0 + - - +
343J THR* 3.6 41.0 + - + +
328K ALA 5.6 0.4 + - - -
333K GLN* 4.6 10.5 + - - +
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Residues in contact with GLU 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J LYS* 2.9 27.4 + - + +
272J LEU* 3.2 28.0 - - - +
274J THR* 1.3 77.4 - - - +
276J TYR* 1.3 62.1 + - - +
278J MET* 3.1 9.7 + - - +
279J GLU* 3.0 35.5 + - + +
319J LYS* 3.2 35.6 + - - -
320J HIS* 3.9 4.7 - - + -
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Residues in contact with TYR 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J LEU 3.0 8.4 + - - +
273J VAL* 3.7 7.6 - - + +
275J GLU* 1.3 76.4 - - - +
277J ALA* 1.3 61.4 + - - +
279J GLU* 3.2 6.2 + - - +
280J THR* 3.1 46.5 + - + +
288J LEU* 4.1 23.1 - - + -
291J MET* 3.8 23.7 - - + +
292J TYR* 3.6 21.1 - + + -
295J PHE* 3.8 20.0 - + - -
312J SER* 2.7 36.3 + - - -
316J TYR* 3.6 33.7 - + + -
320J HIS* 3.2 25.3 + + + +
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Residues in contact with ALA 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J VAL 3.0 14.4 + - - +
274J THR 3.3 9.6 - - - +
275J GLU 3.1 0.2 - - - -
276J TYR* 1.3 78.2 - - - +
278J MET* 1.3 53.2 + - + +
280J THR* 4.2 0.7 - - - -
281J LYS* 2.8 34.5 + - - -
282J CYS 3.3 3.6 + - - -
288J LEU* 3.8 21.3 - - + -
340J ALA* 3.6 23.8 - - + +
344J VAL* 3.7 18.8 - - + +
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Residues in contact with MET 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J THR* 2.9 22.4 + - + +
275J GLU* 3.1 9.6 + - - +
277J ALA* 1.3 76.5 - - - +
279J GLU* 1.3 67.2 + - - +
281J LYS* 3.6 16.7 - - - +
343J THR* 3.5 46.4 - - + +
344J VAL* 4.3 8.5 - - - +
347J LYS* 3.9 33.0 - - + +
293K LEU* 5.7 4.5 - - + -
297K TYR* 5.2 9.9 - - - +
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Residues in contact with GLU 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J GLU* 3.0 31.2 + - + +
276J TYR* 3.3 8.7 - - - +
277J ALA 3.1 0.2 - - - -
278J MET* 1.3 81.0 - - - +
280J THR* 1.3 63.0 + - + +
281J LYS* 3.0 15.4 + - - +
316J TYR* 3.5 46.4 + - + +
319J LYS* 5.5 5.8 - - - -
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Residues in contact with THR 280 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J TYR* 3.1 40.7 + - + +
277J ALA* 3.8 0.9 + - - -
279J GLU* 1.3 76.8 - - - +
281J LYS* 1.3 72.3 + - - +
282J CYS* 3.1 21.4 + - - +
312J SER* 3.6 32.3 - - - -
316J TYR* 4.6 7.4 - - + -
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Residues in contact with LYS 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277J ALA 2.8 13.2 + - - -
278J MET* 3.6 12.3 - - - +
279J GLU 3.0 14.1 - - - +
280J THR* 1.3 79.5 - - - +
282J CYS* 1.3 62.8 + - - +
283J ASP* 3.1 8.8 + - - +
344J VAL* 3.6 14.5 - - + +
348J LYS* 3.7 20.6 + - - +
363J ASN* 5.7 4.0 - - - +
367J ASP* 3.5 31.0 + - - -
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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