Contacts of the helix formed by residues 269 - 281 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267E GLN 3.9 2.1 + - - -
268E VAL* 1.3 72.7 - - - +
270E TRP* 1.3 62.3 + - - +
271E LYS* 3.7 6.9 + - - +
272E LEU* 3.3 42.4 + - - +
273E VAL* 3.3 9.2 + - - +
323E ASN* 2.6 32.3 + - - -
336E ILE* 4.6 1.0 - - - +
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Residues in contact with TRP 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E VAL* 3.6 24.8 - - + +
269E SER* 1.3 71.6 - - - +
271E LYS* 1.3 58.5 + - - +
272E LEU 3.1 2.5 - - - -
273E VAL* 3.3 3.3 + - - +
274E THR* 2.8 36.9 + - - -
332E ASN* 5.1 8.1 - - + -
335E THR* 3.6 33.2 - - + -
336E ILE* 3.6 46.8 - - + +
339E GLN* 3.2 43.7 - - + +
328F ALA 5.9 0.2 - - - -
329F ASP* 6.2 3.8 - - - -
330F SER 5.2 4.3 - - - +
331F LYS* 3.2 62.1 - - + +
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Residues in contact with LYS 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E SER* 3.6 6.0 - - - +
270E TRP* 1.3 79.6 - - - +
272E LEU* 1.3 59.1 + - + +
274E THR* 3.7 7.7 - - - -
275E GLU* 2.9 38.6 + - - +
296F GLN* 4.5 19.5 - - - +
328F ALA* 4.6 20.9 + - + +
329F ASP* 4.0 28.9 - - - +
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Residues in contact with LEU 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E SER* 3.3 24.3 + - - +
270E TRP 3.1 0.6 - - - -
271E LYS* 1.3 78.3 - - + +
273E VAL* 1.3 64.7 + - - +
275E GLU* 3.1 19.4 + - - +
276E TYR* 3.0 19.2 + - - +
292E TYR* 4.3 0.2 - - - -
319E LYS* 4.9 8.3 - - + +
320E HIS* 3.2 29.5 - - + +
322E ALA* 5.8 3.4 - - + -
323E ASN* 3.5 35.4 - - + +
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Residues in contact with VAL 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E SER 3.3 9.2 - - - +
270E TRP 3.3 5.1 + - - +
272E LEU* 1.3 75.2 - - - +
274E THR* 1.3 58.0 + - - +
276E TYR* 3.3 4.7 + - - +
277E ALA* 3.0 26.0 + - - +
288E LEU* 5.1 4.4 - - + +
292E TYR* 3.5 29.4 - - + -
323E ASN* 3.2 26.0 - - - +
327E PHE* 4.8 2.7 - - + -
336E ILE* 3.6 33.7 - - + +
337E CYS* 4.2 24.7 - - - -
340E ALA* 4.4 4.3 - - + -
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Residues in contact with THR 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E TRP 2.8 23.0 + - - -
271E LYS* 3.7 8.7 - - - -
273E VAL* 1.3 74.4 - - - +
275E GLU* 1.3 61.1 + - - +
277E ALA* 3.2 2.1 + - - +
278E MET* 2.9 31.0 + - + +
336E ILE 5.3 1.4 + - - -
339E GLN* 4.2 13.2 + - - -
340E ALA* 4.0 17.4 + - - +
343E THR* 3.6 39.7 + - + +
333F GLN* 5.3 6.9 + - - +
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Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E LYS* 2.9 28.9 + - + +
272E LEU* 3.2 27.9 - - - +
274E THR* 1.3 76.9 - - - +
276E TYR* 1.3 63.8 + - - +
278E MET* 3.1 9.4 + - - +
279E GLU* 3.0 34.3 + - + +
319E LYS* 3.2 35.8 + - - -
320E HIS* 3.9 4.8 - - + -
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Residues in contact with TYR 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E LEU 3.0 8.6 + - - +
273E VAL* 3.6 7.6 - - + +
275E GLU* 1.3 75.6 - - - +
277E ALA* 1.3 61.1 + - - +
279E GLU* 3.2 6.2 + - - +
280E THR* 3.1 47.3 + - + +
288E LEU* 4.1 22.7 - - + -
291E MET* 3.8 23.1 - - + +
292E TYR* 3.6 21.8 - + + -
295E PHE* 3.8 20.2 - + - -
312E SER* 2.7 36.2 + - - -
316E TYR* 3.6 32.5 - + + -
320E HIS* 3.2 26.4 + + + +
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Residues in contact with ALA 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E VAL 3.0 13.9 + - - +
274E THR 3.3 9.6 - - - +
275E GLU 3.1 0.2 - - - -
276E TYR* 1.3 77.8 - - - +
278E MET* 1.3 52.5 + - - +
280E THR* 4.2 0.9 - - - -
281E LYS* 2.8 34.3 + - - -
282E CYS 3.3 4.0 + - - +
288E LEU* 3.8 20.4 - - + -
340E ALA* 3.6 24.7 - - + +
344E VAL* 3.7 18.8 - - + +
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Residues in contact with MET 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274E THR* 2.9 21.7 + - + +
275E GLU* 3.1 9.6 + - + +
277E ALA* 1.3 76.8 - - - +
279E GLU* 1.3 66.9 + - - +
281E LYS* 3.6 16.1 - - - +
343E THR* 3.5 48.2 - - + +
344E VAL* 4.3 7.9 - - - +
347E LYS* 3.9 33.7 - - + +
293F LEU* 6.2 1.8 - - + -
297F TYR* 5.2 10.1 - - - +
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Residues in contact with GLU 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E GLU* 3.0 31.9 + - + +
276E TYR* 3.3 10.3 - - - +
277E ALA 3.1 0.2 - - - -
278E MET* 1.3 80.6 - - - +
280E THR* 1.3 62.8 + - + +
281E LYS* 3.0 15.4 + - - +
316E TYR* 3.5 44.4 + - + +
319E LYS* 5.5 6.3 - - - -
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Residues in contact with THR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E TYR* 3.1 41.1 + - + +
277E ALA* 3.8 1.0 + - - -
279E GLU* 1.3 76.2 - - - +
281E LYS* 1.3 70.7 + - - +
282E CYS* 3.1 21.7 + - - +
312E SER* 3.6 32.8 - - - -
316E TYR* 4.6 7.4 - - + -
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Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277E ALA 2.8 12.8 + - - -
278E MET 3.6 12.1 - - - +
279E GLU 3.0 14.3 - - - +
280E THR* 1.3 79.3 - - - +
282E CYS* 1.3 63.8 + - - +
283E ASP* 3.1 10.7 + - - +
344E VAL* 3.6 14.5 - - + +
348E LYS* 3.7 16.9 + - - +
363E ASN* 5.7 4.0 - - - +
367E ASP* 3.6 30.8 + - - -
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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