Contacts of the helix formed by residues 269 - 281 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D GLN 3.9 2.5 + - - -
268D VAL* 1.3 73.4 - - - +
270D TRP* 1.3 62.0 + - - +
271D LYS* 3.7 6.8 + - - +
272D LEU* 3.3 42.2 + - - +
273D VAL* 3.3 9.0 + - - +
323D ASN* 2.6 32.3 + - - -
336D ILE* 4.6 1.4 - - - +
329E ASP* 5.7 0.5 + - - -
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Residues in contact with TRP 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268D VAL* 3.6 21.6 - - + +
269D SER* 1.3 72.2 + - - +
271D LYS* 1.3 58.7 + - - +
272D LEU 3.2 2.0 - - - -
273D VAL* 3.3 3.3 + - - +
274D THR* 2.8 37.5 + - - -
332D ASN* 5.1 7.9 - - + -
335D THR* 3.6 33.7 - - + -
336D ILE* 3.6 45.7 - - + +
339D GLN* 3.1 36.8 - - + +
328E ALA 5.3 0.4 - - - -
329E ASP 5.7 4.7 - - - -
330E SER 4.6 6.3 - - - +
331E LYS* 2.8 72.8 - - + +
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Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D SER* 3.5 6.5 - - - +
270D TRP* 1.3 80.6 - - - +
272D LEU* 1.3 59.2 + - + +
274D THR* 3.7 7.0 - - - -
275D GLU* 2.9 39.1 + - - +
296E GLN* 4.1 15.7 - - - +
297E TYR* 6.1 1.8 - - - -
328E ALA* 4.0 34.2 + - + +
329E ASP* 3.5 33.0 - - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D SER* 3.3 22.2 + - - +
270D TRP 3.2 0.4 - - - -
271D LYS* 1.3 78.2 - - + +
273D VAL* 1.3 59.5 + - - +
275D GLU* 3.1 19.5 + - - +
276D TYR* 3.0 24.1 + - - +
292D TYR* 4.1 0.4 - - - +
319D LYS* 4.9 8.5 - - + +
320D HIS* 3.2 27.9 - - + +
322D ALA* 5.8 2.9 - - + -
323D ASN* 3.5 35.4 - - + +
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Residues in contact with VAL 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D SER 3.3 9.6 - - - +
270D TRP 3.3 5.3 + - - +
272D LEU* 1.3 76.2 - - - +
274D THR* 1.3 58.1 + - - +
276D TYR* 3.4 4.0 + - - +
277D ALA* 3.0 26.5 + - - +
288D LEU* 5.1 4.6 - - + +
292D TYR* 3.5 29.8 - - + -
323D ASN* 3.2 26.2 - - - +
327D PHE* 4.7 2.0 - - + -
336D ILE* 3.6 33.0 - - + +
337D CYS* 4.2 24.2 - - - -
340D ALA* 4.4 4.3 - - + -
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Residues in contact with THR 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D TRP* 2.8 22.0 + - - +
271D LYS* 3.7 8.4 - - - -
273D VAL* 1.3 75.6 - - - +
275D GLU* 1.3 61.2 + - - +
277D ALA* 3.2 2.3 + - - +
278D MET* 2.9 29.0 + - + +
336D ILE 5.3 1.2 + - - -
339D GLN* 4.2 13.2 + - - -
340D ALA* 3.9 18.2 + - - +
343D THR* 3.6 40.7 + - + +
293E LEU* 6.4 0.2 - - + -
328E ALA 6.0 0.2 - - - -
333E GLN* 4.8 9.7 + - - +
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D LYS* 2.9 27.4 + - + +
272D LEU* 3.2 28.4 - - - +
274D THR* 1.3 77.4 - - - +
276D TYR* 1.3 64.1 + - - +
278D MET* 3.1 10.5 + - + +
279D GLU* 3.0 34.3 + - + +
319D LYS* 3.2 34.8 + - - -
320D HIS* 3.9 4.1 - - + -
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Residues in contact with TYR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272D LEU 3.0 8.5 + - - +
273D VAL* 3.6 7.6 - - + +
275D GLU* 1.3 75.8 - - - +
277D ALA* 1.3 62.3 + - - +
279D GLU* 3.2 6.1 + - - +
280D THR* 3.1 46.5 + - + +
288D LEU* 4.1 22.7 - - + -
291D MET* 3.8 23.3 - - + +
292D TYR* 3.6 21.5 - + + -
295D PHE* 3.8 19.7 - + - -
312D SER* 2.7 35.9 + - - -
316D TYR* 3.7 33.7 - + + -
320D HIS* 3.2 24.4 + + + +
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Residues in contact with ALA 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D VAL 3.0 14.1 + - - +
274D THR 3.3 9.4 - - - +
275D GLU 3.1 0.2 - - - -
276D TYR* 1.3 78.4 - - - +
278D MET* 1.3 53.5 + - + +
280D THR* 4.2 0.7 - - - -
281D LYS* 2.8 34.7 + - - -
282D CYS 3.3 4.2 + - - +
288D LEU* 3.8 20.0 - - + -
340D ALA* 3.6 24.0 - - + +
344D VAL* 3.7 19.1 - - + +
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Residues in contact with MET 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D THR* 2.9 22.4 + - + +
275D GLU* 3.1 9.8 + - - +
277D ALA* 1.3 76.3 - - - +
279D GLU* 1.3 66.5 + - - +
281D LYS* 3.6 17.3 - - - +
343D THR* 3.5 45.3 - - + +
344D VAL* 4.3 7.9 - - - -
347D LYS* 3.9 33.4 - - + +
293E LEU* 5.8 4.3 - - + -
297E TYR* 5.1 10.3 - - - +
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D GLU* 3.0 30.6 + - + +
276D TYR* 3.3 8.5 - - - +
277D ALA 3.1 0.4 - - - -
278D MET* 1.3 79.5 - - - +
280D THR* 1.3 63.5 + - + +
281D LYS* 3.0 15.4 + - - +
316D TYR* 3.5 46.3 + - + +
319D LYS* 5.5 6.1 - - - -
320D HIS* 5.6 0.2 - - - +
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Residues in contact with THR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D TYR* 3.1 40.9 + - + +
277D ALA* 3.8 1.4 + - - -
279D GLU* 1.3 77.0 - - - +
281D LYS* 1.3 70.5 + - - +
282D CYS* 3.1 20.6 + - - +
312D SER* 3.6 31.9 - - - -
316D TYR* 4.6 7.6 - - + -
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Residues in contact with LYS 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D ALA 2.8 13.2 + - - -
278D MET* 3.6 12.6 - - - +
279D GLU 3.0 13.8 - - - +
280D THR* 1.3 79.3 - - - +
282D CYS* 1.3 62.9 + - - +
283D ASP* 3.1 10.9 + - - +
344D VAL* 3.6 15.0 - - + +
348D LYS* 3.7 18.2 + - - +
363D ASN* 5.7 3.6 - - - +
367D ASP* 3.5 30.4 + - - -
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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