Contacts of the helix formed by residues 273 - 281 (chain D) in PDB entry 3JXI
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 LEU 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229D HIS* 4.5 0.2 - - - -
250D VAL 5.1 0.2 - - - +
251D HIS* 3.3 30.7 - - + +
252D ALA 3.7 1.8 - - - -
253D GLN* 3.3 37.5 - - + +
271D GLY 2.7 17.4 + - - +
272D GLU* 1.3 76.0 - - + +
274D PRO* 1.3 68.4 - - + +
275D LEU* 3.4 5.6 - - + +
276D SER* 3.2 14.4 + - - +
277D LEU* 3.0 25.1 + - - +
302D ARG* 3.9 42.4 - - + +
303D GLN 4.1 11.9 - - - -
304D ASP* 4.3 1.1 - - + +
308D ASN 5.0 1.1 - - - +
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Residues in contact with PRO 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.1 20.6 - - + -
229D HIS* 4.5 12.6 - - + +
232D ILE* 3.3 29.3 - - + +
249D ASP 4.3 0.4 - - - +
250D VAL* 3.3 34.5 - - - +
251D HIS* 4.1 1.8 - - - +
252D ALA* 3.5 17.5 - - + +
272D GLU 3.9 0.4 - - - -
273D LEU* 1.3 85.4 - - + +
275D LEU* 1.3 58.2 + - - +
277D LEU* 3.5 4.9 + - + -
278D ALA* 2.9 30.5 + - - +
290D LEU* 4.2 5.6 - - + -
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Residues in contact with LEU 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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250D VAL 4.8 1.2 + - - +
273D LEU* 3.4 4.4 - - + -
274D PRO* 1.3 80.7 - - + +
276D SER* 1.3 61.8 + - - +
278D ALA* 4.0 0.8 - - - +
279D ALA* 3.3 21.0 + - - +
287D VAL* 4.2 31.6 - - + +
290D LEU* 4.1 13.1 - - + +
291D THR* 4.2 17.7 - - + -
298D ALA* 4.0 22.2 - - + +
299D ASP 3.9 9.0 - - - +
300D LEU* 3.8 37.9 - - + +
310D VAL* 4.0 12.6 - - + +
335D LEU* 4.4 8.7 - - + -
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Residues in contact with SER 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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270D PHE 3.0 21.8 - - - -
271D GLY* 3.8 17.5 + - - -
273D LEU* 3.2 20.3 + - - +
274D PRO 3.2 0.4 - - - -
275D LEU* 1.3 76.1 - - - +
277D LEU* 1.3 53.9 + - - +
279D ALA* 3.2 2.3 + - - +
280D CYS* 2.8 38.5 + - - +
308D ASN 5.2 0.3 + - - -
309D THR 4.6 1.2 - - - -
310D VAL* 3.7 29.1 + - - +
313D ALA* 4.2 7.7 - - - +
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Residues in contact with LEU 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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229D HIS* 3.5 51.6 - - + +
232D ILE* 3.5 20.2 - - + -
233D GLU* 4.3 13.2 - - + +
268D PHE* 4.9 2.0 - - + -
270D PHE* 3.4 46.5 + - + -
273D LEU 3.0 10.3 + - - +
274D PRO* 3.5 8.3 - - + +
276D SER* 1.3 75.7 - - - +
278D ALA* 1.3 49.5 + - - +
281D THR* 2.6 55.9 + - + +
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Residues in contact with ALA 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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232D ILE* 3.9 7.8 - - + +
274D PRO 2.9 17.5 + - - +
275D LEU 4.0 2.0 - - - +
277D LEU* 1.3 74.9 - - - +
279D ALA* 1.3 62.9 + - - +
281D THR* 3.4 10.5 + - - -
282D ASN 3.4 0.3 + - - -
283D GLN* 2.9 30.3 + - + +
286D ILE* 3.6 33.0 - - + -
287D VAL* 3.9 14.4 - - + -
290D LEU* 4.2 4.5 - - + -
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Residues in contact with ALA 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 LEU 3.3 15.5 + - - +
276D SER 3.2 3.2 + - - +
278D ALA* 1.3 79.8 - - - +
280D CYS* 1.3 56.3 + - - +
282D ASN 3.1 14.0 + - - -
287D VAL* 3.6 8.2 - - + +
310D VAL* 3.9 19.7 - - + -
314D LEU* 3.7 10.0 - - + +
327D PHE* 3.3 13.2 - - - -
331D MET* 3.4 36.6 - - + +
335D LEU* 4.3 1.8 - - + -
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Residues in contact with CYS 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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268D PHE* 4.3 8.7 - - + -
270D PHE* 3.8 26.2 - - + -
276D SER* 2.8 23.3 + - - +
277D LEU 4.0 1.6 - - - +
279D ALA* 1.3 70.9 - - - +
281D THR* 1.3 60.0 + - - +
282D ASN 3.3 1.1 - - - -
313D ALA* 3.2 38.1 - - - -
314D LEU* 4.1 6.1 - - - -
317D ILE* 3.5 34.0 - - + +
327D PHE* 3.6 15.5 - - - -
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Residues in contact with THR 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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232D ILE* 4.3 0.7 - - - +
233D GLU* 5.5 9.6 - - + +
235D ARG* 2.8 32.1 + - - -
268D PHE* 4.2 16.8 - - + -
277D LEU* 2.6 40.7 + - + +
278D ALA* 3.4 4.5 + - - -
279D ALA 3.2 0.2 - - - -
280D CYS* 1.3 78.8 - - - +
282D ASN* 1.3 66.3 + - - +
283D GLN* 2.9 28.7 + - - +
327D PHE* 4.9 0.2 - - - -
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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