Contacts of the helix formed by residues 309 - 318 (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 THR 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276D SER* 4.6 2.5 - - - -
300D LEU 4.6 0.9 - - - -
301D ARG 4.0 8.3 - - - +
302D ARG 3.6 9.0 - - - -
303D GLN* 3.5 25.8 - - + +
307D GLY 3.6 1.0 + - - +
308D ASN* 1.3 76.4 - - - +
310D VAL* 1.3 65.2 + - - +
311D LEU* 3.4 16.3 + - - +
312D HIS* 3.1 33.8 + - + +
313D ALA* 3.1 11.4 + - - +
348D LEU* 3.5 31.3 + - + +
351D LEU* 4.4 8.7 - - + -
352D LEU 6.2 0.2 - - - +
359D PRO* 4.6 0.7 - - - +
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Residues in contact with VAL 310 (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* 4.0 20.9 - - + +
276D SER* 3.7 21.1 + - - +
279D ALA* 3.9 19.1 - - + -
300D LEU* 3.9 19.0 + - - +
302D ARG 4.3 4.0 + - - -
309D THR* 1.3 74.5 - - - +
311D LEU* 1.3 71.8 - - + +
313D ALA* 3.4 3.7 + - - +
314D LEU* 3.2 23.1 + - + +
335D LEU* 3.5 44.6 - - + -
348D LEU* 4.4 4.0 - - + -
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Residues in contact with LEU 311 (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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309D THR* 3.1 7.1 - - - +
310D VAL* 1.3 83.3 - - + +
312D HIS* 1.3 64.0 + - - +
314D LEU* 3.3 6.3 + - + +
315D VAL* 3.2 26.0 + - - +
332D TYR* 3.5 62.1 - - + +
335D LEU* 4.5 8.5 - - + -
336D LEU* 4.4 6.3 - - + -
348D LEU* 3.9 44.0 - - + +
349D GLU* 4.0 12.6 - - + -
359D PRO* 3.6 15.5 - - + -
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Residues in contact with HIS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLY 4.3 1.3 - - - -
308D ASN* 3.3 31.6 + - + +
309D THR* 3.1 37.8 + - + +
311D LEU* 1.3 78.1 - - - +
313D ALA* 1.3 55.9 + - - +
315D VAL* 3.4 7.9 + - - +
316D ALA* 3.0 23.2 + - - +
351D LEU 3.5 13.7 + - - -
352D LEU 4.2 0.6 - - - -
353D ASN* 3.7 13.2 + - + -
357D LEU 3.0 27.6 + - - -
358D SER 3.5 1.8 - - - -
359D PRO* 3.5 30.0 - - + +
362D MET* 3.0 32.4 - - + +
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Residues in contact with ALA 313 (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 TYR* 4.8 5.1 - - - +
270D PHE 3.8 9.2 - - - +
271D GLY* 3.7 30.5 - - - +
276D SER* 4.2 8.1 - - - -
280D CYS* 3.2 16.6 - - - -
308D ASN* 4.6 0.6 - - + +
309D THR 3.1 10.2 + - - +
310D VAL 3.6 8.5 - - - +
311D LEU 3.2 0.2 - - - -
312D HIS* 1.3 75.1 - - - +
314D LEU* 1.3 59.9 + - - +
316D ALA* 3.3 9.2 - - - +
317D ILE* 3.1 22.5 + - - +
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Residues in contact with LEU 314 (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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279D ALA* 3.7 34.8 - - + +
280D CYS* 4.0 9.9 - - - +
310D VAL* 3.2 22.0 + - + +
311D LEU* 3.3 10.0 + - - +
313D ALA* 1.3 74.3 - - - +
315D VAL* 1.3 61.1 + - + +
317D ILE* 3.6 13.5 - - + +
318D ALA* 3.0 28.1 + - - +
328D VAL* 3.7 23.6 - - + +
331D MET* 4.1 7.9 - - + -
332D TYR* 3.8 27.8 - - + +
335D LEU* 3.7 28.7 - - + -
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Residues in contact with VAL 315 (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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311D LEU 3.2 14.9 + - - +
312D HIS 3.6 8.3 - - - +
313D ALA 3.3 0.2 - - - -
314D LEU* 1.3 76.3 - - - +
316D ALA* 1.3 50.8 + - - +
318D ALA* 3.4 12.3 + - - +
332D TYR* 4.8 3.4 - - + -
359D PRO* 3.8 25.4 - - + +
362D MET* 3.8 15.7 - - + -
363D ALA* 3.5 36.1 - - + +
366D THR* 4.4 0.7 - - - +
368D LYS* 2.7 37.5 + - + +
371D ILE* 4.4 20.6 - - + -
375D ILE* 5.3 1.1 - - + -
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Residues in contact with ALA 316 (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 TYR* 3.8 35.4 - - + +
306D ARG* 5.5 0.7 - - - +
308D ASN* 5.7 0.4 - - - +
312D HIS 3.0 14.4 + - - +
313D ALA 3.3 9.2 - - - +
314D LEU 3.3 0.2 - - - -
315D VAL* 1.3 76.8 - - - +
317D ILE* 1.3 59.6 + - - +
318D ALA 4.0 0.2 - - - +
362D MET* 5.0 5.1 - - - -
368D LYS* 2.8 19.8 + - - +
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Residues in contact with ILE 317 (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* 3.6 24.2 - - + -
269D TYR 3.4 24.7 - - - +
280D CYS* 3.5 42.4 - - + +
313D ALA 3.1 7.8 + - - +
314D LEU* 3.6 8.1 - - + +
316D ALA* 1.3 73.1 - - - +
318D ALA* 1.3 59.3 + - - +
319D ASP* 2.9 11.8 + - - +
324D ASN* 3.1 15.6 + - - +
327D PHE* 3.4 24.0 - - + -
328D VAL* 3.2 33.0 - - + -
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Residues in contact with ALA 318 (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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314D LEU 3.0 18.7 + - - +
315D VAL* 3.4 12.1 - - - +
316D ALA 3.2 1.0 - - - +
317D ILE* 1.3 74.4 - - - +
319D ASP* 1.3 63.5 + - - +
320D ASN* 5.5 1.6 - - - +
324D ASN* 3.5 10.3 - - - +
325D THR* 6.0 2.0 - - - -
328D VAL* 4.2 13.5 - - + -
368D LYS* 2.7 47.5 + - + +
371D ILE* 4.2 8.3 - - + +
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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