Contacts of the helix formed by residues 310 - 320 (chain D) in PDB entry 2ABJ
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 310 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250D ASP* 3.3 37.0 - - + +
251D HIS 3.5 4.7 - - - -
252D GLN* 4.2 12.6 - - + +
253D ILE* 4.3 6.4 - - - +
308D TYR* 5.3 3.1 - - + -
309D LEU* 1.3 80.2 - - - +
311D MET* 1.3 64.6 + - - +
312D ASP* 3.4 8.5 + - - +
313D ASP* 3.1 35.3 + - - +
314D LEU* 3.2 22.3 + - - +
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Residues in contact with MET 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ALA* 5.2 0.2 - - - -
244D LEU* 4.1 8.5 - - - -
246D LEU* 3.8 17.0 - - + -
250D ASP 4.4 0.4 + - - -
251D HIS* 3.1 25.0 + - + +
253D ILE* 3.5 21.1 - - - -
310D THR* 1.3 73.6 - - - +
312D ASP* 1.3 60.4 + - - +
314D LEU* 3.3 17.3 + - + +
315D THR* 2.9 36.6 + - + +
341D ILE* 4.1 14.4 - - + -
343D TYR* 3.6 60.1 - - + +
348D ILE* 4.1 10.8 - - + -
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Residues in contact with ASP 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ASP 5.2 3.2 + - - +
251D HIS* 6.2 1.7 - - - -
310D THR* 3.2 7.9 + - - +
311D MET* 1.3 78.9 - - - +
313D ASP* 1.3 63.6 + - - +
314D LEU 3.2 0.2 - - - -
315D THR* 3.5 8.9 + - - -
316D THR* 2.8 35.1 + - - +
343D TYR* 5.9 1.6 - - - -
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Residues in contact with ASP 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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263D LEU* 6.3 0.4 - - + -
265D TRP* 3.7 17.8 - - + -
268D GLU* 4.1 14.8 - - - +
307D ARG* 3.6 16.9 + - - -
308D TYR 3.8 1.7 - - - +
309D LEU* 3.7 7.0 - - + -
310D THR* 3.1 44.9 + - - +
312D ASP* 1.3 74.9 - - - +
314D LEU* 1.3 58.2 + - - +
316D THR* 3.8 4.4 - - - -
317D ALA* 3.0 29.3 + - - +
322D ARG* 4.8 1.6 + - - -
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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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253D ILE* 4.6 11.2 - - + -
263D LEU* 4.1 16.6 - - + -
265D TRP* 4.9 2.0 - - - -
310D THR 3.2 9.3 + - - +
311D MET* 3.5 22.2 - - + +
312D ASP 3.2 0.6 - - - -
313D ASP* 1.3 77.1 - - - +
315D THR* 1.3 59.9 + - + +
317D ALA* 3.2 5.1 + - - +
318D LEU* 2.9 53.7 + - + +
323D VAL* 3.9 21.8 - - + -
326D MET* 3.7 24.0 - - + -
341D ILE* 3.7 29.4 - - + -
348D ILE* 4.8 3.1 - - + -
350D ILE* 4.0 2.0 - - + -
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Residues in contact with THR 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 MET* 2.9 32.0 + - + +
312D ASP* 3.5 14.9 + - - -
314D LEU* 1.3 71.6 - - + +
316D THR* 1.3 59.0 + - - +
318D LEU* 3.7 7.5 - - + +
319D GLU* 3.1 43.4 + - - +
343D TYR* 5.7 2.2 - - + -
346D GLU* 5.5 3.1 - - - +
348D ILE* 4.1 34.1 - - + -
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Residues in contact with THR 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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312D ASP* 2.8 25.6 + - - +
313D ASP* 3.8 5.2 - - - -
315D THR* 1.3 76.6 + - - +
317D ALA* 1.3 63.0 + - - +
319D GLU* 3.5 15.0 + - - +
320D GLY* 3.3 16.8 + - - -
322D ARG* 4.1 15.2 + - - +
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Residues in contact with ALA 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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265D TRP* 3.5 29.4 - - + -
313D ASP 3.0 18.8 + - - +
314D LEU 3.2 5.1 + - - +
316D THR* 1.3 76.3 - - - +
318D LEU* 1.3 62.1 + - - +
320D GLY 3.2 2.8 + - - -
321D ASN 3.1 4.3 + - - -
322D ARG* 2.8 48.2 + - + +
323D VAL* 3.7 10.8 - - + -
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Residues in contact with LEU 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* 2.9 31.2 + - + +
315D THR* 3.7 7.9 - - - +
316D THR 3.3 0.2 - - - -
317D ALA* 1.3 75.3 - - - +
319D GLU* 1.3 64.6 + - + +
321D ASN* 3.2 18.3 + - - +
322D ARG 4.8 0.9 - - - +
323D VAL* 3.8 20.6 - - + +
348D ILE* 3.5 31.9 - - + -
349D HIS 3.5 18.4 - - - +
350D ILE* 3.8 13.2 - - + -
351D PRO* 3.7 24.0 - - + -
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Residues in contact with GLU 319 (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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315D THR* 3.1 31.9 + - - +
316D THR* 3.7 14.4 + - - +
318D LEU* 1.3 75.1 - - + +
320D GLY* 1.3 57.6 + - - +
321D ASN* 3.3 13.0 + - - -
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Residues in contact with GLY 320 (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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316D THR 3.3 7.6 + - - -
317D ALA 3.2 6.5 + - - -
319D GLU* 1.3 75.1 - - - +
321D ASN* 1.3 71.5 + - - +
322D ARG* 3.2 20.2 + - - +
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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