Contacts of the helix formed by residues 310 - 320 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250J ASP* 3.4 39.9 - - + +
251J HIS 3.5 4.9 - - - -
252J GLN* 4.2 12.1 - - + -
253J ILE* 4.3 7.2 - - - +
308J TYR* 5.4 3.8 - - + -
309J LEU* 1.3 80.0 - - - +
311J MET* 1.3 64.2 + - - +
312J ASP* 3.6 6.7 + - - +
313J ASP* 3.1 37.0 + - - +
314J LEU* 3.1 20.8 + - - +
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Residues in contact with MET 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J LEU* 3.9 14.1 - - - -
246J LEU* 3.8 12.1 - - + -
250J ASP 4.4 0.2 + - - -
251J HIS* 3.1 24.0 + - + +
253J ILE* 3.5 21.3 - - - +
310J THR* 1.3 75.3 - - - +
312J ASP* 1.3 61.4 + - - +
314J LEU* 3.2 20.8 + - + +
315J THR* 2.9 36.1 + - + +
341J ILE* 4.4 7.4 - - + -
343J TYR* 3.5 65.5 - - + +
348J ILE* 4.3 11.9 - - + -
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Residues in contact with ASP 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J ASP 5.2 4.6 + - - +
251J HIS* 6.0 2.2 + - - -
310J THR* 3.3 7.2 + - - +
311J MET* 1.3 77.6 - - - +
313J ASP* 1.3 67.0 + - - +
315J THR* 3.3 9.0 + - - -
316J THR* 2.8 36.1 + - - +
343J TYR* 5.6 2.9 + - - -
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Residues in contact with ASP 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265J TRP* 3.6 20.1 - - + -
268J GLU* 4.1 13.7 - - - +
307J ARG* 3.7 14.0 + - - -
308J TYR 4.1 2.3 - - - +
309J LEU* 3.9 5.6 - - + -
310J THR* 3.1 41.4 + - - +
312J ASP* 1.3 77.1 - - - +
314J LEU* 1.3 57.0 + - - +
316J THR* 3.9 4.7 - - - -
317J ALA* 3.1 27.9 + - - +
322J ARG* 4.9 1.6 + - - -
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Residues in contact with LEU 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253J ILE* 4.4 14.1 - - + -
263J LEU* 4.3 19.7 - - + -
265J TRP* 4.9 3.1 - - - -
310J THR 3.1 10.3 + - - +
311J MET* 3.3 26.7 - - + +
313J ASP* 1.3 80.2 - - - +
315J THR* 1.3 58.4 + - + +
317J ALA* 3.2 4.7 + - - +
318J LEU* 3.0 43.8 + - + +
323J VAL* 3.9 20.6 - - + -
326J MET* 4.2 11.2 - - + -
341J ILE* 3.6 31.4 - - + -
348J ILE* 6.0 0.7 - - + -
350J ILE* 4.4 10.1 - - + -
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Residues in contact with THR 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311J MET* 2.9 30.8 + - + +
312J ASP* 3.3 14.2 + - - -
314J LEU* 1.3 71.8 - - + +
316J THR* 1.3 67.5 + - - +
318J LEU* 3.5 12.6 + - + +
319J GLU* 3.1 26.1 + - - +
343J TYR* 5.4 4.3 - - + -
348J ILE* 4.3 26.0 - - + -
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Residues in contact with THR 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312J ASP* 2.8 24.9 + - - +
313J ASP* 3.9 4.9 - - - -
315J THR* 1.3 78.3 + - - +
317J ALA* 1.3 62.6 + - - +
319J GLU* 3.5 16.8 + - - +
320J GLY* 3.3 16.8 + - - -
322J ARG* 4.0 14.5 + - - +
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Residues in contact with ALA 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J TRP* 3.6 27.4 - - + -
313J ASP 3.1 20.5 + - - +
314J LEU 3.2 4.7 + - - +
316J THR* 1.3 78.0 - - - +
318J LEU* 1.3 57.0 + - - +
320J GLY 3.4 1.0 + - - -
321J ASN 3.2 3.8 + - - -
322J ARG* 2.7 54.8 + - + +
323J VAL* 3.7 10.5 - - + -
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Residues in contact with LEU 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314J LEU* 3.0 33.4 + - + +
315J THR* 3.9 9.2 - - - +
316J THR 3.3 0.2 - - - -
317J ALA* 1.3 73.2 - - - +
319J GLU* 1.3 65.9 + - - +
321J ASN* 3.2 19.0 + - - +
322J ARG 4.8 0.4 - - - +
323J VAL* 3.7 18.2 - - + -
348J ILE* 3.6 30.3 - - + -
349J HIS 3.6 19.3 - - - +
350J ILE* 3.8 16.4 - - + -
351J PRO* 3.7 23.6 - - + -
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Residues in contact with GLU 319 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J THR 3.1 16.7 + - - +
316J THR* 3.5 20.9 + - - +
318J LEU* 1.3 76.0 - - - +
320J GLY* 1.3 57.3 + - - +
321J ASN* 3.3 8.4 + - - -
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Residues in contact with GLY 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316J THR 3.3 10.2 + - - -
317J ALA 3.4 1.5 + - - -
318J LEU 3.2 0.6 - - - -
319J GLU* 1.3 78.6 - - - +
321J ASN* 1.3 71.4 + - - +
322J ARG* 3.2 19.8 + - - +
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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