Contacts of the helix formed by residues 369 - 386 (chain A) in PDB entry 2XLR
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368A VAL* 1.3 84.3 - - + +
370A ALA* 1.3 65.9 + - - +
371A GLU* 3.8 12.3 + - - +
372A GLU* 2.7 56.1 + - - +
373A MET* 3.1 15.8 + - - +
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A TRP* 4.0 28.1 - - + -
368A VAL 4.1 0.6 + - - -
369A THR* 1.3 72.9 - - - +
371A GLU* 1.3 64.4 + - - +
373A MET* 3.1 13.4 + - - +
374A TYR* 3.1 16.1 + - - +
403A LEU* 5.5 2.2 - - + -
406A LYS* 4.9 19.7 - - + -
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Residues in contact with GLU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A THR* 3.1 11.2 + - - +
370A ALA* 1.3 79.4 - - - +
372A GLU* 1.3 59.5 + - + +
374A TYR* 3.9 3.5 + - - +
375A THR* 2.6 41.2 + - - +
400A LYS* 5.3 9.4 - - - +
403A LEU* 3.9 40.6 - - + +
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A THR* 4.6 10.4 - - - +
367A LEU* 4.0 20.1 - - + +
368A VAL* 3.0 18.0 + - - +
369A THR* 2.7 52.3 + - - +
371A GLU* 1.3 80.7 - - + +
373A MET* 1.3 58.2 + - - +
375A THR* 3.5 6.4 + - - -
376A TYR* 2.9 28.4 + - - +
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Residues in contact with MET 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.7 28.9 - - + +
324A TRP* 3.7 34.8 - - + -
367A LEU* 3.9 28.0 - - + +
368A VAL 3.7 25.1 - - - +
369A THR 3.1 9.8 + - - +
370A ALA* 3.1 8.2 + - - +
372A GLU* 1.3 74.1 - - - +
374A TYR* 1.3 65.2 + - - +
375A THR 3.1 1.1 - - - -
376A TYR* 3.0 6.1 + - - +
377A GLN* 2.9 23.8 + - - +
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Residues in contact with TYR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A TRP* 4.2 26.7 - - + -
325A TYR* 3.8 5.6 - - + -
370A ALA 3.1 12.0 + - - +
371A GLU* 4.2 5.4 - - - +
373A MET* 1.3 74.7 - - - +
375A THR* 1.3 64.2 + - - +
377A GLN* 3.2 1.5 + - - +
378A GLY* 2.8 21.8 + - - -
399A ASN* 3.8 18.4 - - + +
402A PHE* 4.5 24.9 - - + -
403A LEU* 6.0 2.7 - - + -
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 2.6 32.8 + - - +
372A GLU* 3.7 7.4 - - - -
374A TYR* 1.3 79.6 - - - +
376A TYR* 1.3 56.7 + - - +
378A GLY* 3.4 1.2 + - - -
379A ASP* 2.9 41.3 + - - +
399A ASN* 3.8 23.7 + - - +
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Residues in contact with TYR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.8 40.8 - - + -
299A TRP* 3.4 19.8 - + - +
360A TRP* 2.9 56.4 + + - -
363A LYS* 3.7 31.6 - - + -
364A GLU* 3.9 11.2 - - + -
367A LEU* 3.7 17.3 - - + -
372A GLU 2.9 15.2 + - - +
373A MET 3.0 7.6 + - - +
375A THR* 1.3 76.1 - - - +
377A GLN* 1.3 68.6 + - - +
379A ASP* 3.0 12.0 + - + +
380A TYR* 2.9 22.6 + - + +
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Residues in contact with GLN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.6 20.8 + - + +
321A GLN* 4.2 7.5 - - - +
322A ASP 3.0 22.8 + - - -
324A TRP* 2.8 32.2 + - + +
325A TYR* 2.8 25.7 + - + +
329A MET* 3.6 28.5 - - - -
373A MET 2.9 14.0 + - - +
374A TYR* 4.0 4.5 - - - +
376A TYR* 1.3 80.6 - - - +
378A GLY* 1.4 52.8 + - - +
380A TYR* 2.9 12.7 + - + +
381A ILE* 2.8 41.8 + - + +
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Residues in contact with GLY 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.6 13.9 - - - -
374A TYR 2.8 21.1 + - - -
375A THR 3.6 2.2 - - - -
377A GLN* 1.4 70.4 - - - +
379A ASP* 1.3 62.1 + - - +
381A ILE* 3.8 3.3 - - - +
382A GLN* 3.0 25.1 + - - +
395A ILE* 3.7 30.3 - - - +
399A ASN* 4.7 0.7 - - - -
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A TRP* 4.2 11.3 - - + -
363A LYS* 5.7 3.3 + - - -
375A THR* 2.9 31.3 + - - +
376A TYR* 3.0 13.4 + - + +
378A GLY* 1.3 78.4 - - - +
380A TYR* 1.4 59.4 + - - +
382A GLN* 3.6 7.1 - - - +
383A ASN* 2.9 28.8 + - - +
395A ILE* 5.9 0.9 - - - +
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Residues in contact with TYR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU 6.0 0.4 - - - -
299A TRP* 3.7 26.2 - + + -
305A LYS* 2.5 34.0 + - + -
306A GLY* 3.4 6.2 - - - -
307A VAL* 3.7 0.5 - - - +
321A GLN* 4.7 9.2 - - + -
329A MET* 4.2 18.2 - - + -
333A GLN* 2.9 32.1 + - - +
360A TRP* 3.6 25.1 - + + -
376A TYR* 2.9 14.8 + - + +
377A GLN* 2.9 15.3 + - + +
379A ASP* 1.4 77.6 - - - +
381A ILE* 1.3 68.9 + - + +
383A ASN* 3.1 15.3 + - + +
384A LEU* 3.1 38.3 + - + +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A TYR* 3.4 49.1 - - + -
328A ASN* 4.8 3.4 - - + +
329A MET* 3.8 28.9 - - + +
332A ALA* 4.0 16.4 - - + -
377A GLN* 2.8 22.4 + - + +
378A GLY* 3.8 4.0 - - - +
380A TYR* 1.3 82.1 - - + +
382A GLN* 1.3 62.0 + - - +
384A LEU* 3.1 9.6 + - - +
385A ILE* 3.0 29.6 + - + +
393A PHE* 4.4 10.5 - - + -
395A ILE* 4.3 11.4 - - + -
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Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A GLY 3.0 19.8 + - - +
379A ASP* 3.6 8.7 - - - +
381A ILE* 1.3 73.6 - - - +
383A ASN* 1.3 67.2 + - - +
385A ILE* 3.5 10.8 - - - +
386A ASP* 2.8 64.3 + - - +
392A SER* 3.5 19.2 + - - -
393A PHE 4.6 4.5 - - - +
395A ILE* 3.4 24.7 + - + +
396A PRO* 5.4 2.4 - - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LYS* 3.0 32.9 + - - +
360A TRP* 4.5 19.3 - - + -
379A ASP 2.9 14.8 + - - +
380A TYR* 3.1 11.0 + - + +
382A GLN* 1.3 77.1 - - - +
384A LEU* 1.3 61.8 + - - +
386A ASP* 3.8 11.0 + - - +
387A MET* 3.4 24.6 + - - +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A LYS* 4.0 23.1 - - + +
307A VAL* 5.2 0.4 - - + -
329A MET* 5.0 0.4 - - + +
332A ALA* 3.9 24.3 - - + +
333A GLN* 3.8 20.2 - - + +
336A TYR* 4.1 25.3 - - + +
380A TYR* 3.1 49.5 + - + +
381A ILE* 3.1 10.1 + - + +
383A ASN* 1.3 73.4 - - - +
385A ILE* 1.3 65.0 + - - +
386A ASP 3.2 1.8 - - - -
387A MET* 3.2 32.0 + - + +
388A THR* 3.8 11.3 + - - +
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ALA* 3.8 20.2 - - + +
381A ILE* 3.0 25.3 + - + +
382A GLN* 3.5 34.3 - - - +
384A LEU* 1.3 73.0 - - - +
386A ASP* 1.3 59.7 + - - +
387A MET 3.3 0.2 + - - -
388A THR* 3.1 30.5 + - - +
390A TYR* 3.7 34.2 - - + +
392A SER* 3.6 28.7 - - - +
393A PHE* 4.3 9.6 - - + +
395A ILE* 4.1 16.2 - - + -
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A GLN* 2.8 52.2 + - - +
383A ASN* 4.0 8.7 - - - +
384A LEU 3.2 0.6 - - - -
385A ILE* 1.3 76.8 - - - +
387A MET* 1.3 61.7 + - + +
388A THR 3.4 1.9 + - - +
392A SER* 4.3 4.0 + - - -
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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