Contacts of the helix formed by residues 366 - 381 (chain A) in PDB entry 2N5T
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 ARG 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A MET* 2.7 40.0 + - - +
347A PHE* 3.4 27.7 - - - -
357A TRP* 4.4 11.1 - - + -
362A ILE* 2.8 13.1 + - + +
363A ALA 3.2 8.6 - - - +
365A ASP* 1.3 88.5 - - + +
367A ARG* 1.3 64.1 + - - +
368A GLU* 3.2 9.9 - - + +
369A ILE* 2.9 36.7 + - + +
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Residues in contact with ARG 367 (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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363A ALA 3.6 10.1 - - - +
364A MET* 4.5 17.8 + - - +
365A ASP 4.0 1.6 - - - -
366A ARG* 1.3 68.0 - - - +
368A GLU* 1.3 73.0 + - - +
369A ILE 2.7 3.6 + - - -
370A LEU* 3.1 5.5 + - + +
371A ARG* 2.6 28.1 + - + +
405A GLU* 4.0 25.8 + - - +
409A TYR* 4.5 11.8 + - - +
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Residues in contact with GLU 368 (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 ARG* 3.2 7.5 + - + +
367A ARG* 1.3 81.7 + - - +
369A ILE* 1.3 58.4 + - + +
371A ARG* 4.4 7.9 - - - +
372A ASP* 2.9 43.9 + - - +
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Residues in contact with ILE 369 (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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301A PHE* 5.4 9.0 - - + -
307A LEU* 4.3 22.7 - - + -
313A GLN* 5.0 1.4 + - - +
334A MET* 3.7 33.7 - - + -
345A MET* 4.4 16.4 - - + -
347A PHE* 5.0 0.2 - - + -
362A ILE* 3.8 15.5 - - + -
363A ALA* 4.3 2.7 - - + -
366A ARG* 2.9 42.0 + - + +
367A ARG 2.7 5.5 + - - -
368A GLU* 1.3 73.5 - - + +
370A LEU* 1.3 66.3 + - - +
372A ASP* 4.0 4.3 - - - +
373A GLN* 3.1 27.5 + - + +
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Residues in contact with LEU 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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333A THR* 5.3 6.3 - - + -
360A ILE* 4.9 2.5 - - + -
363A ALA* 3.3 39.9 - - + +
364A MET* 4.7 4.0 - - + -
366A ARG 3.8 1.2 + - - -
367A ARG* 3.1 8.0 + - + +
369A ILE* 1.3 80.2 - - - +
371A ARG* 1.3 57.2 + - - +
373A GLN* 3.8 5.0 - - - +
374A LEU* 2.8 59.7 + - + +
390A PHE* 4.4 14.8 - - + -
402A LEU* 4.0 21.8 - - + -
405A GLU* 3.9 30.5 - - + +
409A TYR* 4.5 3.1 - - + +
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A GLU* 4.7 2.0 + - - -
367A ARG* 2.6 24.5 + - + +
368A GLU* 4.0 5.6 - - - +
370A LEU* 1.3 70.1 - - - +
372A ASP* 1.3 79.1 + - - +
374A LEU* 4.2 0.3 - - - +
375A ARG* 2.8 69.4 + - - +
409A TYR* 3.4 36.5 + - + +
412A GLU* 3.4 23.6 + - - -
416A GLU* 4.8 4.4 + - - -
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Residues in contact with ASP 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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307A LEU* 4.7 13.4 - - + +
309A THR* 4.8 2.1 - - - -
310A GLU* 3.6 30.5 + - - +
313A GLN* 3.8 16.6 - - - +
368A GLU* 2.9 32.2 + - - +
369A ILE* 4.0 3.1 - - - +
371A ARG* 1.3 87.6 + - - +
373A GLN* 1.3 59.9 + - - +
375A ARG* 3.4 4.8 - - - +
376A ALA* 2.8 30.5 + - - +
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Residues in contact with GLN 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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297A THR* 2.9 39.8 + - - +
301A PHE* 4.8 4.3 - - + -
313A GLN* 3.1 24.9 - - - +
317A TYR* 3.4 10.3 + - + +
333A THR* 3.4 21.9 - - + +
334A MET* 3.0 32.9 + - - +
369A ILE* 3.1 17.7 + - + +
370A LEU* 3.9 5.4 - - + +
372A ASP* 1.3 80.5 - - - +
374A LEU* 1.3 63.7 + - + +
376A ALA* 3.0 4.2 + - - +
377A ILE* 2.8 31.6 + - + +
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Residues in contact with LEU 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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333A THR* 3.6 28.5 - - + -
370A LEU* 2.8 51.9 + - + +
373A GLN* 1.3 71.4 - - + +
375A ARG* 1.3 64.9 + - - +
377A ILE* 3.2 5.6 + - + +
378A LEU* 2.8 35.7 + - + +
388A ILE* 3.8 29.6 - - + -
390A PHE* 4.2 8.7 - - + -
402A LEU 4.8 2.0 - - - +
406A ILE* 4.1 17.7 - - + +
409A TYR* 3.9 25.8 - - + -
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Residues in contact with ARG 375 (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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310A GLU* 2.7 42.5 + - - +
371A ARG* 2.8 68.3 + - + +
372A ASP 3.4 3.8 - - - +
374A LEU* 1.3 72.7 - - - +
376A ALA* 1.3 56.5 + - - +
378A LEU* 3.3 3.7 + - - +
379A ARG* 2.9 36.5 + - - +
409A TYR* 4.3 14.5 + - + +
412A GLU* 3.3 34.1 + - - +
413A LEU* 3.6 26.4 - - + +
416A GLU* 2.8 33.5 + - - -
418A LYS* 3.8 5.7 - - - +
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Residues in contact with ALA 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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310A GLU* 3.4 27.5 - - + +
313A GLN* 3.6 13.0 - - + -
314A PHE* 3.5 21.7 - - - +
317A TYR* 3.7 4.4 - - + -
372A ASP 2.8 20.0 + - - +
373A GLN 3.4 4.3 - - - +
375A ARG* 1.3 73.3 - - - +
377A ILE* 1.3 64.9 + - - +
379A ARG* 3.3 4.0 + - - +
380A ALA* 2.8 25.1 + - - +
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Residues in contact with ILE 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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317A TYR* 3.7 21.5 - - + -
331A VAL* 3.6 34.5 - - + +
333A THR* 3.8 28.7 - - + -
373A GLN* 2.8 29.5 + - + +
374A LEU* 3.7 12.3 - - + +
376A ALA* 1.3 69.7 - - - +
378A LEU* 1.3 66.8 - - - +
380A ALA* 2.8 15.7 + - - +
381A SER* 2.9 10.4 + - - -
386A LEU* 3.6 14.6 - - + +
387A ARG 4.7 1.3 - - - +
388A ILE* 3.6 27.1 - - + -
424A ILE* 4.4 6.3 - - + -
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Residues in contact with LEU 378 (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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374A LEU* 2.8 27.7 + - + +
377A ILE* 1.3 75.9 - - - +
379A ARG* 1.3 64.9 + - - +
381A SER* 2.3 30.0 + - - +
388A ILE* 3.9 11.9 - - + -
406A ILE* 4.4 8.5 - - + -
409A TYR* 4.4 8.3 - - + -
410A LYS* 4.0 32.5 - - + +
413A LEU* 3.5 24.9 - - + -
420A PHE* 3.3 22.4 - - + +
424A ILE* 3.8 38.6 - - + -
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Residues in contact with ARG 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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310A GLU* 3.4 36.3 + - - +
311A GLU* 3.6 20.8 + - - +
314A PHE* 3.5 49.5 - - + +
375A ARG 2.9 18.1 + - - +
376A ALA* 3.7 1.1 - - - +
378A LEU* 1.3 76.5 - - - +
380A ALA* 1.3 61.4 + - - +
382A ALA* 3.1 21.3 + - - +
383A PHE* 3.6 1.9 - - - -
413A LEU* 3.5 27.4 - - + -
418A LYS* 4.0 30.2 - - + +
419A ALA 3.9 13.1 - - - +
420A PHE* 4.6 0.2 - - - -
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Residues in contact with ALA 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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314A PHE* 3.6 13.2 - - - +
317A TYR* 3.5 29.2 - - + -
318A LYS 3.9 10.8 - - - +
321A ALA* 4.5 2.8 - - - +
376A ALA 2.8 13.8 + - - +
377A ILE 2.8 9.7 + - - +
379A ARG* 1.3 72.3 - - - +
381A SER* 1.3 55.1 + - - +
382A ALA 3.0 5.6 - - - -
383A PHE* 2.9 29.0 + - - +
384A GLY 3.9 2.1 + - - -
386A LEU* 3.5 12.2 - - + +
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Residues in contact with SER 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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377A ILE 2.9 6.1 + - - -
378A LEU* 2.3 28.1 + - - -
380A ALA* 1.3 72.3 - - - +
382A ALA* 1.3 58.1 + - - +
383A PHE 2.9 7.4 + - - -
384A GLY 3.5 14.9 + - - +
386A LEU* 3.4 16.8 - - - +
420A PHE* 3.8 0.7 - - - +
421A ASP* 3.0 41.8 + - - +
424A ILE* 3.8 23.5 - - - +
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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