Contacts of the helix formed by residues 380 - 392 (chain A) in PDB entry 2JDQ
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 ASN 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A LEU* 4.0 16.8 - - + +
377A ILE 3.1 12.7 + - - -
378A ASP 3.1 3.0 - - - +
379A ALA* 1.3 82.7 - - - +
381A ILE* 1.3 63.2 + - - +
382A PHE 3.4 2.5 - - - +
383A PRO* 3.6 29.7 - - - +
384A ALA* 4.7 2.3 + - - +
418A TYR* 3.9 10.3 + - - -
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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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340A LEU* 3.7 20.0 - - + +
343A LEU* 4.9 0.2 - - + -
344A LEU* 3.5 39.7 - - + +
347A LEU* 4.2 2.7 - - + -
362A ILE* 3.6 30.1 - - + -
376A VAL* 3.4 40.1 + - + +
377A ILE 4.5 0.2 + - - -
379A ALA* 3.7 13.7 - - + -
380A ASN* 1.3 79.2 - - - +
382A PHE* 1.3 64.7 + - - +
384A ALA* 3.2 8.3 + - - +
385A LEU* 3.1 32.2 + - + -
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Residues in contact with PHE 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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366A THR* 3.9 17.0 - - + -
373A ILE* 4.5 4.7 - - + -
376A VAL* 3.6 20.2 - - + -
377A ILE* 3.7 35.8 + - + -
380A ASN* 4.5 0.2 - - - +
381A ILE* 1.3 73.7 - - - +
383A PRO* 1.3 74.3 - - + +
385A LEU* 3.2 19.3 + - + +
386A ILE* 2.9 28.1 + - + +
403A ALA 4.6 1.3 - - - -
404A ILE* 3.6 23.3 - - + -
407A ALA* 3.7 31.2 - - + -
418A TYR* 4.5 2.7 + + + -
419A LEU* 3.4 24.2 - - + -
422A LEU* 3.8 17.0 - - + -
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Residues in contact with PRO 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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380A ASN* 3.6 38.1 - - - +
382A PHE* 1.3 91.2 - - + +
384A ALA* 1.3 55.2 + - - +
386A ILE* 3.3 6.7 + - + +
387A SER* 2.9 28.8 + - - -
418A TYR* 4.1 2.0 - - - +
422A LEU* 3.8 29.6 - - + -
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Residues in contact with ALA 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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344A LEU* 4.1 16.4 - - + -
347A LEU* 4.0 22.4 - - + -
380A ASN 4.7 1.3 + - - +
381A ILE 3.2 9.3 + - - +
382A PHE 3.2 0.8 - - - -
383A PRO* 1.3 76.0 - - - +
385A LEU* 1.3 60.6 + - - +
387A SER* 3.4 7.0 + - - -
388A ILE* 3.0 36.0 + - + +
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Residues in contact with LEU 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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347A LEU* 4.0 17.7 - - + -
359A CYS* 4.0 27.4 - - - -
362A ILE* 4.2 11.0 - - + -
381A ILE* 3.1 33.4 + - + +
382A PHE* 3.7 28.5 - - + +
384A ALA* 1.3 76.3 - - - +
386A ILE* 1.3 57.8 + - - +
388A ILE* 3.5 5.6 + - - +
389A LEU* 3.0 28.4 + - - +
400A ALA* 3.8 8.0 - - + +
403A ALA* 3.6 33.4 - - + -
404A ILE* 4.0 13.9 - - + -
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Residues in contact with ILE 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 PHE* 2.9 22.5 + - + +
383A PRO* 3.7 5.2 - - + +
385A LEU* 1.3 73.1 - - - +
387A SER* 1.3 68.0 + - - +
389A LEU* 3.2 16.7 + - + +
390A GLN* 3.4 24.1 + - - +
404A ILE* 4.1 17.3 - - + -
419A LEU* 4.2 3.8 - - + +
422A LEU* 3.6 48.7 - - + +
423A GLY 4.1 11.7 - - - +
424A CYS* 4.0 25.1 - - + -
427A PRO* 4.4 8.1 - - + +
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Residues in contact with SER 387 (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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383A PRO 2.9 18.7 + - - -
384A ALA* 3.5 8.7 - - - -
386A ILE* 1.3 78.1 - - - +
388A ILE* 1.3 62.0 + - - -
390A GLN* 3.4 14.4 + - - +
391A THR* 3.1 32.6 + - - +
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Residues in contact with ILE 388 (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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347A LEU* 3.7 46.2 - - + +
355A LYS* 3.8 23.1 - - + +
359A CYS* 3.9 7.2 - - - -
384A ALA* 3.0 23.8 + - + +
385A LEU* 3.7 5.8 - - - +
386A ILE 3.3 0.2 - - - -
387A SER* 1.3 75.9 - - - +
389A LEU* 1.3 60.0 + - - +
391A THR* 4.5 1.8 - - - -
392A ALA* 3.0 44.9 + - + +
396A THR* 3.7 19.3 - - + +
397A ARG* 3.5 3.3 - - - +
400A ALA* 3.8 16.6 - - + -
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Residues in contact with LEU 389 (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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385A LEU 3.0 19.2 + - - +
386A ILE* 3.2 12.0 + - + +
388A ILE* 1.3 76.8 - - - +
390A GLN* 1.3 56.5 + - - +
397A ARG* 3.1 50.7 + - + +
400A ALA* 4.4 5.4 - - + +
401A ALA* 4.0 12.8 - - + +
404A ILE* 4.3 12.6 - - + -
424A CYS* 4.9 2.2 - - - +
427A PRO* 3.4 31.3 - - + +
428A LEU* 3.8 26.0 - - + -
431A LEU* 3.5 23.8 - - + -
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Residues in contact with GLN 390 (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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386A ILE* 3.5 25.1 - - - +
387A SER* 3.5 15.6 - - - +
389A LEU* 1.3 80.7 - - - +
391A THR* 1.3 70.1 + - + +
397A ARG* 4.7 11.1 + - - +
423A GLY 5.4 0.6 + - - -
426A LYS* 5.5 4.4 - - - +
427A PRO* 4.0 29.0 - - + +
430A ASP* 5.8 3.1 - - - +
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Residues in contact with THR 391 (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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387A SER* 3.1 23.4 + - - +
388A ILE* 4.5 1.4 - - - -
390A GLN* 1.3 93.0 - - + +
392A ALA* 1.3 67.9 + - - +
393A GLU 4.0 0.2 + - - -
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Residues in contact with ALA 392 (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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352A GLU* 4.2 5.2 - - - +
355A LYS* 5.4 4.3 - - + +
388A ILE* 3.0 40.0 + - + +
391A THR* 1.3 83.7 + - - +
393A GLU* 1.3 66.5 + - - +
394A PHE 3.7 0.3 + - - -
396A THR* 4.0 16.6 - - + -
397A ARG* 3.1 19.6 + - - +
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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