Contacts of the helix formed by residues 381 - 394 (chain A) in PDB entry 5IXC
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 LEU 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A TYR* 5.2 4.9 - - + +
342A LEU* 3.7 16.8 - - + +
343A LEU* 3.7 37.0 - - + +
346A GLN* 3.4 34.1 + - + +
351A LEU* 4.6 6.3 - - + -
370A LEU* 3.4 35.4 - - + -
376A TRP* 3.9 18.6 - - + +
379A ARG 4.5 0.4 - - - +
380A ASP* 1.3 73.1 + - - +
382A GLU* 1.3 60.8 + - - +
383A GLY 3.1 6.4 + - - -
384A PRO* 3.2 8.6 - - + +
385A ILE* 3.0 32.4 + - + +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 4.0 29.8 - - - +
347A LYS* 4.5 8.1 + - - -
380A ASP* 3.3 18.7 + - - +
381A LEU* 1.3 77.5 - - - +
383A GLY* 1.3 63.5 + - - +
385A ILE* 3.6 13.0 - - + +
386A ARG* 3.2 20.6 + - - +
389A ARG* 4.8 9.8 + - - +
779A GLU* 5.3 1.9 - - - +
782A LEU* 4.6 11.6 - - - +
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Residues in contact with GLY 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 ASP* 3.6 7.3 + - - +
381A LEU 3.1 1.8 - - - -
382A GLU* 1.3 77.8 - - - +
384A PRO* 1.4 67.7 - - - +
386A ARG* 3.1 18.9 + - - +
387A TYR* 3.2 11.2 + - - +
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Residues in contact with PRO 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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339A TYR* 4.1 13.5 + - + -
369A HIS* 4.2 16.7 - - + +
370A LEU* 3.9 30.1 - - + -
373A ASP* 6.0 2.7 - - + +
376A TRP* 5.7 4.7 - - + +
380A ASP 3.5 12.8 - - - +
381A LEU* 3.2 15.7 - - + +
383A GLY* 1.4 82.2 - - - +
385A ILE* 1.3 63.1 + - - +
387A TYR* 3.4 10.1 - - + +
388A ALA* 3.0 22.9 + - - +
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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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339A TYR* 3.4 45.1 - - + +
343A LEU* 5.3 5.6 - - + -
381A LEU* 3.0 29.7 + - + +
382A GLU* 3.6 23.1 - - + +
383A GLY 3.2 0.2 - - - -
384A PRO* 1.3 75.6 - - - +
386A ARG* 1.3 58.1 + - - +
388A ALA* 3.2 6.8 + - - +
389A ARG* 2.9 37.3 + - - +
778A PHE* 3.6 25.7 - - + -
782A LEU* 3.7 23.3 - - + -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU 3.2 9.9 + - - +
383A GLY* 3.1 13.3 + - - +
385A ILE* 1.3 77.8 - - - +
387A TYR* 1.3 58.5 + - - +
389A ARG* 3.3 25.6 + - - +
390A GLU* 2.8 71.6 + - - +
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Residues in contact with TYR 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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369A HIS* 3.4 37.7 - + + -
383A GLY 3.2 8.0 + - - +
384A PRO* 3.4 10.8 - - + +
386A ARG* 1.3 80.1 - - - +
388A ALA* 1.3 67.2 + - - +
390A GLU* 4.0 4.6 - - - +
391A HIS* 2.7 63.6 + + - -
436A LEU 3.7 5.8 - - - -
437A HIS* 2.7 40.9 + + - +
438A GLY 4.9 0.2 + - - -
439A GLN* 5.8 1.0 - - - +
441A MET* 4.2 11.2 - - + -
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Residues in contact with ALA 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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335A MET* 4.8 13.8 - - + +
339A TYR* 3.6 37.0 - - + +
384A PRO 3.0 6.8 + - - +
385A ILE 3.2 7.2 + - - +
387A TYR* 1.3 84.4 - - + +
389A ARG* 1.3 58.3 + - - +
391A HIS* 3.8 2.6 - - - +
392A LEU* 2.8 32.6 + - - +
436A LEU 6.0 0.2 - - - -
778A PHE* 4.2 9.9 - - + -
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Residues in contact with ARG 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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382A GLU* 4.8 10.1 + - - +
385A ILE* 2.9 30.4 + - - +
386A ARG* 3.6 36.2 - - - +
388A ALA* 1.3 76.7 - - - +
390A GLU* 1.3 61.0 + - - +
392A LEU* 3.3 2.6 + - - +
393A ALA* 2.9 28.4 + - - +
773A TYR 4.7 0.9 - - - +
775A GLU* 3.1 41.3 + - + +
778A PHE* 3.6 36.9 - - + -
779A GLU* 2.8 34.0 + - - +
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Residues in contact with GLU 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 ARG* 2.8 64.7 + - + +
387A TYR* 4.0 5.0 - - - +
389A ARG* 1.3 76.6 + - - +
391A HIS* 1.3 68.2 + - + +
393A ALA* 3.3 2.8 + - - +
394A LYS* 3.0 23.4 + - - +
775A GLU* 4.3 20.6 - - - +
809B LEU* 5.7 1.0 - - - +
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Residues in contact with HIS 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 TYR* 2.7 65.9 + + - +
388A ALA* 3.9 3.1 - - - +
390A GLU* 1.3 79.8 - - + +
392A LEU* 1.3 52.9 + - - +
394A LYS* 3.5 23.2 - - + +
396A LYS* 2.5 30.9 + - - -
435A MET 4.0 5.1 - - - +
436A LEU* 3.6 18.8 - - - +
437A HIS* 3.7 23.6 - - - -
438A GLY* 3.8 14.1 + - - -
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Residues in contact with LEU 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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332A ALA* 4.2 7.0 - - + -
335A MET* 3.7 17.5 - - + -
336A THR* 3.6 31.6 - - + -
388A ALA 2.8 17.4 + - - +
389A ARG* 3.7 5.4 - - - +
390A GLU 3.2 0.2 - - - -
391A HIS* 1.3 77.3 - - - +
393A ALA* 1.3 58.4 + - - +
396A LYS* 3.6 6.0 + - - +
435A MET 5.8 1.1 - - - +
436A LEU* 6.1 0.7 - - + -
771A MET* 3.3 46.4 - - + +
772A THR* 3.3 11.6 - - - -
773A TYR* 3.0 48.9 + - + -
778A PHE* 4.0 7.2 - - + -
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG 2.9 17.2 + - - +
390A GLU 3.3 3.8 + - - +
392A LEU* 1.3 73.5 - - - +
394A LYS* 1.3 66.6 + - - +
395A SER* 3.3 3.8 + - - -
772A THR* 5.1 3.8 - - - -
773A TYR 3.1 21.2 + - - +
774A LYS* 4.8 1.6 - - - -
775A GLU* 3.7 30.3 - - + +
809B LEU* 3.9 22.1 - - + +
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Residues in contact with LYS 394 (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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390A GLU 3.0 13.0 + - - +
391A HIS* 3.5 27.1 - - + +
392A LEU 3.8 0.9 - - - +
393A ALA* 1.3 76.7 - - - +
395A SER* 1.3 71.2 + - - +
396A LYS* 2.8 33.5 + - - +
398A GLU* 5.6 2.4 + - - +
404A ARG* 4.0 30.5 - - - +
434A SER 4.9 11.4 - - - -
435A MET 6.0 1.1 - - - +
437A HIS 5.1 0.7 - - - -
438A GLY* 5.0 11.7 - - - -
772A THR* 4.2 1.2 - - - +
808B THR 5.8 0.9 - - - +
809B LEU* 3.6 21.7 - - - +
810B GLU 3.8 21.4 + - - -
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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