Contacts of the helix formed by residues 396 - 411 (chain A) in PDB entry 1UN0
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 GLU 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A GLU* 3.0 37.3 + - + +
395A ALA* 1.3 73.2 - - - +
397A ASP* 1.3 66.8 + - - +
398A LYS* 3.2 31.7 + - + -
399A THR* 2.9 16.0 + - - +
400A LYS* 3.0 10.4 + - - -
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Residues in contact with ASP 397 (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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395A ALA 4.7 0.5 - - - +
396A GLU* 1.3 72.4 - - - +
398A LYS* 1.3 62.0 + - - +
400A LYS* 3.3 22.8 + - - +
401A LYS* 3.1 33.9 + - - +
439A ILE* 3.1 34.2 - - + +
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Residues in contact with LYS 398 (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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355A GLU* 4.0 13.2 - - - +
356A ASN* 2.8 35.1 + - - +
359A LYS* 3.8 29.9 - - + +
396A GLU* 3.2 29.3 + - + +
397A ASP* 1.3 78.1 - - - +
399A THR* 1.3 66.2 + - - +
401A LYS* 3.5 13.7 + - - +
402A GLU* 3.4 22.9 + - - +
51C LYS* 5.6 1.0 - - - +
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Residues in contact with THR 399 (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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355A GLU* 3.4 27.0 + - - +
358A LYS* 4.4 4.9 - - + -
359A LYS* 3.9 27.3 - - - +
362A CYS* 4.2 18.7 - - - -
391A LEU* 4.3 13.2 - - + -
395A ALA* 3.7 20.4 - - + -
396A GLU 2.9 8.3 + - - -
398A LYS* 1.3 76.6 - - - +
400A LYS* 1.3 61.1 + - - +
402A GLU* 3.3 4.9 + - - +
403A ALA* 2.9 26.7 + - - +
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Residues in contact with LYS 400 (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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391A LEU 3.6 15.0 - - - +
392A LEU* 3.4 26.3 + - + +
393A GLU 3.5 22.6 + - - -
394A VAL 4.4 0.9 - - - -
395A ALA 3.2 27.1 - - - +
396A GLU 3.0 7.6 + - - +
397A ASP* 3.5 23.5 + - - +
399A THR* 1.3 74.5 - - - +
401A LYS* 1.3 64.1 + - - +
403A ALA* 3.2 6.0 + - - -
404A CYS* 2.9 25.1 + - - +
436A LEU* 4.1 24.4 - - + +
439A ILE* 6.3 0.2 - - + -
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Residues in contact with LYS 401 (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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397A ASP* 3.1 25.0 + - - +
398A LYS* 3.8 12.3 - - - +
399A THR 3.2 0.2 - - - -
400A LYS* 1.3 75.3 - - + +
402A GLU* 1.3 67.3 + - - +
404A CYS* 3.1 8.7 + - - +
405A TRP* 3.0 28.7 + - + -
436A LEU* 5.2 2.2 - - + -
439A ILE* 4.5 17.0 - - + -
441A ASP* 3.3 35.9 + - - +
444A ILE* 3.6 33.2 - - + +
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Residues in contact with GLU 402 (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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359A LYS* 3.5 11.8 - - + +
362A CYS* 3.7 12.2 - - + +
363A TRP* 3.2 43.4 - - + +
366A SER* 4.1 3.1 - - - -
398A LYS 3.4 11.9 + - - +
399A THR 3.3 9.4 + - - +
400A LYS 3.3 0.2 - - - -
401A LYS* 1.3 84.2 - - - +
403A ALA* 1.3 59.7 + - - +
405A TRP* 3.4 6.2 + - - +
406A ALA* 3.2 18.9 + - - +
38C ARG* 2.7 41.1 + - - -
40C LYS* 3.6 16.5 + - - +
41C ILE* 5.3 5.4 - - - +
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Residues in contact with ALA 403 (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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362A CYS* 3.9 17.5 - - - +
388A LEU* 3.8 26.0 - - + +
391A LEU* 4.5 2.7 - - + -
392A LEU* 4.3 13.7 - - + +
399A THR 2.9 16.3 + - - +
400A LYS* 3.2 6.5 + - - +
402A GLU* 1.3 74.0 - - - +
404A CYS* 1.3 60.2 + - - +
406A ALA* 3.1 8.5 + - - +
407A ILE* 3.0 32.0 + - - +
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Residues in contact with CYS 404 (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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392A LEU* 3.7 10.4 - - + +
400A LYS 2.9 12.7 + - - +
401A LYS* 3.3 11.0 - - - +
403A ALA* 1.3 73.4 - - - +
405A TRP* 1.3 59.3 + - - +
407A ILE* 4.0 4.3 - - - +
408A SER* 2.8 34.4 + - - -
433A LEU* 4.2 13.1 - - - +
436A LEU* 3.2 21.5 - - + -
444A ILE* 3.9 9.0 - - - -
447A VAL* 4.3 13.5 - - - -
448A THR* 3.1 28.0 - - - -
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Residues in contact with TRP 405 (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 SER* 3.8 3.4 - - - -
401A LYS* 3.0 28.3 + - + -
402A GLU* 3.5 7.4 - - - +
403A ALA 3.2 0.2 - - - -
404A CYS* 1.3 77.1 - - - +
406A ALA* 1.3 59.3 + - - +
409A ASN* 2.9 61.9 + - - -
443A ARG* 3.6 40.7 - - + +
444A ILE* 3.3 21.6 - - + +
447A VAL* 3.2 37.9 - - + -
37C ASN* 4.3 9.2 - - - -
38C ARG* 3.1 62.5 - - + +
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Residues in contact with ALA 406 (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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362A CYS 4.2 4.5 - - - +
365A ILE* 4.2 3.6 - - + -
366A SER* 3.5 30.7 - - - +
369A THR* 3.0 19.1 + - - +
385A ILE* 5.6 1.1 - - - +
388A LEU* 4.2 25.8 - - + -
402A GLU 3.2 6.8 + - - +
403A ALA* 3.1 11.5 + - - +
405A TRP* 1.3 79.9 - - - +
407A ILE* 1.3 63.7 + - - +
410A ALA* 3.4 12.5 + - - +
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Residues in contact with ILE 407 (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 ILE* 4.8 12.6 - - + -
388A LEU* 4.0 15.9 - - + +
389A VAL* 3.9 37.5 - - + +
392A LEU* 3.9 19.3 - - + -
403A ALA 3.0 19.1 + - - +
404A CYS* 4.0 3.6 - - - +
406A ALA* 1.3 76.1 - - - +
408A SER* 1.3 64.6 + - - +
410A ALA* 3.2 14.6 + - - +
411A SER* 3.3 13.4 + - - -
424A LEU* 4.0 13.5 - - + +
429A CYS* 4.4 20.9 - - + -
433A LEU* 4.4 19.7 - - + -
451A ALA* 5.5 0.7 - - + -
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Residues in contact with SER 408 (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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404A CYS* 2.8 23.8 + - - -
405A TRP 4.1 0.4 - - - -
407A ILE* 1.3 70.1 - - - +
409A ASN* 1.3 66.2 + - - +
410A ALA 3.0 1.3 - - - -
411A SER* 2.6 23.1 + - - -
412A SER* 3.6 3.8 + - - -
433A LEU* 5.4 0.8 - - - +
447A VAL* 2.8 41.3 + - - +
450A ASP* 4.4 4.3 - - - +
451A ALA* 3.3 26.7 + - - +
454A ASN* 4.7 1.2 + - - -
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Residues in contact with ASN 409 (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 SER* 2.7 31.1 + - - -
367A ASN* 5.3 0.2 + - - -
369A THR* 2.9 32.6 - - - +
370A ALA* 3.6 11.9 - - - +
376A ILE* 4.1 1.0 - - - +
405A TRP* 2.9 50.7 + - - +
408A SER* 1.3 73.0 - - - +
410A ALA* 1.3 58.8 + - - +
412A SER* 3.1 26.8 + - - -
447A VAL* 5.3 0.2 - - - +
37C ASN* 3.7 16.6 + - - +
38C ARG* 5.3 1.0 - - - +
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Residues in contact with ALA 410 (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* 3.9 16.6 - - + -
376A ILE* 3.8 19.7 - - + +
380A ILE* 6.0 0.9 - - + -
385A ILE* 5.1 5.6 - - + -
406A ALA 3.4 12.8 + - - +
407A ILE* 3.2 13.2 + - - +
408A SER 3.0 0.8 - - - -
409A ASN* 1.3 77.3 - - - +
411A SER* 1.3 59.3 + - - +
412A SER 3.2 5.6 + - - -
413A GLY 3.6 7.8 + - - -
414A GLY 4.1 0.2 + - - -
420A ILE* 3.4 19.4 - - + +
424A LEU* 4.3 16.4 - - + -
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Residues in contact with SER 411 (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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407A ILE* 3.3 8.3 + - - -
408A SER 2.6 21.4 + - - -
410A ALA* 1.3 77.2 - - - +
412A SER* 1.3 61.4 + - - +
413A GLY 3.3 0.4 - - - -
414A GLY* 3.3 10.4 + - - +
415A LEU* 4.5 1.2 + - - +
421A ILE* 3.4 28.0 - - - +
424A LEU* 4.0 7.5 - - - +
451A ALA* 3.7 18.1 - - - -
454A ASN* 3.2 32.6 + - - +
455A ILE* 5.2 2.7 - - - -
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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