Contacts of the helix formed by residues 382 - 401 (chain A) in PDB entry 5IJ0
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 382 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A HIS 4.1 3.9 + - - -
310A GLY* 3.4 18.2 - - - -
311A LYS* 4.3 10.0 + - + +
313A MET* 5.3 9.4 - - + -
344A VAL* 6.3 1.1 - - + -
381A THR* 1.3 72.2 - - - +
383A ALA* 1.3 58.8 + - - +
384A ILE 2.9 2.2 - - - -
385A ALA* 2.6 33.8 + - - +
386A GLU* 2.9 8.0 + - - +
432A TYR* 3.8 39.5 - - + +
433A GLU* 6.1 0.2 - - - -
435A VAL* 5.9 0.2 - - + -
436A GLY* 4.0 17.5 - - - +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A CYS* 3.1 20.6 - - - -
306A ASP 3.0 30.1 - - - +
307A PRO* 4.5 1.1 - - + -
309A HIS* 4.2 14.8 - - + -
310A GLY* 4.3 7.0 - - - +
381A THR* 3.4 7.0 - - - +
382A THR* 1.3 81.3 + - - +
384A ILE* 1.3 56.0 + - - +
386A GLU* 3.0 17.3 + - + +
387A ALA* 2.9 22.0 + - - +
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Residues in contact with ILE 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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172A TYR* 4.8 6.7 - - + -
203A MET* 4.9 7.6 - - + -
267A PHE* 4.7 10.5 - - + +
269A LEU* 3.5 35.0 - - + -
303A VAL* 4.3 9.0 - - + -
305A CYS* 3.3 21.6 - - + -
381A THR* 3.0 25.6 + - - +
382A THR 2.9 0.6 - - - -
383A ALA* 1.3 78.8 - - - +
385A ALA* 1.3 59.0 + - - +
387A ALA* 3.1 13.6 + - + +
388A TRP* 2.8 49.2 + - + +
432A TYR* 3.5 25.8 - - + +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A THR* 2.6 20.6 + - - +
384A ILE* 1.3 73.7 - - - +
386A GLU* 1.3 51.7 + - - -
388A TRP* 3.1 11.5 + - - -
389A ALA* 2.7 30.1 + - - +
429A GLU* 2.8 24.5 - - - +
432A TYR* 3.4 39.0 - - + -
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Residues in contact with GLU 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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309A HIS* 5.1 14.1 - - + +
382A THR 2.9 12.6 + - - +
383A ALA* 3.0 20.4 + - + +
385A ALA* 1.3 76.7 - - + +
387A ALA* 1.3 60.2 + - - +
389A ALA* 2.9 22.3 + - - +
390A ARG* 2.9 14.8 + - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A TYR* 3.2 32.3 + - + +
305A CYS* 4.9 7.9 - - + -
383A ALA 2.9 11.7 + - - +
384A ILE* 3.1 19.0 + - + +
386A GLU* 1.3 74.5 - - - +
388A TRP* 1.3 61.6 + - - +
390A ARG* 2.9 37.1 - - - +
391A LEU* 3.0 6.9 + - - +
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Residues in contact with TRP 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PHE* 3.9 27.6 - + - -
172A TYR* 3.5 31.6 + + - -
187A SER* 5.4 1.6 - - - -
188A ILE* 5.9 1.8 - - + -
191A THR* 4.1 18.8 - - + -
203A MET* 4.3 6.3 - - + -
267A PHE* 3.4 41.3 - + - -
384A ILE* 2.8 48.5 + - + +
385A ALA* 3.1 8.5 + - - +
387A ALA* 1.3 73.2 - - - +
389A ALA* 1.3 56.1 + - - +
391A LEU* 3.5 13.4 + - + +
392A ASP* 2.8 31.2 + - - +
425A MET* 3.6 26.8 - - + +
428A LEU* 4.1 17.2 - - + +
429A GLU* 3.0 17.4 - - - +
432A TYR* 4.5 3.1 - + - -
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Residues in contact with ALA 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 ALA 2.7 12.0 + - - +
386A GLU* 2.9 24.9 + - - +
388A TRP* 1.3 70.8 - - - +
390A ARG* 1.3 58.9 + - - +
392A ASP* 3.1 6.8 + - - +
393A HIS* 2.8 29.4 + - - +
429A GLU* 2.7 18.9 + - - +
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Residues in contact with ARG 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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172A TYR* 3.2 22.0 - - - -
173A PRO 3.2 19.8 + - - -
174A ALA 3.9 2.6 + - - -
175A PRO* 3.4 49.9 - - - +
205A ASP* 4.4 1.2 + - - -
304A LYS* 5.7 1.2 - - - +
386A GLU 2.9 10.9 + - - +
387A ALA* 2.9 34.0 + - - +
389A ALA* 1.3 75.0 - - - +
391A LEU* 1.3 95.5 + - - +
393A HIS* 3.1 8.8 + - - +
394A LYS* 2.9 38.4 + - - +
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Residues in contact with LEU 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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172A TYR* 3.1 37.5 - - + +
173A PRO* 3.7 29.6 - - + -
174A ALA 5.2 0.4 - - - +
184A PRO* 4.7 12.0 - - + +
187A SER* 5.2 8.5 - - - +
188A ILE* 4.9 7.4 - - + +
387A ALA 3.0 16.5 + - - +
388A TRP* 3.7 19.5 - - + +
390A ARG* 1.3 101.0 - - - +
392A ASP* 1.3 58.1 + - - +
394A LYS* 3.2 17.4 + - + +
395A PHE* 2.9 30.5 + - - +
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Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 4.5 8.0 - - + +
388A TRP 2.8 19.4 + - - +
389A ALA* 3.1 9.4 + - - +
391A LEU* 1.3 75.8 - - - +
393A HIS* 1.3 52.9 + - - +
395A PHE* 3.5 6.8 + - - +
396A ASP* 2.7 31.0 + - - +
422A ARG* 2.6 53.1 + - - +
425A MET* 3.3 26.5 - - + +
426A ALA* 4.7 2.0 + - - -
429A GLU* 4.9 6.7 - - + +
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 2.8 12.9 + - - +
390A ARG* 3.3 13.5 - - - +
392A ASP* 1.3 75.2 + - - +
394A LYS* 1.3 68.2 + - + +
396A ASP* 3.0 14.9 + - - +
397A LEU* 2.9 55.4 + - + +
422A ARG* 5.5 0.2 - - - +
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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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174A ALA 3.7 8.1 + - - -
175A PRO* 2.7 34.4 + - - +
184A PRO* 4.3 16.4 - - + -
390A ARG* 2.9 29.0 + - - +
391A LEU* 3.5 19.0 - - + +
393A HIS* 1.3 78.7 - - + +
395A PHE* 1.3 63.6 + - - +
397A LEU* 3.2 4.5 + - - +
398A MET* 2.9 29.7 + - + +
346B PRO* 4.1 29.8 - - + +
347B ASN* 3.0 25.0 + - - +
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Residues in contact with PHE 395 (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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184A PRO* 3.9 11.8 - - + +
185A TYR* 3.4 44.9 - + - -
188A ILE* 3.7 39.0 - - + -
391A LEU 2.9 15.7 + - - +
392A ASP 3.6 3.8 - - - +
394A LYS* 1.3 76.8 - - - +
396A ASP* 1.3 61.5 + - - +
398A MET* 4.0 2.6 - - - +
399A TYR* 2.8 50.5 + + + +
418A PHE* 3.7 34.3 - + + -
422A ARG* 4.1 37.2 - - + -
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Residues in contact with ASP 396 (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 ASP 2.7 22.1 + - - +
393A HIS* 3.0 17.8 + - - +
395A PHE* 1.3 76.3 - - - +
397A LEU* 1.3 63.2 + - - +
399A TYR* 3.7 3.0 - - - +
400A ALA* 2.7 41.5 + - - +
422A ARG* 2.5 43.9 + - - +
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Residues in contact with LEU 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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393A HIS* 2.9 46.1 + - + +
394A LYS 3.7 4.5 - - - +
396A ASP* 1.3 80.9 - - - +
398A MET* 1.3 67.7 + - - +
400A ALA* 2.9 18.2 + - + +
401A LYS* 2.9 17.5 + - - +
343B GLU 4.4 12.6 - - - +
344B TRP* 4.1 20.2 - - + +
346B PRO* 4.3 19.3 - - + -
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Residues in contact with MET 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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181A VAL 3.2 29.4 - - - +
184A PRO* 3.7 25.4 - - + -
185A TYR* 2.6 33.8 + - + +
394A LYS* 2.9 17.0 + - + +
395A PHE* 4.0 3.8 - - - +
397A LEU* 1.3 76.7 - - - +
399A TYR* 1.3 56.7 + - - +
401A LYS* 3.7 1.5 + - - +
402A ARG 3.3 2.3 + - - -
403A ALA* 3.1 28.8 + - + +
404A PHE* 5.6 4.7 - - + -
344B TRP* 4.0 8.3 - - - +
345B ILE* 4.3 11.4 - - + -
346B PRO* 3.0 52.3 - - + +
347B ASN* 5.4 1.1 - - + +
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Residues in contact with TYR 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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185A TYR* 3.3 14.1 + + + -
395A PHE* 2.8 38.9 + + + +
396A ASP* 3.9 2.7 - - - +
398A MET* 1.3 74.9 - - - +
400A ALA* 1.3 61.2 + - - +
401A LYS 3.2 0.2 - - - -
402A ARG* 2.6 65.9 + - - +
405A VAL* 5.5 5.4 - - + -
415A GLU* 3.0 38.0 + - + +
418A PHE* 3.4 41.3 - + + -
419A SER* 4.4 12.1 + - - -
422A ARG* 5.5 7.2 - - + -
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ASP* 2.7 28.5 + - - +
397A LEU* 2.9 12.1 + - + +
399A TYR* 1.3 77.8 - - - +
401A LYS* 1.3 65.5 + - + +
402A ARG* 3.4 15.9 + - - +
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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 LEU 2.9 12.0 + - - +
398A MET 4.3 2.5 - - - +
400A ALA* 1.3 80.0 - - + +
402A ARG* 1.3 70.8 + - - +
403A ALA 3.1 2.3 + - - +
260B PHE* 3.5 16.6 - - + -
344B TRP* 3.5 68.0 - - + +
425B TYR* 5.1 8.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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