Contacts of the helix formed by residues 374 - 391 (chain A) in PDB entry 5J3V
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLU* 5.6 2.5 - - - +
274A LEU* 3.3 11.2 - - - +
314A ASP* 4.8 11.8 + - - +
370A ILE* 3.7 9.8 - - - +
371A SER* 3.5 24.8 + - - +
373A TRP* 1.3 82.2 + - - +
375A LEU* 1.3 64.8 + - - +
376A ARG* 3.1 15.5 - - + +
377A LYS* 2.5 42.7 + - - +
378A CYS* 3.1 23.7 + - - +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 4.7 11.9 - - + +
270A GLU* 4.1 28.9 + - + +
273A ALA* 3.7 42.2 - - + +
274A LEU* 3.9 12.0 - - + +
277A CYS* 3.8 17.7 - - + -
307A GLY* 3.8 19.0 - - - +
374A ASN* 1.3 75.3 - - - +
376A ARG* 1.3 56.1 + - - +
378A CYS* 4.5 0.2 - - - -
379A SER* 2.7 44.3 + - - +
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLY 3.5 12.7 + - - +
308A MET* 3.1 28.9 + - - +
309A LYS 4.3 7.2 - - - +
310A TYR* 3.3 43.7 + - - +
314A ASP* 6.1 2.5 - - - -
374A ASN* 3.1 10.4 - - + +
375A LEU* 1.3 77.2 - - - +
377A LYS* 1.3 71.6 + - + +
379A SER* 3.3 2.6 + - - -
380A ALA* 2.9 30.2 + - + +
415A GLU* 2.8 39.0 + - - -
419A LEU* 3.4 30.5 - - + +
457A ILE* 4.7 4.9 - - - +
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 3.5 17.4 - - - +
371A SER 3.5 11.9 + - - -
372A ASP* 3.2 25.4 - - - +
373A TRP* 4.0 15.0 - - + -
374A ASN* 2.5 39.7 + - + +
375A LEU 3.5 0.2 - - - -
376A ARG* 1.3 88.6 - - + +
378A CYS* 1.3 57.6 + - - +
380A ALA* 3.6 7.4 - - - +
381A ALA* 2.9 29.6 + - - +
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Residues in contact with CYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LEU* 3.7 9.9 - - + -
277A CYS* 3.5 39.7 - - - -
278A GLU* 3.7 22.7 - - - -
281A LEU* 4.1 5.5 - - - +
373A TRP* 3.6 22.8 - - + -
374A ASN 3.1 19.3 + - - +
375A LEU 4.0 1.6 - - - +
377A LYS* 1.3 76.9 - - - +
379A SER* 1.3 59.5 + - - +
381A ALA* 3.5 2.3 + - - +
382A ALA* 3.0 25.8 + - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 5.6 1.6 - - - +
277A CYS* 3.4 18.2 - - - -
303A VAL 5.3 0.3 + - - -
304A LEU* 3.4 34.2 + - - +
307A GLY* 4.2 5.6 - - - -
308A MET* 3.6 11.5 - - - +
375A LEU* 2.7 30.6 + - - +
376A ARG 3.8 0.7 - - - -
378A CYS* 1.3 73.3 - - - +
380A ALA* 1.3 60.4 + - - +
382A ALA* 3.7 4.5 - - - +
383A LEU* 3.0 30.1 + - - +
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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
----------------------------------------------------------
308A MET* 3.8 25.0 - - + +
376A ARG 2.9 17.9 + - - +
377A LYS* 3.6 9.4 - - - +
378A CYS 3.3 0.2 - - - -
379A SER* 1.3 76.4 - - - +
381A ALA* 1.3 55.7 + - - +
383A LEU* 3.4 2.8 + - - +
384A ASP* 2.9 27.8 + - - +
419A LEU* 4.4 15.7 - - + -
423A ALA* 3.9 8.1 - - + +
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.5 22.9 - - + -
373A TRP* 4.1 9.2 - - + -
377A LYS 2.9 18.9 + - - +
378A CYS 3.8 4.0 - - - +
380A ALA* 1.3 74.3 - - - +
382A ALA* 1.3 59.0 + - - +
384A ASP* 3.1 7.6 + - - +
385A VAL* 3.0 34.9 + - + +
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A CYS* 4.8 2.7 - - - +
280A TRP* 4.2 20.0 - - + -
281A LEU* 3.6 17.9 - - + +
284A ALA* 5.3 0.2 - - - +
304A LEU* 4.1 21.3 - - + -
378A CYS 3.0 17.7 + - - +
379A SER* 3.7 5.2 - - - +
380A ALA 3.3 0.2 - - - -
381A ALA* 1.3 77.7 - - - +
383A LEU* 1.3 58.0 + - - +
385A VAL* 3.6 1.4 + - - +
386A LEU* 3.1 37.5 + - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.4 12.6 - - + -
304A LEU* 4.6 11.1 - - + +
305A VAL* 4.2 10.5 - - + +
308A MET* 3.7 26.7 - - + -
379A SER 3.0 16.8 + - - +
380A ALA 3.8 4.5 - - - +
382A ALA* 1.3 73.9 - - - +
384A ASP* 1.3 64.5 + - - +
386A LEU* 4.5 2.9 - - + -
387A ALA* 3.2 23.2 + - - +
394A LEU* 4.2 10.5 - - + -
398A ILE* 3.8 20.6 - - + -
420A VAL* 3.7 30.5 - - + -
423A ALA* 4.6 4.0 - - + -
424A ILE* 3.8 15.1 - - + +
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Residues in contact with ASP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ALA 2.9 14.9 + - - +
381A ALA* 3.1 13.2 + - - +
383A LEU* 1.3 77.8 - - - +
385A VAL* 1.3 59.0 + - + +
387A ALA* 3.3 10.7 + - - +
388A ASN* 2.7 37.4 + - - -
423A ALA* 3.2 26.3 - - + +
426A GLU* 4.0 9.9 - - - +
460A TRP* 5.9 0.7 - - - -
464A ARG* 3.8 17.5 + - - -
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU* 3.7 17.5 - - + +
284A ALA* 3.6 35.7 - - + +
285A GLU* 4.6 13.5 - - + +
381A ALA* 3.0 16.4 + - + +
382A ALA 4.1 2.9 - - - +
384A ASP* 1.3 74.9 - - + +
386A LEU* 1.3 65.6 + - - +
388A ASN* 3.0 20.0 + - + +
389A VAL* 3.2 13.5 + - + +
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Residues in contact with LEU 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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280A TRP* 5.2 6.1 - - + +
284A ALA* 3.9 19.3 - - + -
289A CYS* 4.2 3.4 - - - -
293A LEU* 3.9 24.7 - - + -
297A LEU* 5.1 3.1 - - + -
300A LEU* 4.1 15.9 - - + -
301A ILE* 4.8 9.4 - - + -
304A LEU* 3.7 26.5 - - + -
382A ALA* 3.1 23.3 + - + +
383A LEU* 4.2 5.4 - - + +
385A VAL* 1.3 76.6 - - - +
387A ALA* 1.3 56.6 + - - +
389A VAL* 3.3 3.8 + - + -
390A TYR* 3.1 53.3 + - + +
394A LEU* 4.1 10.9 - - + +
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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
----------------------------------------------------------
383A LEU 3.2 19.3 + - - +
384A ASP 3.4 7.6 - - - +
385A VAL 3.1 0.4 - - - -
386A LEU* 1.3 78.1 - - - +
388A ASN* 1.3 56.7 + - - +
391A ARG* 3.0 28.1 + - - +
394A LEU* 3.7 13.9 - - + +
423A ALA 4.5 0.4 - - - +
424A ILE* 3.9 17.7 - - + -
427A GLY* 3.4 14.1 - - - +
428A CYS* 3.7 19.5 - - - -
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Residues in contact with ASN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 2.7 39.4 + - - -
385A VAL* 3.0 12.3 + - + +
387A ALA* 1.3 76.1 - - - +
389A VAL* 1.3 61.3 + - + +
391A ARG* 2.4 35.2 + - - +
426A GLU* 3.4 34.9 + - - +
427A GLY* 3.5 13.4 - - - +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ALA* 3.6 26.7 - - + +
289A CYS* 4.4 11.4 - - + -
290A LYS* 3.7 36.6 - - + +
385A VAL* 3.2 18.8 + - + +
386A LEU* 3.7 9.0 - - - +
387A ALA 3.2 0.4 - - - -
388A ASN* 1.3 83.9 - - + +
390A TYR* 1.3 75.7 + - + +
391A ARG* 3.4 4.1 - - - +
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Residues in contact with TYR 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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289A CYS* 3.3 14.1 + - - -
290A LYS* 3.5 25.8 - - + +
293A LEU* 3.3 24.2 - - + +
294A VAL* 3.4 29.5 + - + -
297A LEU* 3.6 27.8 - - + -
386A LEU* 3.1 39.8 + - + +
389A VAL* 1.3 86.6 - - + +
391A ARG* 1.3 60.2 + - - +
392A ASP 3.0 0.9 + - - -
393A GLU* 2.8 53.6 + - + +
394A LEU* 4.0 24.7 - - + +
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA 3.0 14.1 + - - +
388A ASN* 2.4 51.2 + - - +
389A VAL 3.4 3.8 - - - +
390A TYR* 1.3 77.7 - - - +
392A ASP* 1.3 73.3 + - - +
393A GLU* 3.6 1.1 + - + +
394A LEU* 3.9 4.2 + - - +
426A GLU 6.0 0.2 - - - -
427A GLY* 3.3 20.6 - - - -
428A CYS* 3.1 27.5 - - - -
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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