Contacts of the helix formed by residues 374 - 389 (chain A) in PDB entry 1JPP
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 SER 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A GLU* 3.0 34.7 + - - -
372A ASP* 3.1 4.9 + - - +
373A PRO* 1.3 77.9 - - - +
375A GLN* 1.3 62.3 + - - +
376A ARG* 3.5 6.4 + - - +
377A LEU* 3.3 29.3 + - - -
378A VAL* 3.1 27.2 + - - +
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Residues in contact with GLN 375 (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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373A PRO 3.4 7.1 + - - +
374A SER* 1.3 73.6 + - - +
376A ARG* 1.3 63.2 + - - +
378A VAL* 3.4 5.9 + - - +
379A GLN* 3.2 23.4 + - - +
413A ASP* 4.6 13.5 + - - -
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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
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334A GLU* 3.0 33.5 + - - +
335A LYS* 4.5 10.1 - - - +
338A TRP* 3.3 63.9 - - + +
374A SER* 3.5 8.9 + - - +
375A GLN* 1.3 79.5 - - - +
377A LEU* 1.3 63.9 + - - +
379A GLN* 4.1 4.7 - - - +
380A ASN* 3.1 30.3 + - - +
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Residues in contact with LEU 377 (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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328A MET* 4.9 2.5 - - + -
334A GLU* 4.6 11.4 - - + +
337A LEU* 3.2 49.1 - - + +
338A TRP* 3.9 9.6 - - + -
341A SER* 4.2 9.2 - - - +
369A HIS* 4.1 26.9 - - + +
372A ASP* 4.6 9.6 - - + +
374A SER* 3.3 24.9 + - - +
376A ARG* 1.3 82.4 - - + +
378A VAL* 1.3 61.0 + - + +
380A ASN* 4.2 0.6 - - - -
381A CYS* 3.1 44.9 + - - -
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Residues in contact with VAL 378 (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 3.6 19.5 - - - +
370A LEU* 3.5 26.0 - - + +
372A ASP* 3.5 20.4 - - + +
374A SER 3.1 20.0 + - - +
375A GLN* 3.9 4.9 - - - +
377A LEU* 1.3 77.6 - - + +
379A GLN* 1.3 61.5 + - - +
381A CYS* 3.8 5.0 + - - +
382A LEU* 3.2 37.9 + - + +
408A LEU* 6.0 2.0 - - + -
416A VAL* 5.3 10.3 - - + -
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Residues in contact with GLN 379 (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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375A GLN 3.2 15.1 + - - +
376A ARG* 4.1 6.1 - - - +
377A LEU 3.3 0.2 - - - -
378A VAL* 1.3 76.2 - - - +
380A ASN* 1.3 67.2 + - - +
381A CYS 3.1 1.3 - - - -
382A LEU* 3.1 5.9 + - - +
383A TRP* 3.1 56.8 + - + +
413A ASP* 4.9 2.3 - - - +
415A ASN* 3.8 28.4 + - - +
416A VAL* 4.3 13.9 - - - +
419A CYS* 4.0 16.6 - - - -
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Residues in contact with ASN 380 (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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338A TRP* 3.4 31.3 - - - +
341A SER* 3.6 21.7 + - - +
342A ARG* 3.9 20.6 - - - +
345A LYS* 4.1 25.3 + - + +
376A ARG* 3.1 17.4 + - - +
377A LEU* 4.3 2.2 - - - +
379A GLN* 1.3 78.4 - - - +
381A CYS* 1.3 56.6 + - - +
383A TRP* 4.2 5.0 - - - +
384A THR* 2.7 34.0 + - - +
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Residues in contact with CYS 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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328A MET* 4.6 3.8 - - - -
341A SER* 5.1 2.7 - - - -
366A LEU* 3.8 43.3 - - + +
369A HIS* 4.5 12.8 - - - +
370A LEU* 4.5 9.4 - - + -
377A LEU* 3.1 41.3 + - - +
378A VAL* 3.9 7.2 - - - +
379A GLN 3.1 0.6 - - - -
380A ASN* 1.3 78.3 - - - +
382A LEU* 1.3 58.4 + - - +
384A THR* 3.6 4.6 + - - -
385A LEU* 3.1 34.8 + - + +
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Residues in contact with LEU 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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370A LEU* 3.6 24.2 - - + -
378A VAL* 3.2 26.8 + - + +
379A GLN* 3.1 12.4 + - - +
381A CYS* 1.3 77.0 - - - +
383A TRP* 1.3 66.4 + - - +
384A THR 3.1 1.8 - - - -
385A LEU* 3.2 14.4 + - + +
386A ARG* 3.2 13.5 + - - +
405A LEU* 5.2 6.1 - - + -
408A LEU* 5.0 8.3 - - + -
416A VAL* 3.8 47.3 - - + +
419A CYS* 3.9 21.9 - - + -
420A ALA* 5.2 5.4 - - + +
423A ILE* 4.2 17.1 - - + +
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Residues in contact with TRP 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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345A LYS* 4.4 34.5 - - + -
379A GLN* 3.1 50.2 + - + +
380A ASN* 4.2 5.6 - - - +
381A CYS 3.6 0.2 - - - -
382A LEU* 1.3 75.6 - - - +
384A THR* 1.3 62.9 + - - +
386A ARG* 3.2 25.8 + - - +
387A ASN* 3.2 37.1 + - - +
419A CYS* 4.4 10.3 - - - -
1031C TYR* 4.0 38.4 - + + -
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Residues in contact with THR 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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341A SER* 4.5 3.6 + - - -
344A LEU* 4.3 9.8 - - + +
345A LYS* 3.7 28.6 + - - +
348A SER* 4.0 22.9 - - - +
357A ILE* 6.2 0.9 - - + -
366A LEU* 4.2 20.9 - - + -
380A ASN 2.7 21.9 + - - -
381A CYS* 3.8 4.4 - - - -
382A LEU 3.1 0.4 - - - -
383A TRP* 1.3 80.7 - - - +
385A LEU* 1.3 61.5 + - - +
387A ASN* 3.3 12.9 + - - +
388A LEU* 3.3 21.2 + - + +
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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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363A MET* 3.7 50.0 - - + +
366A LEU* 4.1 28.5 - - + +
367A GLY* 4.9 1.3 - - - +
370A LEU* 4.3 25.8 - - + -
381A CYS 3.1 26.8 + - - +
382A LEU* 3.2 3.3 + - + +
384A THR* 1.3 75.6 - - - +
386A ARG* 1.3 58.0 + - - +
388A LEU* 4.0 4.3 - - + +
389A SER* 3.1 27.9 + - - -
401A LEU* 4.7 10.5 - - + -
405A LEU* 5.5 2.0 - - + -
423A ILE* 3.4 26.8 - - + +
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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
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382A LEU 3.2 10.6 + - - +
383A TRP* 3.2 40.0 + - - +
384A THR 3.2 0.4 - - - -
385A LEU* 1.3 78.7 - - - +
387A ASN* 1.3 61.6 + - - +
389A SER* 2.4 23.9 + - - +
390A ASP* 4.3 1.4 - - - +
418A THR* 4.3 20.8 + - - +
419A CYS* 4.1 34.7 - - - +
422A GLY* 5.1 3.6 - - - -
423A ILE* 3.8 16.3 - - + +
1027C TYR* 3.6 47.0 + - + +
1031C TYR* 3.5 42.4 + - - -
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Residues in contact with ASN 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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345A LYS* 4.9 2.4 + - - +
348A SER* 3.4 41.0 + - - +
349A VAL* 4.1 12.7 - - - +
354A LYS* 2.6 30.6 + - - +
383A TRP* 3.2 27.3 + - - +
384A THR 3.3 8.0 + - - +
386A ARG* 1.3 82.9 + - - +
388A LEU* 1.3 56.7 + - - +
390A ASP* 3.2 8.7 - - - +
1027C TYR* 4.1 6.9 - - - +
1028C SER* 4.0 28.5 + - - +
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Residues in contact with LEU 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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348A SER* 3.8 23.6 - - - -
354A LYS* 4.3 23.7 - - + +
357A ILE* 4.3 34.1 - - + -
358A VAL* 4.3 12.5 - - + +
362A GLY 5.3 2.9 - - - -
363A MET* 3.9 28.3 - - + -
366A LEU* 4.8 10.1 - - + -
384A THR* 3.3 26.8 + - + +
385A LEU* 4.3 0.9 - - - +
387A ASN* 1.3 76.9 - - - +
389A SER* 1.3 67.0 + - - +
390A ASP* 2.9 0.9 + - - +
391A ALA* 2.8 24.0 + - - +
392A ALA* 3.8 4.6 + - - +
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Residues in contact with SER 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A MET* 4.6 11.4 - - - +
385A LEU 3.1 19.4 + - - -
386A ARG* 2.4 26.7 + - - -
388A LEU* 1.3 73.4 - - - +
390A ASP* 1.3 57.5 + - - -
391A ALA 2.9 5.7 + - - -
392A ALA* 3.3 10.8 + - - +
393A THR* 3.9 12.8 + - - +
423A ILE* 4.6 15.0 - - - -
426A ASN* 2.9 36.6 + - - +
427A LEU* 4.4 5.5 - - - +
1027C TYR* 4.2 2.1 - - - -
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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