Contacts of the strand formed by residues 379 - 396 (chain A) in PDB entry 4EWS
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 LYS 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A TYR* 3.2 11.6 - - - -
376A SER 3.1 24.8 + - - +
377A LYS* 3.4 23.8 - - - +
378A LYS* 1.4 78.7 - - - +
380A LEU* 1.3 62.1 + - - +
381A PHE* 3.3 32.3 - - + -
430A THR* 3.8 15.3 - - + +
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Residues in contact with LEU 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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373A ALA* 4.1 22.7 - - + -
374A SER 3.3 17.5 - - - +
375A TYR* 4.1 11.8 - - + -
379A LYS* 1.3 74.2 - - - +
381A PHE* 1.3 64.8 + - - +
382A LEU* 3.7 21.8 - - + -
426A GLU* 3.3 46.3 - - - +
429A PHE* 4.1 18.2 - - + -
430A THR* 3.1 22.5 + - - +
433A MET* 5.1 2.9 - - - -
448A ILE* 5.2 0.9 - - + -
502A 2OB 4.5 30.3 - - + -
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Residues in contact with PHE 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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372A GLN 3.5 1.7 - - - +
373A ALA* 3.4 5.4 - - - -
374A SER* 2.6 55.0 + - - +
376A SER* 3.1 42.8 - - - -
377A LYS* 5.5 2.2 - - + -
379A LYS* 3.3 40.6 - - + -
380A LEU* 1.3 74.1 - - - +
382A LEU* 1.3 62.9 + - - +
383A SER* 4.1 1.0 + - - -
426A GLU* 3.5 10.8 - - - +
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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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371A VAL* 3.9 16.2 - - + -
372A GLN 3.5 1.1 - - - -
373A ALA* 4.0 20.6 - - + -
380A LEU* 3.7 23.1 - - + -
381A PHE* 1.3 71.3 - - - +
383A SER* 1.3 61.1 + - - +
422A MET* 3.7 41.0 - - + +
425A LEU* 4.0 7.4 - - + -
426A GLU* 2.7 31.5 + - + +
502A 2OB 3.7 43.7 - - + +
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 3.4 4.9 - - - -
372A GLN* 2.8 50.4 + - - +
381A PHE* 5.5 0.4 - - - -
382A LEU* 1.3 73.5 - - - +
384A LEU* 1.3 62.1 + - - +
385A LEU* 3.8 6.9 + - - +
422A MET* 3.6 4.3 - - - -
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Residues in contact with LEU 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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369A THR* 3.6 32.8 - - + -
370A THR 3.7 7.0 - - - +
371A VAL* 4.7 0.2 - - + -
383A SER* 1.3 70.9 - - - +
385A LEU* 1.3 64.0 + - - +
386A ASP* 3.6 16.2 - - - +
387A PHE* 3.7 27.6 - - + -
418A ILE* 3.7 23.8 - - + -
422A MET* 3.6 22.2 - - + +
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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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336A LYS* 4.2 8.7 - - + +
370A THR* 2.7 29.6 + - + +
372A GLN* 3.3 50.7 - - + +
383A SER* 4.4 7.0 - - - +
384A LEU* 1.3 75.7 - - - +
386A ASP* 1.3 62.2 + - + +
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Residues in contact with ASP 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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336A LYS* 4.1 12.1 + - - +
369A THR* 3.5 1.0 - - - -
370A THR* 2.7 59.7 + - - +
384A LEU* 3.6 6.3 - - - +
385A LEU* 1.3 81.9 - - + +
387A PHE* 1.3 67.1 + - - +
388A GLN* 3.0 27.7 + - - +
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Residues in contact with PHE 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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367A ILE* 5.3 0.7 - - + -
368A VAL 3.0 13.7 - - - +
369A THR* 4.3 8.7 - - + -
384A LEU* 3.7 25.8 - - + -
386A ASP* 1.3 79.7 - - - +
388A GLN* 1.3 75.4 + - - +
389A ILE* 3.5 33.7 - - + -
414A THR* 3.6 22.2 - - + -
418A ILE* 4.0 8.7 - - + -
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Residues in contact with GLN 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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336A LYS* 5.7 0.9 + - - -
366A ASP 3.7 1.8 - - - +
367A ILE* 3.5 4.5 - - - -
368A VAL* 2.8 59.7 + - + +
386A ASP* 3.0 32.1 + - - +
387A PHE* 1.3 82.5 + - - +
389A ILE* 1.3 65.6 + - - +
390A THR* 5.2 7.2 - - + -
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Residues in contact with ILE 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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365A GLU* 3.3 34.3 - - - +
366A ASP 3.7 2.2 - - - -
367A ILE* 3.8 20.4 - - + -
387A PHE* 3.5 30.4 - - + -
388A GLN* 1.3 79.3 - - - +
390A THR* 1.3 69.7 + - - +
391A PRO* 3.9 7.8 - - + +
410A GLN* 3.7 13.2 - - + +
413A ILE* 5.6 0.4 - - + -
414A THR* 3.2 28.9 - - + +
418A ILE* 3.8 11.9 - - + -
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Residues in contact with THR 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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365A GLU* 3.9 2.2 - - - -
366A ASP* 3.2 34.3 + - - +
388A GLN* 5.2 7.2 - - + -
389A ILE* 1.3 79.9 - - - +
391A PRO* 1.4 67.6 - - - +
392A LYS* 3.3 26.5 + - - +
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Residues in contact with PRO 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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364A GLU 4.9 0.2 - - - +
365A GLU* 3.5 19.5 - - + +
389A ILE* 3.9 7.6 - - + +
390A THR* 1.4 82.8 - - - +
392A LYS* 1.4 63.8 + - - +
393A THR 3.8 0.2 - - - -
394A VAL* 3.9 21.1 - - + -
406A GLN* 5.9 1.1 - - - +
410A GLN* 3.3 26.9 - - + +
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Residues in contact with LYS 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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364A GLU* 2.8 32.8 + - + +
365A GLU* 4.2 0.9 - - - -
366A ASP* 3.5 38.6 + - - +
390A THR* 3.3 24.2 + - - +
391A PRO* 1.4 73.0 - - - +
393A THR* 1.4 66.8 + - - +
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Residues in contact with THR 393 (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 THR 3.2 12.5 - - - +
364A GLU* 3.1 49.9 + - - +
392A LYS* 1.4 82.4 - - - +
394A VAL* 1.3 64.5 + - - +
395A SER* 3.8 10.1 + - - +
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Residues in contact with VAL 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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361A TYR* 3.7 16.2 - - + -
362A THR 3.4 4.3 - - - -
363A PHE* 3.5 52.5 - - + +
364A GLU 5.3 0.4 - - - +
391A PRO* 3.9 23.8 - - + -
392A LYS 4.3 0.2 - - - -
393A THR* 1.3 76.0 - - - +
395A SER* 1.3 63.8 + - - +
406A GLN* 3.7 28.9 - - - +
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Residues in contact with SER 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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360A ALA 4.0 0.2 - - - +
361A TYR* 3.2 11.7 - - - -
362A THR* 2.8 47.4 + - - -
393A THR* 4.1 12.0 + - - +
394A VAL* 1.3 79.1 + - - +
396A ASN* 1.3 64.8 + - - +
397A LEU* 4.3 4.2 - - - +
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Residues in contact with ASN 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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360A ALA 3.4 5.2 - - - +
361A TYR* 4.0 14.3 + - + -
395A SER* 1.3 75.9 - - - +
397A LEU* 1.3 60.0 + - - +
398A THR 3.0 11.3 + - - +
400A SER 5.1 0.9 - - - +
401A SER* 3.0 21.6 + - - -
1B NAG 1.4 75.9 + - - +
4B FUC 3.4 10.0 + - - -
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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