Contacts of the strand formed by residues 359 - 376 (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 VAL 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A VAL* 4.5 18.4 - - + -
348A PHE 3.7 0.7 - - - +
349A LEU* 3.6 1.6 - - - -
350A PHE* 2.9 57.7 + - + -
352A ARG* 5.2 7.1 - - - +
357A HIS 3.6 2.2 + - - +
358A SER* 1.3 72.0 - - - +
360A ALA* 1.3 59.1 + - - +
361A TYR* 3.7 25.6 - - + +
398A THR* 4.0 1.8 - - - -
400A SER* 3.7 31.0 - - - +
405A ILE* 3.8 22.9 - - + -
409A LEU* 4.5 3.4 - - + -
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Residues in contact with ALA 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PHE 3.3 5.4 - - - +
349A LEU* 4.1 22.9 - - + -
358A SER* 3.7 4.6 + - - -
359A VAL* 1.3 73.0 - - - +
361A TYR* 1.3 61.2 + - - +
396A ASN* 3.4 4.5 - - - +
397A LEU* 2.7 56.2 + - + +
398A THR* 3.7 13.9 + - + +
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Residues in contact with TYR 361 (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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346A VAL 3.9 0.7 - - - +
347A LYS* 3.6 0.3 - - - -
348A PHE* 2.9 36.4 + - + +
359A VAL* 3.7 20.4 - - + -
360A ALA* 1.3 76.5 - - - +
362A THR* 1.3 66.3 + - - +
363A PHE* 3.6 29.2 - + + -
394A VAL* 3.7 18.6 - - + -
395A SER 3.2 15.5 - - - -
396A ASN* 4.0 8.7 - - + -
400A SER 4.4 0.7 - - - -
401A SER* 3.3 30.2 - - - -
402A SER 3.2 23.5 + - - -
405A ILE* 3.5 20.0 - - + -
406A GLN* 4.0 16.7 + - + +
409A LEU* 3.8 15.3 - - + -
4B FUC 4.3 7.1 + - - -
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Residues in contact with THR 362 (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 MET* 3.9 19.5 - - + +
346A VAL 3.6 2.9 - - - -
347A LYS* 3.8 32.3 - - + -
360A ALA 5.6 0.2 - - - -
361A TYR* 1.3 77.7 - - - +
363A PHE* 1.3 61.7 + - - +
393A THR 3.2 9.5 + - - +
395A SER* 2.8 50.4 + - - -
397A LEU* 3.7 20.6 - - + +
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Residues in contact with PHE 363 (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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344A VAL 3.8 1.0 - - - +
345A MET* 3.4 4.7 - - - +
346A VAL* 2.8 43.7 + - + +
348A PHE* 4.3 9.4 - + - -
361A TYR* 3.6 28.3 - + + -
362A THR* 1.3 72.7 - - - +
364A GLU* 1.3 60.1 + - - +
365A GLU* 3.9 8.5 + - - +
393A THR 4.3 1.1 - - - -
394A VAL* 3.5 33.9 - - + +
406A GLN* 3.4 34.5 - - + -
409A LEU* 3.6 22.7 - - + -
410A GLN* 3.3 31.4 - - + -
413A ILE* 3.8 23.6 - - + -
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Residues in contact with GLU 364 (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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326A LEU* 3.6 26.7 - - + +
343A SER* 5.6 1.3 - - - +
344A VAL 3.5 4.3 - - - -
345A MET* 4.2 15.4 - - + +
362A THR 3.8 0.2 + - - -
363A PHE* 1.3 69.0 - - - +
365A GLU* 1.3 60.0 + - - +
391A PRO* 3.9 1.3 - - - +
392A LYS* 2.8 35.0 + - + +
393A THR* 3.1 47.4 + - - +
394A VAL* 5.3 0.6 - - - +
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Residues in contact with GLU 365 (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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343A SER* 4.0 0.6 + - - -
344A VAL* 2.8 56.2 + - + +
346A VAL* 5.4 1.6 - - + -
363A PHE* 4.0 11.2 - - - +
364A GLU* 1.3 75.8 - - - +
366A ASP* 1.3 65.5 + - - +
367A ILE* 3.7 6.4 - - + +
389A ILE* 3.3 14.2 - - - +
390A THR 3.4 15.7 - - - +
391A PRO* 3.5 11.6 - - + +
392A LYS* 4.0 2.9 - - - +
410A GLN* 2.9 43.3 + - - +
413A ILE* 3.4 25.9 - - - +
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Residues in contact with ASP 366 (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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327A LYS* 5.9 1.4 - - - -
330A LYS* 5.4 4.9 + - - -
341A ASP* 4.3 16.1 - - - +
342A SER 3.5 2.7 - - - -
343A SER* 2.7 33.3 + - - -
364A GLU* 6.1 0.2 - - - +
365A GLU* 1.3 76.2 - - - +
367A ILE* 1.3 62.0 + - - +
368A VAL* 5.2 2.7 - - + +
388A GLN 3.7 3.6 - - - +
389A ILE* 3.7 0.9 - - - +
390A THR* 3.2 42.5 + - - +
392A LYS* 3.5 28.4 + - - +
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Residues in contact with ILE 367 (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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340A VAL 3.7 1.6 - - - +
341A ASP* 3.6 0.7 - - - -
342A SER* 2.8 42.8 + - - +
344A VAL* 3.5 27.1 - - + -
365A GLU* 3.7 19.5 - - + +
366A ASP* 1.3 76.1 - - - +
368A VAL* 1.3 64.0 + - - +
369A THR* 3.9 23.9 + - + -
387A PHE* 5.3 0.4 - - + -
388A GLN 3.5 6.3 - - - +
389A ILE* 3.8 22.4 - - + -
413A ILE* 4.2 8.7 - - + -
418A ILE* 4.3 9.9 - - + -
502A 2OB 3.7 30.3 - - + -
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Residues in contact with VAL 368 (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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339A VAL* 3.8 27.1 - - + -
340A VAL 3.4 5.8 - - - +
341A ASP* 3.4 30.7 - - + +
366A ASP* 5.2 3.1 - - + +
367A ILE* 1.3 71.7 - - - +
369A THR* 1.3 64.4 + - - +
370A THR* 5.1 2.2 - - - +
387A PHE* 3.0 7.8 - - - +
388A GLN* 2.8 62.5 + - + +
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Residues in contact with THR 369 (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 VAL 3.7 1.4 - - - +
339A VAL* 3.5 2.6 - - - +
340A VAL* 2.9 39.5 + - - +
342A SER* 5.4 0.2 + - - -
367A ILE* 3.9 20.3 + - + -
368A VAL* 1.3 76.0 - - - +
370A THR* 1.4 61.4 + - - +
371A VAL* 3.9 2.6 + - - +
384A LEU* 3.6 22.0 - - + -
386A ASP 3.5 3.8 - - - -
387A PHE* 4.3 4.7 - - + -
418A ILE* 4.0 14.8 - - + -
502A 2OB 3.4 37.9 - - + +
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Residues in contact with THR 370 (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* 3.9 52.2 + - + +
337A GLY* 4.2 6.3 - - - -
338A VAL 3.5 7.9 - - - +
339A VAL* 4.0 13.5 - - + +
368A VAL* 5.1 3.1 - - - +
369A THR* 1.4 71.5 + - - +
371A VAL* 1.3 57.6 + - - +
384A LEU* 3.7 2.9 - - - -
385A LEU* 2.7 39.8 + - + +
386A ASP* 2.7 38.2 + - - +
388A GLN* 5.1 0.7 + - - -
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Residues in contact with VAL 371 (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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337A GLY* 3.5 7.0 - - - -
338A VAL* 2.8 43.5 + - - +
340A VAL* 4.7 1.6 - - + -
369A THR* 4.0 11.7 - - - +
370A THR* 1.3 75.5 - - - +
372A GLN* 1.3 64.1 + - - +
373A ALA 4.4 0.2 - - - -
382A LEU* 3.9 28.5 - - + -
383A SER 3.4 5.2 - - - +
384A LEU* 4.7 0.2 - - + -
385A LEU* 5.1 1.6 - - - -
422A MET* 3.8 23.6 - - + -
450A THR* 5.4 0.2 - - - +
502A 2OB 3.6 51.1 - - + +
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Residues in contact with GLN 372 (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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335A ASN 5.4 0.5 - - - +
336A LYS* 3.0 24.1 - - - +
337A GLY* 4.7 4.7 - - - -
371A VAL* 1.3 77.5 - - - +
373A ALA* 1.3 64.3 + - - +
381A PHE 3.5 3.3 - - - +
382A LEU* 3.5 1.0 - - - -
383A SER* 2.8 44.0 + - - +
385A LEU* 3.3 29.8 - - + +
448A ILE 6.1 0.4 - - - +
450A THR* 4.9 7.0 - - + +
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Residues in contact with ALA 373 (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 VAL* 6.2 0.8 - - + +
371A VAL 4.4 0.2 - - - -
372A GLN* 1.3 78.1 - - - +
374A SER* 1.3 61.9 + - - +
380A LEU* 4.1 6.7 - - + -
381A PHE 3.4 4.5 - - - -
382A LEU* 4.0 10.3 - - + -
448A ILE* 3.7 31.8 + - + +
502A 2OB 3.9 41.0 - - + +
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Residues in contact with SER 374 (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* 1.3 75.2 + - - +
375A TYR* 1.3 60.5 + - - +
376A SER* 5.9 1.0 - - - -
380A LEU* 3.3 7.8 - - - +
381A PHE* 2.6 55.1 + - - -
448A ILE* 3.7 8.1 - - - -
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Residues in contact with TYR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 1.3 75.1 + - - +
376A SER* 1.3 68.5 + - - +
378A LYS* 3.7 38.3 + - + +
379A LYS 3.2 23.3 - - - -
380A LEU* 4.1 8.5 - - + -
381A PHE* 4.6 0.2 - - - -
430A THR* 6.0 1.1 - - + -
433A MET* 3.9 27.1 - - + +
434A ASN* 5.1 0.9 + - - -
438A VAL* 4.4 9.5 + - - +
439A SER* 4.4 14.6 + - - -
443A ILE* 4.3 20.6 - - + +
446A PRO* 3.6 40.3 + - + +
448A ILE* 3.8 8.9 - - + +
502A 2OB 4.0 34.8 - - + -
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A SER* 5.9 1.5 - - - -
375A TYR* 1.3 78.8 - - - +
377A LYS* 1.4 76.0 + - - +
378A LYS 3.1 3.7 + - - +
379A LYS* 3.1 13.0 + - - +
381A PHE* 3.1 27.9 - - - -
446A PRO* 5.7 0.9 - - - -
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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