Contacts of the helix formed by residues 328 - 350 (chain A) in PDB entry 4BEJ
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 ASP 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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326A VAL* 4.5 2.3 - - - -
327A ASP* 1.3 86.6 + - - +
329A LYS* 1.3 61.4 + - - +
330A SER* 2.9 24.8 + - - -
331A ALA* 3.1 24.5 + - + +
332A THR* 2.9 25.1 + - - -
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Residues in contact with LYS 329 (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 VAL* 4.3 16.6 - - + +
327A ASP 4.0 5.2 + - - +
328A ASP* 1.3 71.7 + - - +
330A SER* 1.3 64.9 + - - +
332A THR* 3.4 8.0 + - - -
333A LEU* 3.4 7.3 + - - +
670A LEU* 3.8 25.9 - - + +
671A ASP* 6.0 2.7 - - - +
674A LEU* 3.2 39.9 - - + +
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Residues in contact with SER 330 (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 ASP* 2.9 13.5 + - - -
329A LYS* 1.3 72.0 - - - +
331A ALA* 1.3 64.5 + - - +
333A LEU* 3.3 7.0 + - - +
334A LEU* 3.2 21.9 + - - +
665A TYR* 3.6 25.0 - - - -
670A LEU* 3.6 20.0 - - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASP* 3.1 33.3 + - + +
329A LYS 3.3 0.2 - - - -
330A SER* 1.3 75.0 - - - +
332A THR* 1.3 63.9 + - - +
334A LEU* 3.3 11.6 + - - +
335A GLN* 3.0 30.2 + - - +
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Residues in contact with THR 332 (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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324A GLU* 4.7 13.3 + - - +
326A VAL* 4.2 13.7 - - + +
328A ASP 2.9 16.5 + - - -
329A LYS* 3.5 9.9 + - - -
330A SER 3.3 0.4 - - - -
331A ALA* 1.3 78.1 - - - +
333A LEU* 1.3 56.1 + - - +
335A GLN* 4.9 3.4 - - - -
336A LEU* 2.7 54.4 + - + +
457A PHE* 4.5 11.0 - - + -
674A LEU* 3.7 25.2 - - + +
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Residues in contact with LEU 333 (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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329A LYS 3.4 5.9 + - - +
330A SER* 3.3 10.8 + - - +
331A ALA 3.3 0.4 - - - -
332A THR* 1.3 78.4 - - - +
334A LEU* 1.3 57.0 + - - +
336A LEU* 4.9 1.1 - - + -
337A ILE* 3.0 59.3 + - + +
460A LEU* 3.2 33.2 - - + -
661A VAL* 5.7 0.2 - - - +
664A LEU 3.7 26.7 - - - +
665A TYR* 4.2 16.8 - - + -
669A LEU 6.3 0.2 - - - -
670A LEU* 4.6 15.7 - - + -
673A LEU* 4.3 14.4 - - + -
674A LEU* 3.7 17.5 - - + -
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Residues in contact with LEU 334 (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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330A SER 3.2 9.1 + - - +
331A ALA* 3.4 15.3 - - - +
333A LEU* 1.3 79.3 - - - +
335A GLN* 1.3 53.2 + - + +
337A ILE* 5.2 0.7 - - - -
338A THR* 2.4 36.5 + - - +
661A VAL* 4.8 15.5 - - + -
665A TYR* 3.9 38.1 - - + +
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Residues in contact with GLN 335 (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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331A ALA* 3.0 18.4 + - - +
332A THR* 4.2 2.7 - - - +
334A LEU* 1.3 76.1 - - + +
336A LEU* 1.3 68.4 + - - +
337A ILE 3.1 1.6 - - - -
338A THR* 4.1 3.1 - - - +
339A LYS* 3.0 26.9 + - + +
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Residues in contact with LEU 336 (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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332A THR* 2.7 32.4 + - + +
333A LEU* 4.6 2.0 - - - +
335A GLN* 1.3 75.5 - - - +
337A ILE* 1.3 58.4 + - + +
339A LYS* 4.1 4.8 - - - +
340A PHE* 3.5 18.2 + - + +
455A LEU* 3.5 31.4 - - + -
457A PHE* 3.5 36.8 - - + -
460A LEU* 3.5 30.7 - - + -
464A ILE* 4.3 7.9 - - + -
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Residues in contact with ILE 337 (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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333A LEU* 3.0 39.9 + - + +
334A LEU 5.3 0.2 - - - +
335A GLN 3.1 0.6 - - - -
336A LEU* 1.3 76.5 - - + +
338A THR* 1.3 63.9 + - - +
339A LYS 3.2 1.6 - - - -
340A PHE* 3.3 15.0 + - - +
341A ALA* 3.3 12.5 + - - +
460A LEU* 5.1 4.7 - - + -
464A ILE* 3.9 21.8 - - + -
657A GLN* 5.4 1.3 - - - +
660A LEU* 3.6 21.4 - - + +
661A VAL* 3.7 29.6 - - + -
664A LEU* 3.4 39.0 - - + -
665A TYR* 5.1 2.2 - - + +
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Residues in contact with THR 338 (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 LEU* 2.4 32.7 + - - +
335A GLN* 3.4 5.3 + - - -
337A ILE* 1.3 80.0 - - - +
339A LYS* 1.3 62.0 + - - +
341A ALA* 3.2 8.0 - - - +
342A THR* 3.1 24.5 + - - +
657A GLN* 3.9 22.1 + - - +
661A VAL* 4.8 6.1 - - - +
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Residues in contact with LYS 339 (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 GLN* 3.0 21.2 + - + +
336A LEU* 4.1 4.5 - - - +
338A THR* 1.3 78.1 - - - +
340A PHE* 1.3 53.2 + - - +
342A THR* 3.3 11.1 + - + -
343A GLU* 2.7 67.8 + - - +
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Residues in contact with PHE 340 (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 LEU* 3.5 12.3 + - + +
337A ILE* 3.3 12.3 + - - +
339A LYS* 1.3 78.6 - - - +
341A ALA* 1.3 61.1 + - - +
343A GLU* 3.4 19.9 + - + +
344A TYR* 3.3 24.2 + + + +
443A ILE* 3.6 33.4 - - + -
446A CYS* 3.5 34.8 - - + -
447A SER* 5.3 1.3 - - - -
461A HIS* 6.5 1.8 - + - -
464A ILE* 3.2 39.0 - - + -
465A VAL* 5.4 1.8 - - + -
468A VAL* 4.1 15.5 - - + -
656A LEU* 4.5 3.5 - - + +
660A LEU* 4.5 8.7 - - + -
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Residues in contact with ALA 341 (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 ILE 3.3 9.2 + - - +
338A THR 3.2 6.5 - - - +
340A PHE* 1.3 77.1 - - - +
342A THR* 1.3 58.7 + - - +
344A TYR* 3.0 22.0 + - - +
345A CYS* 3.1 16.9 + - - -
656A LEU* 4.1 17.9 - - + +
657A GLN* 3.0 46.2 - - - +
660A LEU* 4.9 2.0 - - + +
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Residues in contact with THR 342 (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 THR* 3.1 17.2 + - - +
339A LYS* 3.9 13.4 - - + -
341A ALA* 1.3 73.5 - - - +
343A GLU* 1.3 57.2 + - - +
344A TYR 2.8 10.1 + - - -
345A CYS* 4.7 6.3 - - + +
346A ASN* 3.0 52.8 + - - +
657A GLN* 4.1 7.1 + - - -
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Residues in contact with GLU 343 (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 LYS* 2.7 48.2 + - - +
340A PHE* 3.4 21.8 - - + +
342A THR* 1.3 75.1 - - - +
344A TYR* 1.3 56.2 + - - +
346A ASN* 4.7 2.9 - - - +
347A THR* 3.2 20.9 + - - -
446A CYS* 3.4 44.2 - - + +
449A TYR* 4.5 18.4 - - + +
454A LEU* 4.3 18.3 - - - +
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Residues in contact with TYR 344 (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 PHE* 3.3 16.5 + + + +
341A ALA 3.0 9.6 - - - +
342A THR 2.8 2.2 - - - -
343A GLU* 1.3 77.0 - - - +
345A CYS* 1.3 82.9 + - - +
346A ASN 3.0 1.3 - - - -
347A THR* 3.1 13.3 + - - -
348A ILE* 3.1 41.6 + - + +
439A MET* 2.8 37.6 - - + +
442A ILE* 4.3 20.2 - - + -
443A ILE* 5.8 5.4 - - + -
446A CYS* 5.4 2.0 - - - -
468A VAL* 5.6 7.9 - - + -
472A LEU* 4.8 0.8 - - + +
652A VAL* 3.0 29.1 - - + +
653A LYS* 4.0 13.9 - - - -
656A LEU* 3.3 25.8 - - + -
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Residues in contact with CYS 345 (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 ALA* 3.1 21.2 + - - +
342A THR* 4.8 3.8 - - + +
344A TYR* 1.3 82.4 - - - +
346A ASN* 1.3 68.2 + - - +
348A ILE* 3.1 18.3 - - - +
349A GLU* 3.1 18.9 - - - +
653A LYS* 3.5 48.7 - - + -
656A LEU* 5.8 0.9 - - - -
657A GLN* 5.5 7.6 - - - -
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Residues in contact with ASN 346 (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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342A THR* 3.0 39.8 + - - +
343A GLU* 4.7 2.1 - - - +
344A TYR 4.6 0.2 - - - -
345A CYS* 1.3 85.3 - - - +
347A THR* 1.3 55.2 + - - +
349A GLU* 3.4 6.3 - - - +
350A GLY* 2.7 39.4 + - - -
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Residues in contact with THR 347 (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 GLU 3.2 17.9 + - - -
344A TYR 3.1 6.4 + - - -
346A ASN* 1.3 75.9 - - - +
348A ILE* 1.3 57.3 + - - +
350A GLY 3.4 7.7 + - - -
360A LEU 4.0 20.9 - - - +
361A CYS* 4.1 13.0 - - - -
362A GLY* 3.1 6.1 - - - -
363A GLY* 2.6 35.5 + - - -
442A ILE* 4.3 17.3 - - + -
445A HIS* 4.2 14.8 - - + -
446A CYS* 4.4 4.3 - - - -
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Residues in contact with ILE 348 (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 TYR* 3.1 47.8 + - + +
345A CYS 3.1 14.6 - - - +
347A THR* 1.3 75.1 - - - +
349A GLU* 1.3 72.0 + - + +
362A GLY 3.2 22.1 - - - +
363A GLY* 3.2 8.8 - - - +
366A ILE* 4.3 10.2 - - + +
439A MET* 4.8 4.0 - - + -
442A ILE* 4.1 15.0 - - + -
649A VAL* 4.0 28.1 - - + +
653A LYS* 3.4 43.1 - - + -
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Residues in contact with GLU 349 (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 CYS* 3.1 23.0 + - - +
346A ASN* 3.9 5.5 + - - +
347A THR 3.2 0.2 - - - -
348A ILE* 1.3 80.7 - - + +
350A GLY* 1.3 54.7 + - - +
363A GLY* 4.3 4.5 - - - -
653A LYS* 2.3 50.7 + - - +
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Residues in contact with GLY 350 (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 ASN* 2.7 23.3 + - - -
347A THR* 3.4 8.6 + - - -
348A ILE 3.5 0.4 - - - -
349A GLU* 1.3 77.0 - - - +
361A CYS* 3.7 27.1 - - - -
363A GLY* 3.7 7.5 - - - -
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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
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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