Contacts of the helix formed by residues 377 - 394 (chain E) in PDB entry 2ZU6
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 GLU 377 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376E GLY* 1.3 79.0 - - - +
378E SER* 1.3 60.7 + - - +
379E THR 3.5 2.0 - - - -
380E PHE* 3.1 15.4 - - - +
381E LYS* 2.8 29.9 + - + +
428E ARG* 3.1 36.5 + - - -
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Residues in contact with SER 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375E THR 5.3 2.0 + - - -
376E GLY 3.8 0.4 - - - -
377E GLU* 1.3 77.0 - - - +
379E THR* 1.3 55.4 + - - +
381E LYS* 3.0 17.2 + - - +
382E MSE 2.7 65.9 + - - +
352F ASN* 4.0 6.3 + - - -
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Residues in contact with THR 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 3.8 24.0 - - + +
370E MSE 3.6 23.6 - - + +
371E VAL* 3.8 9.0 - - - -
374E SER* 3.2 34.9 - - - +
375E THR 5.4 2.5 + - - -
376E GLY 5.4 0.6 - - - -
377E GLU 3.5 0.6 - - - +
378E SER* 1.3 75.6 + - - +
380E PHE* 1.3 63.7 + - - +
382E MSE 4.0 8.1 - - - +
383E ILE* 3.1 36.4 + - + +
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Residues in contact with PHE 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371E VAL* 3.7 23.8 - - + -
374E SER* 4.6 3.2 + - - +
376E GLY 4.8 3.1 + - - +
377E GLU* 3.1 25.8 + - - +
379E THR* 1.3 77.3 - - - +
381E LYS* 1.3 58.2 + - + +
384E LEU* 3.0 29.0 + - + +
425E VAL* 4.3 9.9 - - + -
428E ARG* 3.1 46.2 - - + +
429E PHE* 3.2 57.6 - + + -
432E GLU* 3.1 33.7 - - + -
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Residues in contact with LYS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E GLU* 2.8 12.2 + - + +
378E SER* 3.0 19.1 + - - +
380E PHE* 1.3 76.4 - - + +
382E MSE 1.3 81.6 + - - +
384E LEU* 3.0 8.6 + - - +
385E ASP* 2.8 42.2 + - - +
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Residues in contact with MSE 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E TYR* 3.2 29.0 + - + +
339E LEU* 3.7 48.0 - - + +
342E GLY* 5.3 7.0 - - - -
378E SER* 2.7 59.9 + - - +
379E THR* 4.0 1.3 - - - +
381E LYS* 1.3 86.2 - - + +
383E ILE* 1.3 67.9 + - - +
384E LEU 2.6 1.9 + - - -
385E ASP* 2.8 13.2 + - - +
386E LEU 2.9 9.4 + - - -
351F THR* 4.6 15.5 - - + +
352F ASN* 3.1 26.7 - - - +
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Residues in contact with ILE 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E LEU* 4.4 14.6 - - + -
338E TYR* 4.4 11.2 - - + -
339E LEU* 4.0 10.3 - - + -
367E ALA* 3.9 21.1 - - + +
370E MSE 3.9 24.5 - - + -
371E VAL* 3.7 29.2 - - + -
379E THR* 3.1 27.8 + - + +
380E PHE 4.5 0.7 - - - +
382E MSE 1.3 79.0 - - - +
384E LEU* 1.3 56.3 + - - +
386E LEU* 3.3 6.8 + - + +
387E LEU* 3.0 55.5 + - + +
429E PHE* 3.9 2.9 - - + -
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Residues in contact with LEU 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380E PHE* 3.0 20.7 + - + +
381E LYS* 3.0 8.0 + - - +
382E MSE 2.6 6.1 + - - -
383E ILE* 1.3 74.4 - - - +
385E ASP* 1.3 66.2 + - - +
387E LEU* 3.5 2.6 + - - +
388E LYS* 3.1 27.8 + - + +
429E PHE* 3.6 15.0 - - + -
432E GLU* 3.5 45.3 - - + +
433E CYS* 3.5 33.0 - - - -
436E ALA* 5.4 5.6 - - + -
438E ILE* 4.6 5.7 - - + +
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Residues in contact with ASP 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E TYR* 4.0 7.8 + - - +
344E ILE* 4.1 14.4 - - + +
381E LYS* 2.8 44.3 + - - +
382E MSE 3.4 8.4 + - - +
384E LEU* 1.3 77.5 - - - +
386E LEU* 1.3 58.2 + - - +
388E LYS* 3.0 14.7 + - - +
389E SER* 2.8 30.8 + - - -
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Residues in contact with LEU 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E LEU* 5.2 2.5 - - + -
335E LEU* 4.0 23.8 - - + -
338E TYR* 3.6 41.0 + - + -
344E ILE* 3.3 36.1 - - + +
347E ALA* 4.5 13.2 - - + -
363E LEU* 5.2 1.3 - - + -
382E MSE 2.9 5.1 + - - -
383E ILE* 3.5 11.2 - - + +
384E LEU 3.2 0.2 - - - -
385E ASP* 1.3 79.4 - - - +
387E LEU* 1.3 62.6 + - + +
389E SER* 3.4 0.7 + - - -
390E LEU* 2.8 51.8 + - + +
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Residues in contact with LEU 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LEU* 4.5 8.3 - - + -
364E VAL* 5.3 7.0 - - + +
367E ALA* 4.4 14.1 - - + -
368E ILE* 4.8 9.0 - - + -
383E ILE* 3.0 37.3 + - + +
384E LEU* 3.5 1.5 + - - +
385E ASP 3.3 0.2 - - - -
386E LEU* 1.3 86.2 - - + +
388E LYS* 1.3 60.0 + - - +
390E LEU* 4.1 14.8 - - + -
391E TRP* 2.8 29.8 + - - +
396E ILE* 5.4 1.1 - - + -
401E MSE 3.3 22.4 - - + +
405E TYR* 4.2 11.7 - - + +
429E PHE* 3.9 22.0 - - + -
438E ILE* 4.0 12.4 - - + +
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Residues in contact with LYS 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E LEU* 3.1 19.9 + - + +
385E ASP* 3.0 19.2 + - - +
387E LEU* 1.3 77.1 - - - +
389E SER* 1.3 60.1 + - - +
391E TRP* 3.0 14.7 + - + +
392E LYS* 2.8 38.5 + - + +
436E ALA* 3.9 31.0 - - + +
438E ILE* 4.3 9.2 - - + -
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Residues in contact with SER 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E ILE* 3.4 36.6 - - - +
348E GLU* 3.7 13.7 + - - +
385E ASP 2.8 10.5 + - - -
386E LEU 3.6 2.7 - - - -
388E LYS* 1.3 74.7 - - - +
390E LEU* 1.3 63.6 + - - -
392E LYS* 3.0 12.4 + - - +
393E SER* 3.0 26.2 + - - -
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Residues in contact with LEU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E ALA 6.4 0.7 - - - -
348E GLU* 3.4 32.5 - - + +
351E LEU* 4.3 8.5 - - + -
363E LEU* 4.4 6.5 - - + -
386E LEU* 2.8 51.3 + - + +
387E LEU* 3.8 13.0 - - + +
389E SER* 1.3 72.4 + - - +
391E TRP* 1.3 59.9 + - - +
393E SER* 3.9 3.8 - - - -
394E SER* 3.2 17.0 + - - -
395E THR* 3.4 30.1 + - + -
396E ILE* 3.4 37.7 + - + +
401E MSE 4.6 3.4 - - + -
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Residues in contact with TRP 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E LEU 2.8 24.3 + - - +
388E LYS* 3.0 16.9 + - + +
390E LEU* 1.3 74.0 - - - +
392E LYS* 1.3 92.7 + - + +
394E SER* 3.3 16.6 + - - -
396E ILE 5.0 3.0 - - - +
398E VAL* 5.5 12.7 - - + +
401E MSE 4.3 13.0 - - + -
436E ALA 3.9 12.8 - - - -
437E GLY* 3.7 24.7 + - - -
438E ILE* 3.6 39.4 + - + +
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Residues in contact with LYS 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLN* 5.4 2.1 - - - +
216D MET* 4.5 7.9 - - - +
221D LEU* 4.7 16.9 - - + +
388E LYS* 2.8 21.4 + - + +
389E SER* 3.0 10.7 + - - +
391E TRP* 1.3 101.8 - - + +
393E SER* 1.3 60.6 + - - +
394E SER* 4.6 2.3 + - - -
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Residues in contact with SER 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D THR* 3.3 2.6 - - - -
216D MET* 2.7 38.9 + - - +
217D PRO* 3.7 23.8 - - - -
348E GLU* 2.8 20.1 + - - -
389E SER 3.0 10.8 + - - -
390E LEU* 3.7 0.3 + - - -
392E LYS* 1.3 75.0 - - - +
394E SER* 1.3 66.4 + - - +
395E THR* 2.7 30.8 + - - -
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Residues in contact with SER 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLN* 3.0 32.4 + - - -
214D ALA 4.1 5.6 - - - -
215D THR* 3.7 9.8 - - - +
390E LEU 3.2 10.4 + - - -
391E TRP 3.3 9.7 + - - -
392E LYS 3.3 3.5 + - - -
393E SER* 1.3 81.6 + - - +
395E THR* 1.3 68.2 + - - +
396E ILE 3.1 16.2 + - - +
397E THR* 3.9 11.4 + - - +
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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