Contacts of the helix formed by residues 323 - 342 (chain B) 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 SER 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ARG* 3.5 5.6 - - - +
386A ASP* 3.5 12.3 - - - -
322B GLN* 1.3 76.6 - - - +
324B VAL* 1.3 64.3 + - - +
325B ASN* 3.3 11.7 + - - +
326B HIS* 2.8 28.8 + - - +
327B LEU* 2.9 15.2 + - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ARG* 4.4 1.3 - - - +
386A ASP* 3.0 46.6 + - - +
389A THR* 3.6 23.6 - - + -
390A PHE* 4.0 26.2 - - + +
322B GLN 3.9 1.6 + - - -
323B SER* 1.3 70.9 - - - +
325B ASN* 1.3 59.2 + - - +
327B LEU* 4.0 9.7 - - - +
328B VAL* 2.8 34.3 + - + +
359B PHE* 4.1 16.8 - - + -
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Residues in contact with ASN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 4.8 1.0 + - - -
323B SER* 2.8 12.0 + - - +
324B VAL* 1.3 82.2 - - - +
326B HIS* 1.3 57.3 + - - +
328B VAL* 3.0 10.6 + - - +
329B LYS* 2.9 33.9 + - - +
139C ASN* 4.7 14.8 - - - +
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Residues in contact with HIS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER* 3.0 42.9 + - - -
322B GLN* 3.4 24.0 - - + +
323B SER* 2.8 23.9 + - - +
325B ASN* 1.3 70.9 - - - +
327B LEU* 1.3 64.3 + - - +
329B LYS* 3.0 22.2 + - + +
330B GLU* 3.0 36.4 + - + +
305C ASP* 5.6 0.2 + - - -
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A PHE* 3.9 16.8 - - + -
318B GLY* 5.0 1.1 - - - -
319B GLY 4.1 9.6 - - - +
320B GLY* 5.6 0.2 - - - -
322B GLN* 3.8 31.9 - - + +
323B SER 2.9 18.5 + - - +
324B VAL* 4.0 8.3 - - - +
326B HIS* 1.3 76.4 - - - +
328B VAL* 1.3 63.8 + - - +
330B GLU* 3.3 6.3 + - - +
331B ILE* 2.9 29.0 + - + +
354B LEU* 4.4 22.6 - - + +
356B VAL* 3.8 31.0 - - + -
359B PHE* 3.8 23.8 - - + -
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Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B VAL* 2.8 29.9 + - + +
325B ASN* 3.0 7.6 + - - +
327B LEU* 1.3 73.4 - - - +
329B LYS* 1.3 59.2 + - - +
331B ILE* 3.3 3.3 + - - +
332B ASP* 2.9 30.9 + - + +
359B PHE* 4.1 8.1 - - + -
362B GLU* 3.5 31.9 - - - +
366B GLU* 3.7 12.7 - - - +
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Residues in contact with LYS 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ASN* 2.9 17.6 + - - +
326B HIS* 3.3 16.4 - - + +
328B VAL* 1.3 78.9 - - - +
330B GLU* 1.3 59.6 + - + +
332B ASP* 3.5 7.5 + - + +
333B MSE 2.9 33.5 + - + +
305C ASP* 6.2 0.2 - - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B SER* 3.3 10.3 + - - +
326B HIS* 3.0 47.9 + - + +
327B LEU* 3.6 4.7 - - - +
329B LYS* 1.3 73.3 - - - +
331B ILE* 1.3 57.8 + - - +
332B ASP 2.9 1.7 + - - -
333B MSE 3.0 5.1 - - - +
334B LEU* 2.7 36.5 + - + +
354B LEU* 3.6 34.1 - - + -
282C ARG* 4.1 13.2 + - - -
305C ASP* 3.2 30.1 - - - +
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Residues in contact with ILE 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 2.9 15.4 + - + +
328B VAL 3.8 3.1 - - - +
330B GLU* 1.3 75.8 - - - +
332B ASP* 1.3 61.2 + - - +
334B LEU* 3.4 9.3 - - - +
335B LEU* 3.2 27.1 + - + +
351B LEU* 5.1 3.6 - - + -
354B LEU* 3.8 19.3 - - + -
356B VAL* 5.7 1.8 - - + -
359B PHE* 3.9 22.4 - - + +
360B HIS* 6.2 0.4 - - + -
362B GLU* 3.6 28.3 - - + -
363B LEU* 3.9 37.5 - - + +
366B GLU* 3.6 24.2 - - - +
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Residues in contact with ASP 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B VAL* 2.9 19.5 + - + +
329B LYS* 3.5 8.2 - - - +
331B ILE* 1.3 75.1 - - - +
333B MSE 1.3 57.0 + - - +
335B LEU* 3.1 3.9 + - - +
336B LYS* 2.8 75.3 + - - +
366B GLU* 3.7 16.2 - - - +
370B MSE 5.1 7.3 - - - +
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Residues in contact with MSE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LYS* 2.9 20.2 + - + +
330B GLU* 3.0 18.6 - - - +
332B ASP* 1.3 73.7 + - - +
334B LEU* 1.3 55.8 + - - +
336B LYS* 3.3 6.5 + - + -
337B GLU* 2.7 36.8 + - + +
282C ARG* 3.6 41.3 - - + +
304C GLY* 4.1 20.0 - - - +
305C ASP* 4.3 9.4 - - - +
331C LEU* 3.6 38.6 - - + -
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU 2.7 17.0 + - - +
331B ILE* 3.4 6.1 - - - +
333B MSE 1.3 73.4 - - - +
335B LEU* 1.3 65.7 + - + +
337B GLU* 3.3 4.2 - - - +
338B TYR* 3.0 25.0 + - + +
347B ALA* 3.8 31.2 - - + +
350B CYS* 3.4 22.7 - - + +
351B LEU* 3.5 32.5 - - + +
354B LEU* 4.1 15.3 - - + -
363B LEU* 4.4 21.3 - - + -
386B LEU* 5.7 1.1 - - + -
282C ARG* 3.6 13.2 - - - +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.2 19.3 + - + +
332B ASP* 3.1 3.9 + - - +
334B LEU* 1.3 78.7 - - + +
336B LYS* 1.3 67.5 + - - +
337B GLU 3.1 1.3 - - - -
338B TYR* 3.0 15.4 + - + +
339B LEU* 3.2 15.9 + - - +
363B LEU* 4.0 19.5 - - + +
366B GLU* 3.6 37.0 - - + +
367B ALA* 3.8 31.4 - - + +
370B MSE 3.5 19.4 - - + +
383B ILE* 4.5 6.3 - - + -
386B LEU* 4.0 23.6 - - + -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B ASP* 2.8 56.2 + - - +
333B MSE 3.6 8.3 - - + +
335B LEU* 1.3 73.6 - - - +
337B GLU* 1.3 61.7 + - - +
339B LEU* 3.3 18.4 + - - +
340B LEU* 3.5 17.0 + - + +
370B MSE 4.4 8.6 - - - +
111C GLU* 3.7 30.2 + - - -
331C LEU* 3.9 23.8 - - + -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MSE 2.7 27.4 + - + +
334B LEU 3.3 5.8 - - - +
336B LYS* 1.3 71.5 - - - +
338B TYR* 1.3 61.6 + - - +
340B LEU* 3.1 5.1 + - - +
341B SER* 2.7 26.8 + - - +
346B GLU* 3.7 26.7 - - + +
350B CYS* 4.2 1.0 - - - -
280C ASN 4.4 9.7 - - - +
281C THR* 3.8 12.8 - - + -
282C ARG* 2.6 61.6 + - - +
329C THR* 5.3 2.3 - - - +
331C LEU* 3.9 10.8 - - + +
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Residues in contact with TYR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B LEU* 3.0 13.7 + - + +
335B LEU* 3.0 10.2 + - + +
337B GLU* 1.3 76.7 - - - +
339B LEU* 1.3 67.8 + - + +
341B SER* 3.6 6.3 - - - -
342B GLY* 2.6 46.8 + - - -
343B ASP 3.6 20.4 - - - -
344B ILE* 3.5 34.7 - - + +
347B ALA* 4.3 14.8 - - + -
382B MSE 2.8 52.3 + - + +
383B ILE* 4.5 4.3 - - + -
385B ASP* 4.0 5.0 - - - +
386B LEU* 3.8 27.8 + - + -
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU 3.2 6.3 + - - +
336B LYS* 3.6 11.2 - - - +
337B GLU 3.2 0.8 - - - -
338B TYR* 1.3 81.1 - - + +
340B LEU* 1.3 64.7 + - + +
342B GLY 4.7 0.3 + - - -
370B MSE 2.9 41.7 - - + -
379B THR* 4.4 19.3 - - + +
382B MSE 3.6 49.7 - - + +
383B ILE* 4.1 11.0 - - + -
351C THR* 4.1 1.6 + - - -
352C ASN* 3.7 21.1 + - - +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LYS* 3.6 15.3 - - + +
337B GLU* 3.1 5.4 + - - +
339B LEU* 1.3 84.8 - - + +
341B SER* 1.3 58.3 + - - +
280C ASN* 3.9 13.9 + - - +
329C THR* 6.2 0.2 - - - -
330C ASP* 3.7 26.5 - - - +
331C LEU* 3.8 33.9 - - + -
350C PRO* 5.6 0.2 - - - +
351C THR* 2.6 27.1 + - - +
352C ASN* 4.0 4.7 - - - +
355C ASN* 3.9 30.5 - - - +
359C ARG* 6.2 0.2 - - - +
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Residues in contact with SER 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 2.7 19.1 + - - +
338B TYR* 3.6 11.4 + - - -
340B LEU* 1.3 72.7 - - - +
342B GLY* 1.3 58.5 + - - +
343B ASP* 2.6 37.8 + - - +
346B GLU* 5.0 0.7 - - - +
280C ASN* 3.9 18.7 + - - +
281C THR* 3.9 27.3 - - - +
351C THR* 3.1 24.1 - - - +
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Residues in contact with GLY 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B TYR* 2.6 33.1 + - - -
339B LEU 4.6 0.4 - - - -
340B LEU 3.6 0.6 - - - -
341B SER* 1.3 71.9 - - - +
343B ASP* 1.3 57.8 + - - +
344B ILE* 3.2 14.1 + - - +
382B MSE 5.4 8.3 - - - -
351C THR* 4.6 4.9 + - - -
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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
------------------------------------------------------------
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