Contacts of the helix formed by residues 281 - 294 (chain D) 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 THR 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279D ILE* 3.5 4.2 - - - +
280D ASN* 1.3 88.6 - - + +
282D ARG* 1.3 57.9 + - - +
284D LYS* 3.2 26.5 + - + +
285D VAL* 3.1 21.3 + - - +
329D THR* 3.5 10.5 - - - +
174E GLU* 5.5 0.2 - - - -
178E HIS* 3.9 19.7 - - + +
180E ASP* 4.5 4.9 - - + +
183E GLU* 3.1 45.9 + - + +
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Residues in contact with ARG 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D THR* 1.3 71.3 - - - +
283D ARG* 1.3 68.8 + - + +
284D LYS 3.1 1.6 - - - -
285D VAL* 2.9 19.0 + - + +
286D ASP* 3.1 18.4 + - - +
303D HIS* 3.4 46.1 + - + +
304D GLY* 4.2 12.1 - - - +
329D THR* 3.6 14.0 - - + +
332D LEU* 3.3 31.1 - - + +
170E PRO* 4.3 23.0 - - - +
171E ILE* 5.6 6.3 - - - +
174E GLU* 2.6 38.2 + - - -
178E HIS* 5.7 0.4 - - - -
183E GLU* 4.3 1.5 + - - +
187E MSE 5.2 10.8 - - - -
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Residues in contact with ARG 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D THR* 3.4 0.6 - - - +
282D ARG* 1.3 78.4 - - + +
284D LYS* 1.3 57.4 + - - +
286D ASP* 3.6 8.8 + - - +
287D TRP* 3.2 25.1 + - - +
183E GLU* 3.0 28.6 + - - +
186E GLU* 3.2 45.9 + - - +
187E MSE 3.6 35.2 - - - +
190E ASP* 5.0 7.5 + - - -
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Residues in contact with LYS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D GLU* 2.9 37.6 + - - +
279D ILE* 3.3 22.4 - - + +
281D THR* 3.2 21.4 + - + +
282D ARG 3.1 0.6 - - - -
283D ARG* 1.3 79.0 - - - +
285D VAL* 1.3 63.2 + - - +
286D ASP 3.3 0.2 - - - -
287D TRP* 4.1 20.9 - - + -
288D LEU* 3.2 23.4 + - - +
347D TYR* 3.8 14.8 - - - -
348D ASP* 3.3 22.9 + - - +
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D ILE* 3.8 16.6 - - + -
281D THR 3.1 15.2 + - - +
282D ARG* 2.9 13.2 + - + +
284D LYS* 1.3 77.9 - - - +
286D ASP* 1.3 59.3 + - - +
288D LEU* 4.0 1.6 - - - +
289D THR* 2.6 38.0 + - - +
301D ALA* 3.9 23.1 - - + -
302D MET 4.0 15.0 - - - +
303D HIS* 4.4 1.8 - - + -
327D ILE* 3.8 13.7 - - + +
328D THR 3.7 32.5 - - - +
329D THR* 3.8 5.6 - - + -
332D LEU* 5.7 0.2 - - + -
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Residues in contact with ASP 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ARG 3.1 10.5 + - - +
283D ARG* 3.9 9.5 - - - +
285D VAL* 1.3 77.9 - - - +
287D TRP* 1.3 59.5 + - - +
289D THR* 3.6 5.1 - - - -
290D GLU* 2.9 33.5 + - - +
301D ALA* 4.5 7.4 - - - +
303D HIS* 3.4 33.5 + - - +
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Residues in contact with TRP 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D GLU* 5.6 2.5 - - - -
260D LEU* 4.2 18.6 - - + -
283D ARG 3.2 15.4 + - - +
284D LYS* 3.8 23.6 - - + +
285D VAL 3.4 0.2 - - - -
286D ASP* 1.3 80.0 - - - +
288D LEU* 1.3 85.7 + - + +
290D GLU* 3.6 12.6 - - - +
291D LYS* 3.4 56.1 + - + +
347D TYR* 3.6 31.6 - + - -
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Residues in contact with LEU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 4.0 22.9 - - + -
263D LEU* 4.9 4.5 - - + -
277D ILE* 4.6 8.1 - - + -
279D ILE* 3.6 26.7 - - + -
284D LYS 3.2 14.8 + - - +
285D VAL 4.2 2.5 - - - +
287D TRP* 1.3 87.8 - - + +
289D THR* 1.3 61.2 - - - +
291D LYS* 3.6 6.0 + - - +
292D MET* 2.8 40.8 - - + +
327D ILE* 4.0 24.7 - - + -
347D TYR* 3.5 35.7 - - + +
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D VAL* 2.6 23.7 + - - +
286D ASP* 3.2 6.7 + - - -
288D LEU* 1.3 77.7 - - - +
290D GLU* 1.3 62.2 + - - +
292D MET* 3.4 10.6 + - - +
293D HIS* 3.1 34.1 + - + +
299D VAL* 4.4 6.7 - - + +
301D ALA* 3.3 38.3 - - + +
327D ILE* 3.3 18.7 - - - +
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Residues in contact with GLU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ASP 2.9 14.2 + - - +
287D TRP* 3.6 17.8 - - - +
289D THR* 1.3 74.3 - - - +
291D LYS* 1.3 70.5 + - + +
292D MET 3.0 9.2 + - - -
293D HIS* 3.4 10.3 + - - +
294D ALA* 3.3 20.3 + - - +
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Residues in contact with LYS 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 3.8 36.0 - - + +
287D TRP* 3.4 46.8 + - + +
288D LEU* 3.6 4.5 + - - +
289D THR 3.4 0.6 - - - -
290D GLU* 1.3 87.4 - - + +
292D MET* 1.3 70.4 + - - +
294D ALA* 4.2 13.7 - - + -
295D ARG* 3.8 21.7 + - - +
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Residues in contact with MET 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260D LEU* 4.4 14.8 - - - -
263D LEU* 3.5 38.8 - - + -
264D CYS* 4.6 8.5 - - - -
267D TYR* 5.6 1.1 - - + -
277D ILE* 5.9 2.5 - - + -
288D LEU* 2.8 35.2 - - + +
289D THR 3.8 6.1 - - - +
290D GLU 3.0 0.8 - - - -
291D LYS* 1.3 90.3 - - - +
293D HIS* 1.3 63.9 + - - +
294D ALA 3.1 1.1 - - - +
295D ARG 3.5 3.6 - - - +
296D ASP 3.0 19.1 + - - -
297D PHE* 3.0 52.6 + - + +
299D VAL* 4.1 25.8 - - + -
327D ILE* 5.0 2.9 - - + -
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Residues in contact with HIS 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D THR* 3.1 35.3 - - + +
290D GLU* 3.4 9.6 + - - +
292D MET* 1.3 77.6 - - - +
294D ALA* 1.3 59.6 + - - +
295D ARG 3.2 1.5 + - - -
296D ASP* 3.9 10.3 + - - +
297D PHE 5.2 7.6 + - - +
299D VAL* 3.3 25.9 + - + -
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Residues in contact with ALA 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D GLU 3.3 15.5 + - - +
291D LYS* 4.2 12.3 - - + -
292D MET 3.1 0.2 - - - -
293D HIS* 1.3 79.0 - - - +
295D ARG* 1.3 63.5 + - + +
296D ASP 3.7 0.4 - - - -
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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
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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