Contacts of the helix formed by residues 230 - 245 (chain E) in PDB entry 1Z6Z
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 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E ASP* 6.1 2.2 - - - -
228E LEU 3.5 4.6 + - - -
229E VAL* 1.3 77.3 - - - +
231E CYS* 1.3 69.0 + - - +
232E LYS* 3.2 26.9 + - - +
233E VAL* 3.1 22.9 + - + +
234E SER* 3.1 18.4 + - - -
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Residues in contact with CYS 231 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15E GLY* 4.2 3.4 - - - -
16E PHE* 4.0 21.9 - - + -
19E THR* 3.5 24.0 - - - +
198E LEU* 4.1 20.9 - - - -
199E ASP* 4.9 7.5 - - - +
200E THR* 3.7 29.4 - - - -
229E VAL 3.4 3.6 + - - -
230E ASP* 1.3 73.7 + - - +
232E LYS* 1.3 57.0 + - - +
234E SER* 3.4 1.9 + - - -
235E ALA* 2.9 31.7 + - - +
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Residues in contact with LYS 232 (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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19E THR* 3.6 18.6 - - + +
23E LEU* 4.1 7.8 - - + +
230E ASP* 3.2 16.7 + - - +
231E CYS* 1.3 76.5 - - - +
233E VAL* 1.3 58.1 + - + +
235E ALA* 3.3 3.4 + - - +
236E GLN* 2.9 42.0 + - - +
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Residues in contact with VAL 233 (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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229E VAL* 4.8 1.3 - - + -
230E ASP* 3.1 30.3 + - + +
232E LYS* 1.3 74.5 - - + +
234E SER* 1.3 63.1 + - - +
236E GLN* 3.3 15.3 + - - +
237E LYS* 3.1 19.9 + - - +
255E PHE* 3.8 24.9 - - + -
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Residues in contact with SER 234 (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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16E PHE* 3.7 5.1 - - - -
193E TYR* 3.1 19.9 + - - -
195E PRO* 2.7 37.8 + - - +
198E LEU* 3.8 19.1 - - - -
229E VAL* 3.9 5.4 - - - -
230E ASP 3.1 10.3 + - - -
231E CYS 3.8 2.2 - - - -
233E VAL* 1.3 76.9 - - - +
235E ALA* 1.3 62.7 + - - +
237E LYS 3.1 2.3 + - - -
238E LEU* 3.0 19.9 + - - +
255E PHE* 3.8 11.3 - - - -
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Residues in contact with ALA 235 (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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16E PHE* 3.6 17.8 - - + -
19E THR* 4.7 2.7 - - + -
20E LEU* 3.8 25.2 - - + +
23E LEU* 3.8 19.1 - - + -
231E CYS 2.9 18.4 + - - +
232E LYS* 3.6 4.9 - - - +
234E SER* 1.3 75.3 - - - +
236E GLN* 1.3 58.2 + - - +
238E LEU* 3.3 4.8 + - - +
239E LEU* 3.0 33.6 + - - +
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Residues in contact with GLN 236 (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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23E LEU* 4.3 19.1 - - + -
232E LYS* 2.9 32.1 + - - +
233E VAL* 3.6 13.0 + - - +
234E SER 3.2 0.2 - - - -
235E ALA* 1.3 73.1 - - - +
237E LYS* 1.3 61.1 + - - +
239E LEU* 3.4 9.9 + - + +
240E SER* 2.9 31.0 + - - -
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Residues in contact with LYS 237 (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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193E TYR* 3.5 17.5 - - + +
233E VAL 3.1 12.6 + - - +
234E SER 3.1 9.6 + - - +
236E GLN* 1.3 73.8 - - - +
238E LEU* 1.3 64.0 + - - +
240E SER* 3.3 12.9 + - - +
241E LEU* 2.9 44.0 + - + +
253E VAL* 5.2 2.4 - - - +
254E ASP 4.0 11.3 + - - -
255E PHE* 3.4 36.2 + - + +
257E ASP* 4.2 13.5 + - - +
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Residues in contact with LEU 238 (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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16E PHE* 4.1 8.7 - - + -
20E LEU* 4.1 29.2 - - + -
95E ILE* 4.8 6.7 - - + -
150E VAL* 4.2 11.0 - - + -
152E ILE* 4.1 20.9 - - + -
191E LEU* 3.7 27.8 - - + -
193E TYR* 3.8 28.6 + - + -
234E SER 3.0 8.2 + - - +
235E ALA* 3.3 8.0 + - - +
237E LYS* 1.3 75.3 - - - +
239E LEU* 1.3 65.1 + - + +
241E LEU* 3.2 11.8 + - - +
242E LEU* 3.0 38.1 + - + +
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Residues in contact with LEU 239 (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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2E LEU* 4.9 5.7 - - + +
20E LEU* 4.1 15.3 - - + -
23E LEU* 3.8 32.8 - - + -
24E LEU* 3.8 28.5 - - + -
27E LEU* 4.1 28.8 - - + +
95E ILE* 5.8 0.4 - - + -
235E ALA 3.0 24.3 + - - +
236E GLN* 3.8 9.9 - - + +
237E LYS 3.3 0.2 - - - -
238E LEU* 1.3 75.1 - - + +
240E SER* 1.3 57.4 + - - +
242E LEU* 3.0 18.7 + - + +
243E GLU* 2.8 29.6 + - - +
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Residues in contact with SER 240 (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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236E GLN 2.9 16.2 + - - -
237E LYS* 3.3 17.7 + - - +
239E LEU* 1.3 78.2 - - - +
241E LEU* 1.3 60.5 + - - +
243E GLU* 3.9 6.2 - - - +
244E LYS* 2.9 43.7 + - - +
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Residues in contact with LEU 241 (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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191E LEU* 4.7 14.6 - - + -
193E TYR* 3.7 36.8 - - + -
237E LYS* 2.9 32.5 + - + +
238E LEU* 3.3 9.2 - - - +
240E SER* 1.3 79.5 + - - +
242E LEU* 1.3 56.9 + - - +
244E LYS* 3.9 6.5 - - + +
245E ASP* 3.0 25.8 + - - -
246E GLU 4.4 0.7 + - - -
247E PHE* 3.7 23.9 - - + +
253E VAL* 3.8 25.8 - - + -
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Residues in contact with LEU 242 (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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2E LEU* 4.7 7.6 - - + -
91E ARG* 3.8 24.3 + - - +
93E LEU* 4.1 28.7 - - + -
95E ILE* 4.9 4.0 - - + -
148E THR* 3.8 29.4 - - + -
150E VAL* 4.0 14.1 - - + -
191E LEU* 4.1 13.0 - - + -
238E LEU* 3.0 34.6 + - + +
239E LEU* 3.0 19.0 + - + +
241E LEU* 1.3 74.9 - - - +
243E GLU* 1.3 63.7 + - - +
245E ASP* 3.4 16.9 + - - +
247E PHE* 4.4 6.7 - - + -
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Residues in contact with GLU 243 (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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0E HIS* 3.6 41.3 - - + +
1E MET 5.6 1.6 - - - +
2E LEU* 4.7 11.6 - - + +
27E LEU* 6.4 1.3 - - + -
91E ARG* 4.8 4.7 + - - +
239E LEU 2.8 15.9 + - - +
240E SER* 3.9 7.2 - - - +
242E LEU* 1.3 77.8 - - - +
244E LYS* 1.3 64.0 + - + +
245E ASP* 3.4 4.2 + - - +
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Residues in contact with LYS 244 (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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240E SER* 2.9 29.3 + - - +
241E LEU* 4.1 7.2 - - + +
243E GLU* 1.3 80.0 - - + +
245E ASP* 1.3 69.5 + - - +
246E GLU* 3.2 41.0 + - + +
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Residues in contact with ASP 245 (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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91E ARG* 5.2 2.9 + - - +
146E ASN* 3.2 26.6 + - - -
148E THR* 4.9 2.3 + - - -
189E ARG* 2.8 45.1 + - - +
241E LEU 3.0 15.2 + - - -
242E LEU 3.6 12.9 - - - +
243E GLU 3.2 4.4 - - - +
244E LYS* 1.3 78.5 - - - +
246E GLU* 1.3 57.5 + - - +
247E PHE* 3.9 9.7 - - - -
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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