Contacts of the helix formed by residues 222 - 233 (chain E) in PDB entry 1ZM9
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 ILE 222 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204E PRO* 3.1 38.4 + - + +
205E ALA* 4.4 3.4 - - - +
207E GLY* 5.4 0.6 - - - -
209E VAL 4.6 1.2 + - - +
211E PHE* 4.0 15.0 - - + -
220E PHE* 4.6 3.1 - - + -
221E THR* 1.3 72.7 - - - +
223E ARG* 1.3 61.6 + - - +
224E GLN 3.1 0.2 + - - -
225E PHE* 3.4 4.4 + - - +
226E ALA* 3.1 23.5 + - - +
241E MET* 3.5 31.4 - - + +
244E LEU* 3.5 21.4 - - + +
245E TRP* 4.4 10.3 - - + +
273E PHE* 3.2 39.5 - - + -
277E ILE* 5.4 2.5 - - + -
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Residues in contact with ARG 223 (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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81E MET* 5.9 1.2 - - - -
85E ASP* 3.0 33.9 + - - +
88E GLU* 3.3 23.2 + - - -
206E ARG 5.1 6.5 - - - -
207E GLY* 4.6 11.7 - - - -
221E THR* 3.0 9.7 + - - +
222E ILE* 1.3 77.0 - - - +
224E GLN* 1.3 55.1 + - - +
226E ALA* 3.7 10.1 - - - +
227E THR* 2.7 33.8 + - - +
237E LYS* 3.8 15.2 - - + +
241E MET* 3.6 28.6 - - + +
336E GLU* 3.1 29.2 + - - +
340E LEU* 3.3 32.8 - - - +
341E HIS* 5.8 2.0 - - - -
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Residues in contact with GLN 224 (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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219E ALA 3.6 2.2 + - - +
220E PHE* 3.0 18.5 - - + +
221E THR* 2.8 39.5 + - - +
223E ARG* 1.3 76.8 - - - +
225E PHE* 1.3 62.6 + - + +
226E ALA 2.9 7.6 + - - -
227E THR* 3.1 15.6 + - - -
228E ARG* 3.4 19.6 + - - +
328E LEU* 4.9 10.1 - - + +
329E PRO* 5.0 4.4 + - - +
332E ASP* 4.4 9.3 + - - +
333E ALA* 3.4 29.4 - - - +
336E GLU* 3.3 12.5 + - - +
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Residues in contact with PHE 225 (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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220E PHE* 4.0 19.3 - + + -
221E THR 3.6 2.5 + - - +
222E ILE* 3.4 7.9 + - - +
224E GLN* 1.3 79.0 - - + +
226E ALA* 1.3 56.4 + - - +
227E THR 3.4 0.2 - - - -
228E ARG* 3.2 39.5 - - - -
229E TYR* 3.0 43.7 + + + +
244E LEU* 4.0 4.1 - - + +
276E PHE 5.0 3.1 - - - -
277E ILE* 3.1 56.5 - - + -
280E PRO* 5.8 2.5 - - + -
281E ILE* 4.2 4.5 - - + -
327E PHE* 3.5 16.6 - + - -
328E LEU* 3.4 36.3 - - + -
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Residues in contact with ALA 226 (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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222E ILE 3.1 17.5 + - - +
223E ARG* 3.7 8.7 - - - +
224E GLN 2.9 0.2 - - - -
225E PHE* 1.3 78.3 - - - +
227E THR* 1.3 58.6 + - - +
228E ARG 3.3 0.9 - - - -
230E ALA* 2.8 26.2 + - - +
237E LYS* 2.9 18.9 - - + +
240E MET* 3.7 5.6 - - - +
241E MET* 3.4 36.8 - - + +
244E LEU* 3.8 5.4 - - + -
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Residues in contact with THR 227 (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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223E ARG* 2.7 22.5 + - - +
224E GLN* 3.1 8.5 + - - -
226E ALA* 1.3 76.5 - - - +
228E ARG* 1.3 64.6 + - - +
230E ALA* 3.8 12.6 - - + +
231E LYS* 3.9 21.5 - - - +
237E LYS* 3.2 34.2 + - + +
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Residues in contact with ARG 228 (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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224E GLN* 3.4 16.5 + - - +
225E PHE* 3.2 32.0 - - + +
226E ALA 3.3 0.4 - - - -
227E THR* 1.3 78.4 - - - +
229E TYR* 1.3 64.4 + - + +
230E ALA 3.0 8.1 + - - -
231E LYS* 3.2 15.4 + - - +
232E LYS* 3.5 15.4 + - - +
303E LEU 5.9 0.8 + - - -
327E PHE* 2.9 57.8 + - - -
328E LEU* 3.7 11.7 - - - +
329E PRO* 5.2 2.2 - - - +
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Residues in contact with TYR 229 (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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225E PHE* 3.0 36.3 + + + +
228E ARG* 1.3 79.2 - - + +
230E ALA* 1.3 62.6 + - - +
231E LYS 3.3 0.4 - - - -
232E LYS* 3.5 42.1 + - + -
233E PHE* 3.1 52.9 + + + +
240E MET* 3.9 11.5 - - + +
244E LEU* 4.7 5.2 - - + -
276E PHE* 2.7 56.8 + + + -
277E ILE* 3.9 9.0 - - + -
280E PRO* 3.8 12.5 - - - +
303E LEU* 6.0 0.5 - - - +
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Residues in contact with ALA 230 (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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226E ALA 2.8 24.9 + - - +
227E THR* 3.8 13.5 - - + +
228E ARG 3.0 0.4 - - - -
229E TYR* 1.3 80.2 - - - +
231E LYS* 1.3 62.8 + - + +
233E PHE 3.7 11.3 - - - +
234E GLY* 4.4 0.9 - - - -
235E VAL 3.4 25.9 + - - +
236E ASP* 5.2 0.7 - - - -
237E LYS* 3.9 14.6 - - + +
240E MET* 4.2 3.4 - - - -
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Residues in contact with LYS 231 (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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227E THR* 3.9 23.8 - - - +
228E ARG* 3.2 6.4 + - - +
230E ALA* 1.3 78.3 - - + +
232E LYS* 1.3 66.2 + - + +
233E PHE 3.0 7.8 - - - +
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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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228E ARG* 3.5 11.1 + - - +
229E TYR* 3.5 47.0 + - + +
230E ALA 3.5 0.4 - - - -
231E LYS* 1.3 76.1 - - + +
233E PHE* 1.3 73.7 + - + +
303E LEU* 6.0 4.4 - - - +
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Residues in contact with PHE 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 TYR* 3.1 38.0 + + + +
230E ALA 3.7 4.1 - - - +
231E LYS 3.0 10.9 - - - +
232E LYS* 1.3 93.3 - - + +
234E GLY* 1.3 61.9 + - - +
235E VAL* 3.8 10.1 - - + +
240E MET* 3.5 34.1 - - + -
243E ARG* 5.6 1.1 - - - +
250E PHE* 4.2 24.7 - + - -
257E TRP* 4.0 16.6 - + - -
276E PHE* 3.9 30.7 - + - -
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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