Contacts of the helix formed by residues 222 - 231 (chain E) in PDB entry 2I2X
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 GLN 222 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166E MET 6.3 0.4 - - - -
167E GLY 3.9 10.6 - - - +
168E GLY* 3.2 30.9 + - - -
169E LYS* 4.6 4.3 - - - -
172E PHE* 2.9 52.0 - - + +
187E SER 3.4 18.2 + - - -
188E ILE* 3.2 26.1 - - + +
219E ASP* 2.7 30.0 + - - +
220E CYS 3.1 0.2 - - - -
221E ALA* 1.3 88.7 - - + +
223E ALA* 1.3 69.6 + - - +
224E ASN 3.3 0.7 - - - -
225E THR 3.1 2.8 + - - -
226E ALA 2.9 9.4 + - - -
253E ARG* 4.6 1.7 + - - +
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Residues in contact with ALA 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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188E ILE* 5.3 0.2 - - - +
219E ASP* 2.8 28.8 + - + +
222E GLN* 1.3 73.7 - - - +
224E ASN* 1.3 65.5 + - - +
226E ALA* 3.1 18.5 + - - +
227E MET 3.1 9.2 + - - -
243E ALA 5.2 1.6 - - - +
246E ALA* 5.0 8.3 - - - -
247E ARG* 3.4 34.4 + - - +
250E SER* 3.7 17.3 - - - +
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Residues in contact with ASN 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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218E THR* 3.9 0.4 - - - +
219E ASP 3.5 3.0 + - - -
220E CYS* 3.2 39.2 - - - +
222E GLN 3.3 0.6 - - - -
223E ALA* 1.3 76.5 - - - +
225E THR* 1.3 64.0 + - - +
227E MET* 2.9 10.7 + - + +
228E PHE* 2.8 46.8 + - + -
247E ARG* 2.9 33.2 + - - +
269E CYS* 2.7 34.5 + - - +
271E TYR* 3.6 7.4 - - - -
295E HIS* 6.2 0.2 + - - -
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Residues in contact with THR 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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172E PHE* 3.8 19.1 - - + -
173E ASP* 4.5 3.4 - - - +
220E CYS 3.5 8.6 + - - -
221E ALA 3.5 13.9 + - - -
222E GLN 3.1 9.1 + - - -
224E ASN* 1.3 76.7 - - - +
226E ALA* 1.3 62.5 + - - +
228E PHE* 3.3 8.2 + - - +
229E ILE* 3.0 42.1 + - + +
138F ILE* 3.9 15.9 - - + -
500F B13 3.5 33.4 - - + +
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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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172E PHE* 3.8 8.2 - - + -
176E VAL* 4.2 10.1 - - + -
222E GLN 2.9 12.1 + - - +
223E ALA 3.3 9.0 - - - +
225E THR* 1.3 76.7 - - - +
227E MET* 1.3 57.5 + - - +
229E ILE* 3.3 1.4 + - - +
230E GLY* 2.8 25.1 + - - -
238E LEU* 3.4 26.1 - - + +
243E ALA* 4.2 7.8 - - - +
246E ALA* 4.0 24.9 - - + -
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Residues in contact with MET 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 ALA 3.1 4.6 + - - +
224E ASN* 2.9 15.4 + - - +
226E ALA* 1.3 72.5 - - - +
228E PHE* 1.3 80.6 + - + +
230E GLY* 3.1 3.0 + - - +
231E GLY* 2.9 26.4 + - - +
243E ALA* 4.4 5.5 + - + +
247E ARG* 3.5 25.1 - - - +
271E TYR* 3.6 34.8 - - + +
296E SER 5.2 2.7 - - - +
297E ASP* 4.5 10.5 - - + -
298E VAL* 5.6 1.3 - - + -
299E MET* 4.1 23.6 - - - +
366E GLN* 3.3 30.2 + - - +
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Residues in contact with PHE 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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220E CYS* 5.3 4.5 - - - -
224E ASN* 2.8 52.1 + - + +
225E THR* 3.9 6.1 - - - +
227E MET* 1.3 82.9 - - + +
229E ILE* 1.3 61.1 + - + +
231E GLY* 3.4 12.9 + - - +
235E ASN* 5.7 0.3 + - - -
295E HIS* 3.2 59.9 - + + -
296E SER 4.3 8.7 - - - -
500F B13 3.2 57.7 - - + +
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Residues in contact with ILE 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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176E VAL* 4.0 21.5 - - + +
177E LEU* 4.2 9.9 - - + -
225E THR* 3.0 29.7 + - + +
226E ALA* 3.7 3.8 - - - +
228E PHE* 1.3 74.4 - - + +
230E GLY* 1.3 68.2 + - - +
231E GLY* 3.2 1.9 + - - -
235E ASN* 4.5 3.5 + - - -
237E ASN* 3.5 44.9 + - + +
238E LEU* 3.8 9.0 - - + -
95F LEU* 4.9 7.9 - - + -
138F ILE* 3.7 37.9 - - + -
142F ILE* 5.9 2.0 - - + -
500F B13 4.8 15.7 - - + +
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Residues in contact with GLY 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 14.8 + - - -
227E MET* 3.1 6.3 + - - -
229E ILE* 1.3 75.7 - - - +
231E GLY* 1.3 59.0 + - - +
235E ASN* 3.2 16.6 - - - +
238E LEU* 3.5 27.3 + - - +
240E HIS* 2.9 24.1 + - - -
243E ALA* 5.2 3.8 - - - -
366E GLN* 5.6 0.9 - - - -
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Residues in contact with GLY 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 MET* 2.9 14.0 + - - +
228E PHE* 3.4 12.1 + - - -
229E ILE 3.1 2.7 - - - -
230E GLY* 1.3 71.9 - - - +
232E GLY* 1.3 68.3 + - - +
235E ASN* 4.0 11.0 - - - -
240E HIS* 3.3 13.0 - - - -
298E VAL* 6.0 1.9 - - - +
366E GLN* 5.2 2.3 + - - -
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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