Contacts of the helix formed by residues 222 - 231 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167I GLY 3.2 15.0 + - - +
168I GLY 2.9 34.5 + - - +
169I LYS* 4.5 5.6 - - - -
172I PHE* 2.8 42.7 - - + +
187I SER 3.2 16.8 + - - -
188I ILE* 3.4 30.9 - - + +
219I ASP* 2.6 39.7 + - - +
220I CYS 3.1 0.2 + - - -
221I ALA* 1.3 77.8 - - + +
223I ALA* 1.3 66.7 + - - +
224I ASN 3.3 0.8 + - - -
225I THR 3.3 1.7 + - - -
226I ALA 3.0 7.6 + - - -
253I ARG* 4.3 4.9 + - - -
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Residues in contact with ALA 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188I ILE* 4.6 0.6 - - - +
219I ASP* 3.0 23.3 + - + +
222I GLN* 1.3 77.0 - - - +
224I ASN* 1.3 59.4 + - - +
226I ALA* 3.3 8.2 + - - +
227I MET* 3.0 26.0 + - - +
243I ALA 5.3 2.3 - - - +
246I ALA* 4.5 8.4 - - - +
247I ARG* 3.3 37.1 + - - +
250I SER* 3.8 15.0 - - - +
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Residues in contact with ASN 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I ASP 3.8 0.6 + - - -
220I CYS* 3.1 48.4 + - - +
223I ALA* 1.3 73.0 - - - +
225I THR* 1.3 67.1 + - - +
227I MET* 2.9 7.5 + - - +
228I PHE* 2.8 43.9 + - + -
247I ARG* 2.7 37.6 + - - +
269I CYS* 2.7 32.2 + - - +
271I TYR* 3.4 12.4 - - - -
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Residues in contact with THR 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I PHE* 3.5 22.0 - - + -
173I ASP* 4.3 1.6 - - - +
220I CYS 3.1 7.3 + - - -
221I ALA* 3.1 17.6 + - - -
222I GLN 3.3 8.5 + - - -
224I ASN* 1.3 74.2 - - - +
226I ALA* 1.3 62.0 + - - +
228I PHE* 3.3 4.8 + - - +
229I ILE* 3.0 40.5 + - + +
138J ILE* 3.7 16.8 - - + -
500J B13 3.1 39.3 - - + +
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Residues in contact with ALA 226 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I PHE* 3.7 13.0 - - + -
176I VAL* 4.0 13.2 - - + -
222I GLN 3.0 13.5 + - - +
223I ALA 3.5 9.4 - - - +
224I ASN 3.1 0.2 - - - -
225I THR* 1.3 75.5 - - - +
227I MET* 1.3 58.0 + - - +
229I ILE* 3.5 1.6 + - - +
230I GLY* 3.0 23.7 + - - -
238I LEU* 3.3 23.3 - - + +
243I ALA* 4.1 5.7 - - - +
246I ALA* 4.1 20.6 - - + -
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Residues in contact with MET 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I ALA 3.0 12.9 + - - +
224I ASN* 2.9 11.9 + - - +
226I ALA* 1.3 76.3 - - - +
228I PHE* 1.3 87.1 + - + +
230I GLY* 3.3 3.6 + - - -
231I GLY* 2.9 26.0 + - - +
243I ALA* 4.4 3.3 - - - +
247I ARG* 3.6 19.1 - - - +
271I TYR* 3.8 30.5 - - + +
295I HIS* 4.3 0.7 - - + -
296I SER 4.5 1.8 - - - +
297I ASP* 4.1 14.1 - - + -
298I VAL* 5.7 1.3 - - + -
299I MET* 4.3 23.3 - - - +
366I GLN* 3.3 29.0 + - - +
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Residues in contact with PHE 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I CYS* 5.2 2.5 - - - -
224I ASN* 2.8 45.1 + - + +
225I THR* 3.9 4.9 - - - +
227I MET* 1.3 89.8 - - + +
229I ILE* 1.3 65.9 + - - +
231I GLY* 3.0 15.1 + - - +
235I ASN* 4.8 1.7 + - - -
295I HIS* 3.5 53.2 - + + -
296I SER 4.4 4.9 - - - -
500J B13 3.0 62.9 - - + +
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Residues in contact with ILE 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I VAL* 4.1 25.6 - - + +
177I LEU* 4.3 15.0 - - + -
225I THR* 3.0 41.2 + - + +
226I ALA* 3.8 3.4 - - - +
228I PHE* 1.3 75.3 - - - +
230I GLY* 1.3 64.0 + - - +
231I GLY 3.2 0.9 + - - -
235I ASN* 4.0 6.6 + - - -
237I ASN* 3.4 47.2 + - + +
238I LEU* 3.9 8.7 - - + -
95J LEU* 5.1 2.7 - - + -
138J ILE* 4.1 12.8 - - + -
142J ILE* 5.4 2.9 - - + -
500J B13 4.2 24.7 - - + -
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Residues in contact with GLY 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226I ALA 3.0 14.7 + - - -
227I MET* 3.5 5.8 - - - -
229I ILE* 1.3 77.0 - - - +
231I GLY* 1.3 60.1 + - - +
235I ASN* 3.4 14.6 - - - +
238I LEU* 3.6 27.1 + - - +
240I HIS* 2.7 28.7 + - - -
243I ALA* 5.4 1.8 - - - -
366I GLN* 5.9 0.2 - - - -
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Residues in contact with GLY 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227I MET* 2.9 14.8 + - - +
228I PHE* 3.0 17.3 + - - -
230I GLY* 1.3 78.8 - - - +
232I GLY* 1.3 58.0 + - - -
235I ASN* 3.6 10.5 - - - -
240I HIS* 3.3 14.2 + - - -
298I VAL* 5.9 2.4 - - - +
366I GLN* 5.2 1.9 + - - -
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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
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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