Contacts of the helix formed by residues 222 - 231 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166M MET 5.9 0.4 - - - -
167M GLY 3.3 12.9 + - - +
168M GLY 3.1 31.9 + - - -
169M LYS* 4.3 5.6 - - + -
172M PHE* 2.8 46.2 - - + +
187M SER 3.2 21.4 + - - -
188M ILE* 3.6 25.0 - - + +
219M ASP* 2.6 35.6 + - - +
221M ALA* 1.3 84.8 - - + +
223M ALA* 1.3 65.2 + - - +
224M ASN 3.3 0.9 - - - -
225M THR 3.1 3.1 + - - -
226M ALA 3.1 8.3 + - - -
253M ARG* 4.4 4.2 + - - +
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Residues in contact with ALA 223 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M ILE* 4.8 0.2 - - - +
219M ASP* 3.0 25.4 + - + +
222M GLN* 1.3 72.0 - - - +
224M ASN* 1.3 64.0 + - - +
226M ALA* 3.4 8.8 + - - +
227M MET* 3.0 21.7 + - - +
243M ALA 5.1 2.8 - - - +
246M ALA* 4.1 15.9 - - - +
247M ARG* 3.4 30.6 + - - +
250M SER* 3.8 16.6 - - - +
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Residues in contact with ASN 224 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219M ASP 3.7 1.0 + - - -
220M CYS* 3.2 37.3 + - - +
222M GLN 3.3 0.8 - - - -
223M ALA* 1.3 74.3 - - - +
225M THR* 1.3 64.9 + - - +
227M MET* 3.0 7.6 + - - +
228M PHE* 2.9 41.2 + - + -
247M ARG* 2.6 39.5 + - - +
269M CYS* 2.8 44.1 + - - +
271M TYR* 3.5 9.1 - - - -
287M GLU* 5.1 0.2 + - - -
295M HIS* 6.1 0.2 + - - -
500N B13 5.8 1.1 - - + -
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Residues in contact with THR 225 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M PHE* 3.7 19.3 - - + -
173M ASP* 4.4 4.9 - - - +
176M VAL* 5.2 0.2 - - + -
220M CYS 3.4 4.0 + - - -
221M ALA* 3.3 15.8 + - - -
222M GLN 3.1 9.7 + - - -
224M ASN* 1.3 75.8 - - - +
226M ALA* 1.3 62.2 + - - +
228M PHE* 3.3 4.4 + - - +
229M ILE* 3.1 29.3 + - + +
138N ILE* 3.4 33.0 - - + -
500N B13 3.4 32.5 - - + +
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Residues in contact with ALA 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M PHE* 3.9 2.8 - - + -
176M VAL* 4.1 17.5 - - + -
222M GLN 3.1 12.4 + - - +
223M ALA 3.5 8.7 - - - +
225M THR* 1.3 77.0 - - - +
227M MET* 1.3 56.8 + - - +
228M PHE 3.2 0.2 + - - -
229M ILE* 3.4 1.2 + - - +
230M GLY* 2.9 26.9 + - - -
238M LEU* 3.3 27.8 - - + +
242M ILE* 6.4 0.2 - - + -
243M ALA* 4.2 13.4 - - - +
246M ALA* 4.3 12.8 - - + -
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Residues in contact with MET 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223M ALA 3.0 13.0 + - - +
224M ASN* 3.0 15.1 + - - +
226M ALA* 1.3 76.4 - - - +
228M PHE* 1.3 82.7 + - + +
230M GLY* 3.3 2.4 + - - -
231M GLY* 2.9 24.3 + - - +
243M ALA* 4.4 2.6 - - - +
247M ARG* 3.8 16.2 - - - +
271M TYR* 3.8 30.3 - - + +
295M HIS* 4.3 7.2 - - + +
296M SER 4.8 3.1 - - - +
297M ASP* 4.4 9.9 - - + -
298M VAL* 5.6 1.3 - - + -
299M MET* 4.3 24.9 - - - +
366M GLN* 3.3 30.0 + - - +
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Residues in contact with PHE 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220M CYS* 6.1 0.7 - - - -
224M ASN* 2.9 41.2 + - + +
225M THR* 3.9 4.0 - - - +
226M ALA 3.2 0.2 - - - -
227M MET* 1.3 93.9 - - + +
229M ILE* 1.3 68.5 + - - +
230M GLY 3.1 1.1 - - - -
231M GLY* 3.0 16.2 + - - +
235M ASN* 5.1 1.6 + - - -
295M HIS* 3.2 52.0 - + + -
296M SER 5.1 2.5 - - - -
500N B13 3.7 68.3 - - + +
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Residues in contact with ILE 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176M VAL* 4.0 25.8 - - + +
177M LEU* 4.4 4.9 - - + -
225M THR* 3.1 36.3 + - + +
226M ALA* 3.8 3.6 - - - +
228M PHE* 1.3 76.9 - - + +
230M GLY* 1.3 62.9 + - - +
231M GLY* 3.4 0.9 + - - -
235M ASN* 4.5 3.5 + - - -
237M ASN* 3.4 50.5 + - + +
238M LEU* 3.9 7.6 - - + -
95N LEU* 5.0 8.3 - - + -
138N ILE* 3.9 29.4 - - + -
142N ILE* 5.8 2.5 - - + -
500N B13 4.8 17.4 - - + +
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Residues in contact with GLY 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M ALA 2.9 15.8 + - - -
227M MET* 3.6 5.6 - - - -
228M PHE 3.1 0.2 - - - -
229M ILE* 1.3 77.5 - - - +
231M GLY* 1.3 60.7 + - - +
235M ASN* 3.3 16.9 - - - +
238M LEU* 3.5 25.6 + - - +
240M HIS* 2.8 25.6 + - - -
243M ALA* 5.4 1.3 - - - -
366M GLN* 5.6 0.2 - - - -
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Residues in contact with GLY 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M MET 2.9 14.3 + - - +
228M PHE* 3.0 14.8 + - - -
230M GLY* 1.3 75.8 - - - +
232M GLY* 1.3 62.0 + - - +
235M ASN* 3.8 11.4 - - - -
240M HIS* 3.2 13.2 - - - -
298M VAL* 5.9 3.1 - - - +
366M GLN* 5.1 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