Contacts of the helix formed by residues 189 - 200 (chain B) 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 TYR 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A PRO* 5.2 13.2 - - + -
50A GLU* 6.2 0.4 - - - -
185B THR 4.4 12.3 - - - +
186B THR 5.9 0.9 - - - -
187B THR* 3.0 3.8 - - - +
188B MET* 1.3 89.5 - - + +
190B ALA* 1.3 54.6 + - - +
191B PHE 3.0 6.3 - - - -
192B LYS* 3.0 51.7 - - + +
193B GLU* 3.7 2.6 + - - +
218B PHE* 3.6 28.6 - + - -
221B GLN* 4.1 13.9 + - - -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 6.2 0.2 - - - +
131B ALA* 3.7 19.1 - - + -
132B GLU* 3.7 28.3 - - + +
161B VAL 5.8 0.4 - - - +
163B ALA* 5.4 0.2 - - - +
187B THR 3.1 15.5 + - - +
189B TYR* 1.3 75.3 - - - +
191B PHE* 1.3 64.7 + - - +
193B GLU* 3.8 13.7 + - + +
194B VAL* 3.3 28.8 + - + +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 4.9 5.6 - - - -
131B ALA* 4.3 9.4 - - + -
180B GLY* 3.7 31.2 - - - -
181B THR 3.9 3.4 - - - -
182B ALA* 3.5 33.4 - - + -
188B MET 3.5 14.8 - - - +
189B TYR 3.0 0.8 - - - -
190B ALA* 1.3 80.0 - - - +
192B LYS* 1.3 54.7 + - - +
194B VAL* 3.4 1.3 + - - +
195B ASN* 2.8 37.4 + - - +
207B PHE* 3.8 21.3 - + + -
209B CYS* 3.5 29.4 - - + -
210B GLY 4.0 2.5 - - - -
214B VAL* 3.7 27.4 - - + -
218B PHE* 4.2 5.8 - + - -
219B VAL* 5.2 0.4 - - + -
222B PHE* 3.9 17.5 - + + -
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B TYR* 3.0 31.9 + - + +
191B PHE* 1.3 79.9 - - - +
193B GLU* 1.3 65.5 + - + +
195B ASN* 3.0 8.0 + - - -
196B ASP* 3.0 44.6 + - - +
221B GLN* 5.5 7.3 + - - -
222B PHE* 3.3 39.0 - - + -
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Residues in contact with GLU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B GLU* 3.3 26.8 - - - +
162B PRO 4.3 6.4 - - - +
163B ALA* 4.4 10.6 - - + +
164B GLU* 4.8 8.1 - - - +
189B TYR 3.7 2.9 + - - +
190B ALA* 3.9 15.8 - - + +
191B PHE 3.5 0.2 - - - -
192B LYS* 1.3 78.8 - - + +
194B VAL* 1.3 58.4 + - - +
196B ASP* 4.0 4.6 - - - +
197B MET* 2.9 36.0 + - + +
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B HIS* 3.9 21.5 - - + +
161B VAL 5.6 1.3 - - - +
163B ALA* 3.9 27.1 - - + -
166B VAL* 4.2 12.1 - - + -
178B LEU* 3.8 23.1 - - + -
190B ALA* 3.3 18.3 + - + +
191B PHE* 3.7 3.8 - - - +
192B LYS 3.1 1.0 + - - -
193B GLU* 1.3 78.2 - - - +
195B ASN* 1.3 64.4 + - - +
197B MET* 3.3 5.0 + - + +
198B LEU* 3.1 28.2 + - + +
207B PHE* 3.7 23.1 - - + -
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Residues in contact with ASN 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B PHE 2.8 21.3 + - - +
192B LYS 3.6 1.8 - - - +
194B VAL* 1.3 75.1 - - - +
196B ASP* 1.3 74.9 + - - +
198B LEU* 3.1 12.5 + - - +
199B LEU* 3.2 26.9 + - - +
207B PHE* 4.6 8.4 - - + -
222B PHE* 3.6 23.9 - - + +
223B ALA* 3.4 9.4 + - - +
224B LEU* 2.9 55.0 - - - +
225B GLY 4.2 0.8 - - - +
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Residues in contact with ASP 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LYS* 3.0 46.9 + - - +
193B GLU* 4.0 3.9 - - - +
195B ASN* 1.3 86.6 - - - +
197B MET* 1.3 54.8 + - - +
198B LEU 3.1 0.7 + - - -
199B LEU* 3.2 8.2 + - - +
200B GLU* 2.7 52.9 + - + +
222B PHE* 5.1 1.2 - - - -
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Residues in contact with MET 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ALA* 3.2 36.6 - - + +
164B GLU* 3.8 26.2 - - - +
166B VAL* 5.4 0.9 - - + -
167B LEU* 3.3 30.0 - - + +
193B GLU* 2.9 19.3 + - + +
194B VAL* 3.6 9.0 - - + +
196B ASP* 1.3 75.4 - - - +
198B LEU* 1.3 59.3 + - + +
200B GLU* 4.0 15.4 - - + +
201B ASN* 3.6 18.2 - - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 5.3 0.7 - - + -
167B LEU* 3.9 25.8 - - + +
170B VAL* 4.7 11.2 - - + -
178B LEU* 3.9 27.4 - - + -
194B VAL* 3.1 18.1 + - + +
195B ASN 3.6 7.6 - - - +
196B ASP 3.1 0.8 - - - -
197B MET* 1.3 81.2 - - + +
199B LEU* 1.3 53.3 + - - +
201B ASN* 3.1 5.8 + - - +
202B GLY 2.8 12.5 + - - -
203B ILE* 2.7 60.2 + - + +
205B ILE* 4.9 14.1 - - + +
207B PHE* 5.6 2.7 - - + -
224B LEU* 3.7 20.4 - - + -
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B ASN* 3.2 30.2 + - - +
196B ASP* 3.6 8.3 - - - +
198B LEU* 1.3 72.9 - - - +
200B GLU* 1.3 56.8 + - + +
201B ASN 3.0 4.9 - - - -
202B GLY* 3.0 18.3 + - - +
203B ILE 4.0 7.6 - - - +
204B LYS* 5.4 5.2 - - + -
223B ALA* 4.1 20.9 - - + -
224B LEU* 3.7 29.8 - - + -
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ASP* 2.7 41.1 + - + +
197B MET* 3.9 12.2 + - + +
199B LEU* 1.3 72.3 - - + +
201B ASN* 1.3 62.8 + - - +
202B GLY 3.5 0.2 - - - -
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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