Contacts of the helix formed by residues 189 - 201 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49K PRO* 6.1 3.4 - - + -
185L THR 4.6 4.7 - - - -
186L THR 6.0 1.8 - - - +
187L THR 3.0 2.4 + - - +
188L MET* 1.3 105.4 - - + +
190L ALA* 1.3 54.9 + - - +
191L PHE 3.1 5.4 - - - -
192L LYS* 3.1 59.5 - - + +
193L GLU* 4.0 6.3 + - - +
218L PHE* 3.6 24.8 - + - -
221L GLN* 4.4 11.4 + - - -
222L PHE* 4.8 2.7 - + - -
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Residues in contact with ALA 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L ALA* 3.6 26.0 - - + -
132L GLU* 3.6 33.4 - - + +
161L VAL 5.6 0.4 - - - +
163L ALA* 5.5 0.2 - - - +
187L THR 3.2 6.3 + - - +
189L TYR* 1.3 74.4 - - - +
191L PHE* 1.3 64.3 + - - +
192L LYS 3.1 1.1 - - - -
193L GLU* 3.5 15.2 + - - +
194L VAL* 3.2 28.8 + - + +
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Residues in contact with PHE 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L HIS* 4.5 4.3 - - - -
131L ALA* 3.8 25.6 - - + -
180L GLY* 3.4 38.8 - - - -
181L THR 3.6 3.6 - - - -
182L ALA* 3.8 12.1 - - + -
188L MET 3.2 18.9 + - - +
189L TYR 3.1 0.2 - - - -
190L ALA* 1.3 77.7 - - - +
192L LYS* 1.3 57.3 + - - +
194L VAL 3.9 0.2 - - - -
195L ASN* 3.1 30.3 + - - +
207L PHE* 3.7 19.1 - + + -
209L CYS* 3.4 35.0 - - + -
210L GLY 4.2 0.9 - - - -
214L VAL* 3.8 24.9 - - + -
218L PHE* 4.3 6.3 - + - -
222L PHE* 4.0 19.5 - + + -
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Residues in contact with LYS 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L TYR* 3.1 46.9 + - + +
191L PHE* 1.3 75.5 - - - +
193L GLU* 1.3 63.6 + - + +
195L ASN* 3.2 2.8 + - - +
196L ASP* 2.9 52.2 + - - +
221L GLN* 5.5 5.4 + - - -
222L PHE* 3.4 28.2 - - + -
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Residues in contact with GLU 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132L GLU* 3.3 24.8 - - - +
163L ALA* 4.2 15.2 - - + +
189L TYR 4.2 4.7 - - - +
190L ALA* 3.5 23.5 + - - +
192L LYS* 1.3 80.8 - - + +
194L VAL* 1.3 58.3 + - - +
196L ASP* 4.4 5.3 - - - +
197L MET* 3.1 33.8 + - + +
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Residues in contact with VAL 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L HIS* 3.9 20.2 - - + +
161L VAL 5.7 0.7 - - - +
163L ALA* 4.3 11.9 - - + +
166L VAL* 4.1 23.8 - - + -
178L LEU* 3.8 20.4 - - + -
190L ALA* 3.2 20.0 + - + +
192L LYS 3.2 0.6 - - - -
193L GLU* 1.3 75.7 - - - +
195L ASN* 1.3 64.3 + - - +
197L MET* 4.1 6.6 - - - +
198L LEU* 3.2 33.9 + - + +
207L PHE* 3.5 29.8 - - + -
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Residues in contact with ASN 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L PHE 3.1 20.7 + - - +
192L LYS 3.6 2.2 - - - +
194L VAL* 1.3 76.1 - - - +
196L ASP* 1.3 73.1 + - - +
198L LEU* 3.3 5.0 + - - +
199L LEU* 3.1 34.7 + - - +
207L PHE* 4.1 10.7 - - + -
222L PHE* 3.7 25.7 - - + +
223L ALA* 3.5 12.9 + - - +
224L LEU* 3.1 50.8 - - - +
225L GLY 4.4 0.4 - - - +
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Residues in contact with ASP 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L LYS* 2.9 43.8 + - - +
193L GLU* 4.4 4.9 + - - +
195L ASN* 1.3 85.1 - - - +
197L MET* 1.3 57.8 + - - +
199L LEU* 3.4 12.1 + - - +
200L GLU* 3.1 43.4 + - - +
222L PHE* 5.5 1.2 - - - -
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Residues in contact with MET 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163L ALA* 3.1 47.8 - - + +
164L GLU* 3.5 22.7 - - - +
166L VAL* 5.5 0.4 - - + -
167L LEU* 3.6 30.3 - - + +
193L GLU* 3.1 20.1 + - - +
194L VAL* 4.1 5.2 - - - +
196L ASP* 1.3 75.6 - - - +
198L LEU* 1.3 65.1 + - + +
200L GLU* 3.5 9.9 + - + +
201L ASN* 3.3 33.2 + - - +
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Residues in contact with LEU 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L VAL* 5.7 0.9 - - + -
167L LEU* 4.3 13.2 - - + +
170L VAL* 4.0 22.7 - - + -
178L LEU* 3.7 26.7 - - + -
194L VAL* 3.2 29.1 + - + +
195L ASN* 3.3 4.2 + - - +
197L MET* 1.3 76.1 - - + +
199L LEU* 1.3 56.8 + - - +
201L ASN 3.6 0.7 + - - -
202L GLY 3.4 2.9 + - - -
203L ILE* 2.7 70.0 + - + +
205L ILE* 5.6 6.1 - - + +
207L PHE* 4.9 4.7 - - + -
224L LEU* 3.8 22.4 - - + -
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Residues in contact with LEU 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195L ASN* 3.1 37.2 + - - +
196L ASP* 3.6 15.0 - - - +
198L LEU* 1.3 76.1 - - - +
200L GLU* 1.3 58.5 + - + +
201L ASN 3.2 1.8 - - - -
202L GLY* 3.1 17.3 + - - +
203L ILE 4.5 5.2 - - - +
204L LYS* 5.8 2.9 - - + -
223L ALA* 3.8 26.5 - - + -
224L LEU* 4.0 21.5 - - + -
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Residues in contact with GLU 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L ASP* 3.1 33.5 + - - +
197L MET* 3.5 10.9 + - + +
198L LEU 3.4 0.4 - - - -
199L LEU* 1.3 76.2 - - + +
201L ASN* 1.3 64.2 + - - +
202L GLY 3.4 1.3 - - - -
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Residues in contact with ASN 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167L LEU* 4.1 13.6 - - - +
171L GLN* 3.3 26.5 - - - +
197L MET* 3.3 22.8 + - - +
198L LEU 3.6 0.6 + - - +
199L LEU 3.2 0.4 - - - -
200L GLU* 1.3 82.1 - - - +
202L GLY* 1.3 63.2 + - - +
203L ILE* 3.3 23.1 + - + +
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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