Contacts of the helix formed by residues 189 - 201 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185J THR 4.8 3.6 - - - -
186J THR 6.5 0.2 - - - -
187J THR 2.7 7.5 + - - -
188J MET* 1.3 98.0 - - + +
190J ALA* 1.3 51.4 + - - -
191J PHE 2.8 5.8 - - - -
192J LYS* 2.8 54.6 + - + +
193J GLU* 3.3 8.8 + - - +
218J PHE* 3.5 26.8 - + - -
221J GLN* 4.4 11.1 + - - -
222J PHE* 4.6 4.5 - + - -
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Residues in contact with ALA 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131J ALA* 3.5 21.1 - - + -
132J GLU* 3.7 30.3 - - + +
161J VAL 5.7 0.7 - - - +
163J ALA* 5.0 1.6 - - + +
187J THR 3.0 14.2 + - - +
189J TYR* 1.3 76.1 - - - +
191J PHE* 1.3 57.2 + - - +
193J GLU* 3.4 16.4 + - - +
194J VAL* 3.1 33.6 + - + +
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Residues in contact with PHE 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J HIS* 4.9 3.4 - - - -
131J ALA* 3.8 17.9 - - + -
180J GLY* 3.3 31.0 - - - -
181J THR 3.4 12.3 - - - -
182J ALA* 3.7 23.8 - - + -
188J MET 3.0 19.1 - - - +
190J ALA* 1.3 76.5 - - - +
192J LYS* 1.3 58.0 + - - +
194J VAL* 3.5 1.0 + - - -
195J ASN* 2.9 30.2 + - - +
207J PHE* 3.7 20.0 - + + -
209J CYS* 3.4 36.8 - - + -
210J GLY 4.0 0.9 - - - -
214J VAL* 3.9 16.2 - - + -
218J PHE* 4.3 11.7 - + - -
222J PHE* 4.3 15.0 - + + -
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Residues in contact with LYS 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189J TYR* 2.8 38.5 + - + +
191J PHE* 1.3 71.2 - - - +
193J GLU* 1.3 56.6 + - + +
195J ASN* 3.1 4.5 + - - +
196J ASP* 2.6 68.4 + - - +
221J GLN* 5.5 5.6 - - - -
222J PHE* 3.1 36.4 - - + -
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Residues in contact with GLU 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J GLU* 3.6 23.4 - - - +
162J PRO 5.3 0.2 - - - +
163J ALA* 4.4 16.2 - - + +
189J TYR 3.3 8.9 + - - +
190J ALA* 3.6 18.0 + - - +
191J PHE 3.3 0.4 - - - -
192J LYS* 1.3 77.2 - - + +
194J VAL* 1.3 62.1 + - - +
196J ASP* 3.9 5.4 - - - +
197J MET* 3.0 31.3 + - + +
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Residues in contact with VAL 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J HIS* 3.8 22.7 - - + +
161J VAL 5.9 0.2 - - - +
163J ALA* 3.9 26.9 - - + +
166J VAL* 4.2 12.8 - - + -
178J LEU* 3.8 28.7 - - + -
190J ALA* 3.1 16.7 + - + +
191J PHE 3.8 3.8 - - - +
193J GLU* 1.3 77.1 - - - +
195J ASN* 1.3 64.6 + - - +
197J MET* 3.9 5.3 - - - +
198J LEU* 3.3 27.0 + - + +
207J PHE* 3.8 15.7 - - + -
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Residues in contact with ASN 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J PHE 2.9 18.9 + - - +
192J LYS* 3.1 5.1 + - - +
194J VAL* 1.3 78.7 - - - +
196J ASP* 1.3 70.2 + - - +
197J MET 3.3 0.5 + - - -
198J LEU* 3.5 8.8 + - - +
199J LEU* 3.4 30.4 + - - +
207J PHE* 4.5 8.9 - - + -
222J PHE* 3.3 29.7 - - + +
223J ALA 4.0 3.3 + - - -
224J LEU* 3.0 51.0 - - - +
225J GLY 4.0 1.2 - - - +
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Residues in contact with ASP 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J LYS* 2.6 53.2 + - - +
193J GLU* 3.9 4.8 - - - +
195J ASN* 1.3 81.3 - - - +
197J MET* 1.3 60.9 + - - +
199J LEU* 3.8 7.0 + - - +
200J GLU* 3.3 36.9 + - - +
222J PHE* 5.9 0.5 - - - -
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Residues in contact with MET 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163J ALA* 3.2 49.6 - - + +
164J GLU* 3.1 24.2 - - - +
167J LEU* 3.7 28.4 - - + +
193J GLU* 3.0 19.6 + - + +
194J VAL* 3.9 6.5 - - - +
195J ASN 3.2 0.2 - - - -
196J ASP* 1.3 77.0 - - - +
198J LEU* 1.3 59.4 + - + +
200J GLU* 3.6 6.1 + - - +
201J ASN* 3.2 39.6 + - - +
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Residues in contact with LEU 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166J VAL* 5.7 0.9 - - + -
167J LEU* 4.1 17.3 - - + -
170J VAL* 4.2 23.6 - - + -
178J LEU* 3.8 27.4 - - + -
194J VAL* 3.3 24.7 + - + +
195J ASN* 4.1 0.7 - - - +
196J ASP 3.5 0.2 - - - -
197J MET* 1.3 74.7 - - + +
199J LEU* 1.3 56.2 + - - +
201J ASN* 3.4 2.7 - - - +
202J GLY 3.0 7.8 + - - -
203J ILE* 2.6 65.0 + - + +
205J ILE* 5.5 5.2 - - + +
207J PHE* 5.5 1.3 - - + -
224J LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195J ASN* 3.4 35.3 + - - +
196J ASP* 4.1 8.1 - - - +
197J MET 3.4 0.2 - - - -
198J LEU* 1.3 76.2 - - - +
200J GLU* 1.3 65.0 + - + +
202J GLY* 3.3 11.8 + - - +
203J ILE 3.9 11.2 - - - +
204J LYS* 5.0 7.4 - - + -
223J ALA* 4.3 21.1 - - + -
224J LEU* 3.9 24.9 - - + -
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Residues in contact with GLU 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196J ASP* 3.3 25.5 + - - +
197J MET* 3.9 7.9 - - - +
198J LEU 3.3 0.2 - - - -
199J LEU* 1.3 78.5 - - + +
201J ASN* 1.3 60.4 + - - +
202J GLY 3.2 4.4 + - - -
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Residues in contact with ASN 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167J LEU* 4.2 22.2 - - + +
171J GLN* 3.8 18.2 - - - +
197J MET* 3.2 27.5 + - - +
198J LEU 3.4 5.4 + - - +
199J LEU 3.3 0.2 - - - -
200J GLU* 1.3 78.8 - - - +
202J GLY* 1.3 61.1 + - - +
203J ILE* 3.4 12.0 + - + +
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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