Contacts of the helix formed by residues 189 - 200 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C PRO* 6.2 4.7 - - + -
185D THR 4.6 4.3 - - - +
186D THR 6.2 0.7 - - - -
187D THR* 2.9 3.1 + - - +
188D MET* 1.3 101.1 - - + +
190D ALA* 1.3 54.6 + - - +
191D PHE 3.1 4.7 - - - +
192D LYS* 3.1 42.7 - - + +
193D GLU* 3.6 7.8 - - - +
218D PHE* 3.5 30.9 - + - -
221D GLN* 4.1 14.1 + - - -
222D PHE* 5.1 1.3 - + - -
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Residues in contact with ALA 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D HIS* 5.3 1.1 + - - -
131D ALA* 3.6 17.7 - - + -
132D GLU* 3.8 26.9 - - + +
161D VAL 5.6 0.4 - - - +
163D ALA* 5.4 0.5 - - - +
187D THR 3.0 15.9 + - - +
189D TYR* 1.3 73.3 - - - +
191D PHE* 1.3 64.8 + - - +
192D LYS 3.1 1.6 - - - -
193D GLU* 3.3 20.3 + - - +
194D VAL* 3.5 27.2 + - - +
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Residues in contact with PHE 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D HIS* 4.7 4.5 - - - -
131D ALA* 3.7 23.8 - - + -
180D GLY* 3.3 10.8 - - - -
181D THR* 3.3 31.4 - - - -
182D ALA* 3.5 14.6 - - + -
188D MET 3.2 16.8 - - - +
189D TYR 3.1 0.2 - - - -
190D ALA* 1.3 79.9 - - - +
192D LYS* 1.3 57.3 + - - +
194D VAL* 4.7 0.9 - - - -
195D ASN* 3.1 30.0 + - - +
207D PHE* 4.0 15.9 - + + -
209D CYS* 3.4 42.2 - - + -
210D GLY 4.2 5.2 - - - -
214D VAL* 4.3 15.3 - - + -
218D PHE* 4.8 5.8 - + + -
219D VAL* 5.2 1.3 - - + -
222D PHE* 4.2 18.6 - + + -
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Residues in contact with LYS 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D TYR* 3.1 34.1 + - + +
191D PHE* 1.3 73.8 - - - +
193D GLU* 1.3 69.5 - - + +
195D ASN* 3.0 3.5 + - - -
196D ASP* 2.8 56.9 + - - +
222D PHE* 3.7 29.0 - - + -
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Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D GLU* 3.1 23.9 - - - +
163D ALA* 4.0 17.6 - - + +
189D TYR 3.6 5.7 + - - +
190D ALA* 3.3 31.2 + - - +
191D PHE 3.7 0.2 - - - -
192D LYS* 1.3 78.5 - - + +
194D VAL* 1.3 53.5 + - - +
196D ASP* 3.7 5.0 - - - +
197D MET* 2.8 42.3 + - + +
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Residues in contact with VAL 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D HIS* 4.2 9.9 - - + +
161D VAL 6.0 0.2 - - - +
163D ALA* 4.0 27.1 - - + +
166D VAL* 4.1 21.5 - - + -
178D LEU* 3.8 22.4 - - + -
190D ALA 3.5 17.5 + - - +
191D PHE 4.3 0.4 - - - +
192D LYS 3.1 1.0 - - - -
193D GLU* 1.3 76.2 - - - +
195D ASN* 1.3 60.1 + - - +
197D MET* 3.8 6.6 - - + +
198D LEU* 2.9 39.8 + - + +
207D PHE* 3.6 28.0 - - + -
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Residues in contact with ASN 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D PHE 3.1 18.9 + - - +
192D LYS 3.0 2.2 + - - +
194D VAL* 1.3 78.8 - - - +
196D ASP* 1.3 65.5 + - - +
198D LEU* 3.9 2.3 - - - +
199D LEU* 3.1 43.7 + - - +
207D PHE* 4.6 7.5 - - + -
222D PHE* 3.4 39.3 - - + +
223D ALA* 3.8 1.5 + - - +
224D LEU* 3.2 52.5 - - - +
225D GLY 4.2 0.6 - - - +
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Residues in contact with ASP 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LYS* 2.8 54.4 + - - +
193D GLU* 3.8 4.6 + - - +
195D ASN* 1.3 88.9 - - - +
197D MET* 1.3 50.6 + - - +
199D LEU* 3.2 13.0 + - - +
200D GLU* 2.7 50.2 + - - +
222D PHE* 4.6 3.6 - - - -
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D ALA* 3.1 44.9 - - + +
164D GLU* 3.6 23.6 - - - +
166D VAL* 6.0 0.2 - - + -
167D LEU* 3.3 41.9 - - + +
193D GLU* 2.8 20.7 + - - +
194D VAL* 3.8 6.3 - - + +
196D ASP* 1.3 70.8 - - - +
198D LEU* 1.3 65.8 + - + +
200D GLU* 3.9 12.6 - - + +
201D ASN* 3.6 11.5 + - - +
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D VAL* 5.1 1.1 - - + -
167D LEU* 4.2 19.1 - - + +
170D VAL* 4.2 17.0 - - + -
178D LEU* 3.8 26.2 - - + -
194D VAL* 2.9 29.8 + - + +
195D ASN* 3.9 0.4 - - - +
197D MET* 1.3 76.8 - - + +
199D LEU* 1.3 59.7 - - - +
201D ASN 3.7 0.7 + - - -
202D GLY 3.4 3.3 + - - -
203D ILE* 2.8 71.4 + - + +
205D ILE* 4.8 9.6 - - + +
207D PHE* 5.6 2.7 - - + -
224D LEU* 3.7 26.2 - - + -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D ASN* 3.1 38.3 + - - +
196D ASP* 3.2 12.1 + - - +
198D LEU* 1.3 73.5 - - - +
200D GLU* 1.3 52.9 + - + +
201D ASN 2.8 16.1 + - - -
202D GLY* 2.9 13.4 + - - +
203D ILE 4.5 7.6 - - - +
204D LYS* 6.2 2.5 - - + -
223D ALA* 4.6 17.7 - - + +
224D LEU* 4.5 20.2 - - + -
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ASP* 2.7 35.7 + - - +
197D MET* 3.9 12.8 + - + +
198D LEU 3.4 0.4 - - - -
199D LEU* 1.3 70.3 - - + +
201D ASN* 1.3 67.3 + - - +
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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