Contacts of the helix formed by residues 197 - 206 (chain X) in PDB entry 2XB2
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 PHE 197 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4R U 3.0 26.2 - - - -
5R U 3.0 35.0 - - - -
114X PRO* 3.5 33.0 - - + -
164X PRO* 3.7 29.6 - - + -
191X GLU* 3.4 41.7 - - + +
192X MET* 3.3 12.7 - - - +
194X ASN 3.0 2.4 + - - +
196X GLY* 1.3 79.9 - - - +
198X LYS* 1.3 62.6 + - - +
199X GLU 3.4 2.2 - - - -
200X GLN* 3.6 19.2 + - - +
201X ILE* 3.2 27.9 + - - +
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Residues in contact with LYS 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218S TRP* 4.0 33.2 - - + +
192X MET 3.9 7.9 - - - -
193X LEU* 3.4 28.0 - - + +
194X ASN 3.5 7.3 + - - +
195X LYS* 4.5 14.7 - - + +
196X GLY 4.0 0.4 - - - +
197X PHE* 1.3 77.2 - - - +
199X GLU* 1.3 73.9 + - + +
201X ILE* 3.2 4.3 + - - +
202X TYR* 2.9 27.3 + - + +
228X MET* 3.8 32.4 - - + +
231X LYS* 6.1 3.0 - - - +
232X PHE* 6.1 0.2 - - - -
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Residues in contact with GLU 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X GLY 5.5 3.6 - - - +
197X PHE 3.4 0.6 - - - +
198X LYS* 1.3 86.8 - - + +
200X GLN* 1.3 69.0 + - + +
202X TYR* 3.2 16.6 + - - +
203X ASP* 3.0 32.7 + - - +
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Residues in contact with GLN 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R U 2.8 49.7 + - - +
164X PRO* 3.7 19.1 - - + +
165X GLY* 3.9 4.2 + - - -
168X PHE* 5.2 3.1 - - + +
196X GLY 3.7 18.1 + - - +
197X PHE* 3.8 22.7 - - + +
198X LYS 3.3 0.6 - - - -
199X GLU* 1.3 78.7 - - + +
201X ILE* 1.3 62.4 + - - +
203X ASP* 3.5 11.7 + - - +
204X VAL* 3.4 25.3 + - - +
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Residues in contact with ILE 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218S TRP* 3.5 23.6 - - + -
112X LEU* 4.3 7.6 - - + -
164X PRO* 3.8 27.8 - - + -
184X LEU* 5.3 6.0 - - + +
186X LEU* 4.2 34.5 - - + -
192X MET* 3.4 31.2 - - + +
193X LEU* 4.7 1.6 - - + -
197X PHE* 3.2 15.0 + - + +
198X LYS* 3.2 8.8 + - - +
200X GLN* 1.3 73.3 - - - +
202X TYR* 1.3 68.3 + - - +
204X VAL* 3.1 9.6 + - - +
205X TYR* 2.9 20.3 + - + +
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Residues in contact with TYR 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217S ARG 5.3 1.0 + - - -
218S TRP* 3.5 60.9 - + + -
219S GLU* 4.3 7.6 + - - +
221S ASP* 4.1 6.1 + - - -
198X LYS* 2.9 13.6 + - + +
199X GLU* 3.2 22.2 + - - +
201X ILE* 1.3 76.9 - - - +
203X ASP* 1.3 70.9 + - - +
205X TYR* 2.9 14.3 + + + +
206X ARG* 3.0 61.1 + - + +
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Residues in contact with ASP 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X PHE* 3.4 38.6 - - + -
199X GLU* 3.0 23.4 + - - +
200X GLN* 3.5 13.0 - - - +
202X TYR* 1.3 85.7 - - - +
204X VAL* 1.3 59.9 + - - +
206X ARG* 3.6 18.9 + - - +
207X TYR* 3.3 23.7 - - - -
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Residues in contact with VAL 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X LEU* 3.6 26.2 - - + -
112X LEU* 4.6 15.9 - - + -
164X PRO* 4.7 5.6 - - + +
167X VAL* 4.1 9.6 - - + -
168X PHE* 4.1 29.4 - - + +
171X ILE* 3.4 23.1 - - + -
184X LEU* 5.5 1.1 - - + -
200X GLN 3.4 14.8 - - - +
201X ILE 3.1 6.9 + - - +
203X ASP* 1.3 74.6 - - - +
205X TYR* 1.3 67.4 + - - +
207X TYR* 2.9 17.3 + - - +
208X LEU* 3.4 12.9 + - + +
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Residues in contact with TYR 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217S ARG* 5.5 3.1 + - - -
218S TRP* 3.4 55.3 + + + -
219S GLU* 4.3 6.1 - - - -
220S HIS* 2.8 62.9 + + - -
184X LEU* 4.1 18.8 - - + +
201X ILE* 2.9 14.3 + - + +
202X TYR* 2.9 11.6 + + - +
204X VAL* 1.3 78.4 - - - +
206X ARG* 1.3 59.7 + - - +
208X LEU* 3.2 17.6 + - + +
212X THR* 5.5 2.3 + - - -
214X VAL* 4.1 14.5 - - + +
232X PHE* 3.4 36.6 + + + -
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Residues in contact with ARG 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219S GLU 3.8 16.4 - - - +
220S HIS* 3.4 13.0 - - - +
221S ASP* 2.9 37.2 + - - +
222S LYS* 3.4 40.3 - - + +
223S PHE 3.4 19.6 + - - -
202X TYR* 3.0 52.6 + - + +
203X ASP* 3.7 18.8 + - - +
204X VAL 3.0 0.4 + - - -
205X TYR* 1.3 76.8 - - - +
207X TYR* 1.3 58.7 + - - +
208X LEU 3.3 0.6 + - - -
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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