Contacts of the helix formed by residues 193 - 209 (chain X) in PDB entry 2BOD
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 TRP 193 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191X TYR 3.6 2.2 + - - -
192X ARG* 1.3 75.4 - - - +
194X THR* 1.3 69.4 + - - +
195X ALA* 4.2 8.5 - - + +
196X ASP* 3.1 27.5 + - - +
197X GLU* 3.0 18.4 + - - +
222X ASN* 3.9 6.3 - - - +
223X GLY 3.6 19.5 - - - -
224X ASN* 3.4 28.0 - - - -
225X GLY* 3.5 15.5 - - - -
226X PRO* 3.8 14.2 - - + +
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Residues in contact with THR 194 (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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193X TRP* 1.3 74.9 - - - +
195X ALA* 1.3 59.7 + - - +
197X GLU* 3.0 6.9 + - - +
198X VAL* 2.8 34.2 + - + +
217X ILE* 5.2 2.5 - - + -
219X THR* 3.7 11.2 - - + +
222X ASN* 3.0 25.7 + - - +
241X THR* 5.2 3.7 + - - +
255X PHE* 3.7 38.6 - - + -
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Residues in contact with ALA 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193X TRP* 3.2 5.9 - - + +
194X THR* 1.3 79.2 - - - +
196X ASP* 1.3 64.2 + - - +
198X VAL* 3.5 7.3 + - - +
199X ALA* 3.1 23.4 + - - +
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Residues in contact with ASP 196 (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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160X SER* 3.6 22.0 - - - +
192X ARG* 4.9 4.1 + - + +
193X TRP* 3.1 36.1 + - + +
195X ALA* 1.3 79.0 - - - +
197X GLU* 1.3 58.2 + - - +
199X ALA* 3.5 6.4 + - - +
200X TYR* 3.1 27.7 + - - +
226X PRO* 6.2 0.2 - - - +
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Residues in contact with GLU 197 (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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159X HIS* 3.5 5.2 - - - +
160X SER* 2.6 39.8 + - - -
186X THR* 2.8 33.8 + - - +
187X ASN* 3.3 39.1 + - + +
192X ARG* 3.3 8.7 - - + +
193X TRP 3.0 14.5 + - - +
194X THR 3.0 7.7 + - - +
196X ASP* 1.3 74.6 - - - +
198X VAL* 1.3 59.5 + - - +
200X TYR* 3.3 3.6 + - - +
201X ALA* 2.8 31.9 + - - +
217X ILE* 3.7 21.5 - - + +
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Residues in contact with VAL 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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194X THR* 2.8 35.7 + - + +
195X ALA* 3.9 8.1 - - - +
197X GLU* 1.3 69.9 - - - +
199X ALA* 1.3 58.6 + - - +
201X ALA* 3.9 2.1 - - - +
202X LYS* 3.0 51.2 + - + +
217X ILE* 3.6 19.7 - - + -
247X THR 6.0 0.7 - - - +
249X ASP* 4.3 11.2 - - + +
252X ILE* 4.3 13.0 - - + -
255X PHE* 4.3 9.6 - - + -
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Residues in contact with ALA 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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195X ALA 3.1 17.8 + - - +
196X ASP* 3.7 7.0 - - - +
197X GLU 3.3 0.2 - - - -
198X VAL* 1.3 78.9 - - - +
200X TYR* 1.3 56.1 + - - +
202X LYS* 3.8 5.4 - - - +
203X ALA* 2.9 30.6 + - - +
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Residues in contact with TYR 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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157X ALA* 2.5 30.3 + - + -
158X GLY* 4.5 0.2 - - - -
159X HIS* 3.6 33.9 + - - -
160X SER* 3.8 19.5 - - - -
163X HIS* 3.7 24.6 + - - +
165X PRO* 4.3 16.6 - - + -
168X MET* 3.5 20.6 - - - +
186X THR* 4.0 21.5 - - + -
196X ASP 3.1 17.5 + - - +
197X GLU* 3.3 4.5 + - - +
199X ALA* 1.3 76.6 - - - +
201X ALA* 1.3 63.7 + - - +
203X ALA* 3.1 6.7 + - - +
204X VAL* 3.0 46.8 + - + +
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Residues in contact with ALA 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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184X ILE* 3.8 9.1 - - + +
186X THR* 4.0 17.5 - - + +
197X GLU 2.8 18.7 + - - +
198X VAL* 3.9 2.7 - - - +
200X TYR* 1.3 76.2 - - - +
202X LYS* 1.3 58.4 + - - +
204X VAL* 3.3 2.8 + - - +
205X LEU* 3.0 34.6 + - - +
215X ALA* 3.7 27.1 - - + -
217X ILE* 4.6 2.2 - - + -
252X ILE* 4.2 8.3 - - + -
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Residues in contact with LYS 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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198X VAL* 3.0 34.3 + - + +
199X ALA* 3.9 5.6 - - - +
201X ALA* 1.3 77.6 - - - +
203X ALA* 1.3 56.6 + - - +
205X LEU* 3.8 7.4 - - - +
206X SER* 2.9 30.3 + - - -
249X ASP* 2.8 34.5 + - - +
251X MET* 4.3 17.6 - - + +
252X ILE* 4.3 12.8 - - + -
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Residues in contact with ALA 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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165X PRO* 3.5 27.4 - - + +
199X ALA 2.9 18.1 + - - +
200X TYR* 3.5 6.3 - - - +
202X LYS* 1.3 74.3 - - - +
204X VAL* 1.3 63.9 + - - +
206X SER* 3.4 5.5 + - - -
207X ALA* 3.1 25.1 + - - +
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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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157X ALA* 5.4 0.2 - - + -
165X PRO* 3.9 19.3 - - + +
168X MET* 4.0 8.3 - - + -
169X ALA* 3.9 6.2 - - - +
172X LEU* 3.6 30.1 - - + -
184X ILE* 3.9 16.2 - - + -
200X TYR* 3.0 55.1 + - + +
201X ALA 3.7 4.3 - - - +
203X ALA* 1.3 74.9 - - - +
205X LEU* 1.3 62.8 + - - +
207X ALA* 3.3 3.3 + - - +
208X ILE* 3.1 27.1 + - + +
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Residues in contact with LEU 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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184X ILE* 4.1 17.9 - - + -
201X ALA 3.0 22.5 + - - +
202X LYS* 3.8 5.4 - - - +
204X VAL* 1.3 75.1 - - - +
206X SER* 1.3 61.9 + - - +
208X ILE* 3.3 15.2 + - + +
209X GLY* 3.0 18.7 + - - -
210X ASN 4.3 8.6 + - - +
213X LEU* 3.8 36.1 - - + +
214X ARG 3.9 29.6 - - - +
215X ALA* 4.0 6.3 - - + +
251X MET* 3.9 28.9 - - + +
252X ILE* 5.4 0.4 - - + -
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Residues in contact with SER 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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202X LYS 2.9 18.8 + - - -
203X ALA* 3.8 7.2 - - - -
204X VAL 3.2 0.2 - - - -
205X LEU* 1.3 77.0 - - - +
207X ALA* 1.3 61.1 + - - +
209X GLY* 3.1 16.6 + - - -
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Residues in contact with ALA 207 (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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165X PRO* 4.4 2.2 - - + +
166X ALA* 4.4 16.6 - - + +
169X ALA* 3.5 24.7 - - + +
173X GLN* 4.1 7.3 + - - +
203X ALA 3.1 18.0 + - - +
204X VAL 3.8 0.4 - - - +
206X SER* 1.3 74.1 + - - +
208X ILE* 1.3 63.1 + - - +
209X GLY* 4.7 0.2 - - - -
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Residues in contact with ILE 208 (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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169X ALA* 3.7 22.0 - - + +
172X LEU* 4.1 19.5 - - + -
173X GLN* 3.2 31.0 + - + +
177X ILE* 4.2 16.2 - - + -
178X SER* 4.4 4.3 - - - +
184X ILE* 4.8 0.4 - - + -
204X VAL* 3.1 31.8 + - + +
205X LEU* 3.7 13.2 - - + +
206X SER 3.2 0.2 - - - -
207X ALA* 1.3 77.3 - - - +
209X GLY* 1.3 60.8 + - - +
210X ASN* 4.1 8.2 - - + +
213X LEU* 3.9 31.9 - - + -
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Residues in contact with GLY 209 (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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205X LEU 3.0 9.9 + - - -
206X SER* 3.1 14.0 + - - -
207X ALA 4.5 0.2 - - - -
208X ILE* 1.3 78.3 - - - +
210X ASN* 1.3 59.4 + - - +
211X PRO* 3.5 10.5 - - - +
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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