Contacts of the helix formed by residues 190 - 211 (chain A) 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 CYS 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 3.8 11.2 - - - -
186A TYR* 2.9 16.2 + - + +
189A GLY* 1.3 77.7 - - - +
191A LEU* 1.3 68.4 + - - +
192A GLY 3.3 0.7 - - - -
193A SER* 3.2 3.4 + - - -
194A ILE* 3.0 29.2 + - + +
389A ILE* 4.3 5.3 - - + +
390A TYR* 4.0 26.5 - - - -
436A MET* 5.7 0.7 - - - -
439A PHE* 3.9 19.3 - - - -
440A MET* 3.5 36.8 - - + -
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLY 4.7 0.4 - - - -
168A GLY* 4.0 14.6 - - - -
170A GLU* 4.2 0.2 - - - +
171A VAL* 4.0 15.0 - - + -
186A TYR* 2.8 61.9 + - + +
187A SER* 3.6 10.3 - - - +
190A CYS* 1.3 75.0 - - - +
192A GLY* 1.3 64.5 + - - +
194A ILE* 3.0 14.0 + - - +
195A ASP* 3.1 13.7 + - - +
440A MET* 5.0 1.1 - - + -
454A PHE* 3.9 17.5 - - + -
459A TYR* 3.8 42.0 - - + -
461A PHE* 4.0 13.2 - - + -
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLY* 3.7 19.6 + - - -
187A SER 2.9 15.9 + - - -
188A ILE* 3.3 12.8 + - - -
190A CYS 3.3 0.6 - - - -
191A LEU* 1.3 76.7 - - - +
193A SER* 1.3 61.5 + - - +
195A ASP* 3.3 2.1 + - - +
196A MET* 3.0 27.0 + - - +
222A GLN* 5.0 0.2 - - - -
253A ARG* 3.9 13.7 - - - -
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 5.2 1.1 + - - -
188A ILE 3.6 4.0 + - - -
189A GLY* 2.7 24.5 + - - -
190A CYS 3.2 3.8 + - - -
192A GLY* 1.3 74.6 - - - +
194A ILE* 1.3 63.9 + - - +
196A MET* 3.4 4.7 + - - +
197A GLU* 3.1 21.3 + - - +
252A PRO* 4.0 2.9 + - - +
253A ARG* 3.5 21.2 + - - -
256A VAL* 3.8 24.6 - - - +
389A ILE* 4.0 24.1 + - - +
392A ARG* 4.9 0.7 + - - -
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Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 4.0 14.1 + - - +
190A CYS 3.0 20.8 + - - +
191A LEU* 3.0 10.6 + - - +
193A SER* 1.3 75.0 - - - +
195A ASP* 1.3 63.3 + - - +
197A GLU* 3.3 16.7 + - - +
198A LEU* 3.4 11.1 + - - +
389A ILE* 4.0 17.3 - - + -
436A MET* 5.3 1.8 - - + -
440A MET* 3.8 15.9 - - + -
459A TYR* 3.8 25.4 - - + +
461A PHE* 3.7 29.2 - - + -
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Residues in contact with ASP 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 2.8 45.1 + - - -
138A LEU* 3.4 22.8 - - + +
139A ARG* 5.1 3.7 + - - +
165A SER* 4.3 2.6 + - - -
167A GLY* 3.7 26.9 + - - -
191A LEU 3.1 10.7 + - - +
192A GLY 4.0 1.3 - - - +
194A ILE* 1.3 74.7 - - - +
196A MET* 1.3 67.0 + - - +
198A LEU* 3.1 20.5 + - - +
199A ILE* 3.2 21.3 + - - +
458A ASN 4.7 2.0 - - - +
459A TYR* 4.5 4.2 - - + -
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.6 7.4 - - - +
192A GLY 3.0 24.9 + - - +
193A SER 3.6 5.6 - - - +
194A ILE 3.3 0.2 - - - -
195A ASP* 1.3 76.6 - - + +
197A GLU* 1.3 61.6 + - - +
199A ILE* 4.0 3.4 - - - -
200A TRP* 3.1 43.8 + - + +
217A ASP* 3.3 42.2 - - + +
253A ARG* 3.4 46.2 - - - +
254A SER 3.9 3.8 - - - +
256A VAL* 3.6 13.0 - - + -
257A ALA* 3.6 19.7 - - + +
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Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA* 3.4 34.2 + - - +
5A ARG* 4.6 14.0 + - - +
193A SER 3.1 13.3 + - - +
194A ILE* 3.9 7.6 - - - +
195A ASP 3.2 0.2 - - - -
196A MET* 1.3 74.7 - - - +
198A LEU* 1.3 61.9 + - - +
201A THR* 2.7 38.1 + - - +
256A VAL* 3.4 16.5 - - + +
260A ALA* 4.4 4.0 - - + +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 4.4 9.6 - - - +
139A ARG* 4.1 43.1 - - + +
143A TYR* 3.5 43.8 + - + +
194A ILE 3.4 9.2 + - - +
195A ASP* 3.1 12.2 + - - +
197A GLU* 1.3 79.7 - - - +
199A ILE* 1.3 64.4 + - - +
201A THR* 3.4 10.2 + - - -
202A ASP* 3.4 15.8 + - - +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.3 32.5 - - - +
143A TYR* 3.7 17.0 - - + +
146A PHE* 4.0 14.8 - - + -
147A LEU* 5.3 0.6 - - - +
163A VAL* 4.5 7.6 - - + -
165A SER* 3.4 36.6 - - - +
195A ASP* 3.3 20.6 - - - +
196A MET* 3.5 8.3 - - - +
198A LEU* 1.3 81.5 - - + +
200A TRP* 1.3 77.5 + - + +
202A ASP* 3.2 4.0 + - - +
203A ILE* 2.7 38.8 + - + +
217A ASP* 4.0 0.4 - - - +
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Residues in contact with TRP 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU 3.7 11.7 - - - -
162A SER* 3.9 5.4 - - - -
163A VAL* 3.7 13.5 - - + -
196A MET* 3.1 44.5 + - + +
199A ILE* 1.3 85.0 - - + +
201A THR* 1.3 61.0 + - - +
203A ILE* 3.5 29.6 - - + +
204A SER* 2.8 32.1 + - - -
214A SER* 3.4 26.7 - - - -
216A GLY 3.4 46.4 - - - -
217A ASP* 2.7 33.6 + - + +
257A ALA* 3.7 22.2 - - + +
260A ALA* 3.4 11.7 - - + +
262A ALA* 4.1 6.7 - - + -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA* 5.0 5.2 - - - +
197A GLU* 2.7 29.8 + - - +
198A LEU* 3.4 5.3 + - - -
199A ILE 3.3 0.2 - - - -
200A TRP* 1.3 76.3 - - - +
202A ASP* 1.3 71.1 + - - +
204A SER* 4.0 1.8 - - - -
205A LYS* 3.2 36.2 + - + +
260A ALA* 4.0 17.1 + - - +
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Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 2.5 34.3 + - - +
147A LEU* 3.8 26.6 - - + +
198A LEU* 3.4 11.9 + - - +
199A ILE 3.2 7.7 + - - +
201A THR* 1.3 82.8 - - - +
203A ILE* 1.3 61.9 + - - +
205A LYS* 3.3 26.4 + - - +
206A ILE* 3.1 27.5 + - + +
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 4.8 0.9 - - + -
147A LEU* 5.1 4.5 - - + -
150A PHE* 3.5 55.4 - - + -
161A LEU* 4.5 14.1 - - + +
163A VAL* 4.1 6.7 - - + -
199A ILE* 2.7 37.9 + - + +
200A TRP* 3.5 45.8 - - + -
201A THR 3.4 0.4 - - - -
202A ASP* 1.3 70.3 - - - +
204A SER* 1.3 58.4 + - - +
206A ILE* 3.1 12.4 + - - +
207A ALA* 3.0 23.4 + - - +
214A SER* 4.1 4.3 - - - +
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A TRP* 2.8 22.7 + - - -
201A THR 4.0 2.2 - - - -
203A ILE* 1.3 73.6 - - - +
205A LYS* 1.3 66.2 + - - +
207A ALA* 3.1 2.9 + - - +
208A LYS* 2.9 26.0 + - - +
214A SER* 3.0 26.8 + - - -
260A ALA 3.4 8.3 + - - -
261A GLY* 3.2 26.3 - - - -
262A ALA 3.5 0.9 + - - -
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A THR* 3.2 23.6 + - + +
202A ASP* 3.3 30.5 + - - +
204A SER* 1.3 76.9 - - - +
206A ILE* 1.3 60.2 + - + +
208A LYS* 3.4 10.0 + - + +
209A LYS* 3.0 29.2 + - - +
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Residues in contact with ILE 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.8 46.7 - - + +
150A PHE* 4.3 13.0 - - + +
151A GLU* 3.4 45.3 - - + +
154A ALA* 4.7 0.2 - - + -
161A LEU* 4.5 5.2 - - + -
202A ASP* 3.1 15.1 + - + +
203A ILE* 3.1 8.7 + - - +
205A LYS* 1.3 74.4 - - + +
207A ALA* 1.3 59.9 + - - +
209A LYS* 3.2 7.1 + - + +
210A THR* 2.8 40.2 + - + +
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Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 4.3 5.2 - - + -
203A ILE 3.0 12.3 + - - +
204A SER 3.5 7.4 - - - +
206A ILE* 1.3 75.3 - - - +
208A LYS* 1.3 57.8 + - - +
210A THR* 3.3 0.2 + - - -
211A GLY* 2.8 26.5 + - - -
212A THR* 2.9 34.5 + - - +
213A ILE 4.0 1.1 - - - -
214A SER* 3.5 35.2 - - - +
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A SER 2.9 16.8 + - - +
205A LYS* 3.6 8.7 - - + +
207A ALA* 1.3 77.7 - - - +
209A LYS* 1.3 63.8 + - - +
211A GLY* 3.3 9.6 + - - -
208I LYS* 3.8 37.6 - - + +
209I LYS 4.6 5.8 + - - -
210I THR 4.7 1.4 - - - -
211I GLY* 3.6 25.3 - - - +
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Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLU* 3.3 27.5 + - - +
155A GLU* 5.0 6.8 + - - -
205A LYS 3.0 18.9 + - - +
206A ILE* 3.2 8.9 + - + +
208A LYS* 1.3 77.1 - - - +
210A THR* 1.3 64.0 + - + +
211A GLY 3.8 0.2 + - - -
208I LYS* 4.9 4.9 + - - -
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Residues in contact with THR 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLU* 4.4 7.6 - - + +
154A ALA* 3.6 25.7 - - + +
155A GLU* 4.0 32.8 - - + +
206A ILE* 2.8 28.8 + - + +
207A ALA* 3.3 0.9 + - - -
209A LYS* 1.3 82.6 - - + +
211A GLY* 1.3 60.3 + - - +
212A THR* 3.0 26.3 + - - +
208I LYS* 4.6 3.4 + - - -
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A ALA 2.8 6.7 + - - -
208A LYS 3.3 6.3 + - - -
209A LYS 3.4 0.8 + - - -
210A THR* 1.3 78.5 - - - +
212A THR* 1.3 62.9 + - - +
213A ILE* 5.7 1.2 - - - +
208I LYS* 3.4 28.6 - - - +
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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