Contacts of the helix formed by residues 190 - 211 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185M LEU* 4.0 6.5 - - - -
186M TYR* 3.0 15.6 + - + +
188M ILE 3.4 0.2 - - - -
189M GLY* 1.3 78.7 - - - +
191M LEU* 1.3 67.5 + - - +
192M GLY 3.3 0.4 - - - -
193M SER* 3.2 2.4 + - - -
194M ILE* 3.0 31.6 + - - +
389M ILE* 4.3 7.6 - - + -
390M TYR* 3.9 37.5 - - - -
439M PHE* 3.9 11.9 - - - -
440M MET* 3.8 33.7 - - + -
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Residues in contact with LEU 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168M GLY* 3.9 3.8 - - - -
170M GLU* 4.3 7.9 - - - +
171M VAL* 3.8 23.8 - - + -
186M TYR* 2.9 58.2 + - + +
187M SER* 3.5 16.4 - - - +
190M CYS* 1.3 73.5 - - - +
192M GLY* 1.3 62.1 + - - +
194M ILE* 3.1 5.7 + - + +
195M ASP* 3.1 19.8 + - - +
454M PHE* 4.0 9.2 - - + -
459M TYR* 3.7 47.3 - - + -
461M PHE* 4.1 12.3 - - + -
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Residues in contact with GLY 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167M GLY* 3.5 22.9 + - - -
187M SER 3.0 12.9 + - - -
188M ILE 3.5 10.7 + - - -
190M CYS 3.3 0.6 - - - -
191M LEU* 1.3 75.0 - - - +
193M SER* 1.3 63.8 + - - +
194M ILE 3.1 0.3 + - - -
195M ASP* 3.3 1.4 + - - +
196M MET* 2.9 32.1 + - - +
222M GLN* 4.9 0.7 - - - -
253M ARG* 4.0 9.6 - - - -
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Residues in contact with SER 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5M ARG* 4.8 1.7 + - - -
188M ILE 3.7 4.0 + - - -
189M GLY* 2.5 28.2 + - - -
190M CYS 3.2 4.5 + - - -
192M GLY* 1.3 75.2 - - - +
194M ILE* 1.3 61.4 + - - +
196M MET* 4.3 2.5 - - - -
197M GLU* 3.2 20.4 + - - +
252M PRO* 4.1 4.7 + - - +
253M ARG* 3.6 18.1 + - - +
256M VAL* 3.6 27.3 - - - +
389M ILE* 4.1 23.0 + - - +
392M ARG* 5.1 0.9 + - - -
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Residues in contact with ILE 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M ARG* 3.8 22.6 + - - +
190M CYS 3.0 20.5 + - - +
191M LEU* 3.1 9.6 + - - +
193M SER* 1.3 73.7 - - - +
195M ASP* 1.3 66.0 + - - +
197M GLU* 3.3 15.8 + - - +
198M LEU* 3.4 11.4 + - - +
389M ILE* 3.9 15.5 - - + -
436M MET* 5.7 0.4 - - + -
440M MET* 3.9 16.2 - - + -
459M TYR* 3.8 17.0 - - + +
461M PHE* 3.6 32.1 - - + -
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Residues in contact with ASP 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ARG* 2.9 44.4 + - - -
138M LEU* 3.9 19.5 - - + +
139M ARG* 5.2 2.4 + - - +
165M SER* 4.2 7.1 - - - -
167M GLY* 3.5 23.8 + - - -
191M LEU 3.1 15.0 + - - +
192M GLY 3.8 2.9 - - - +
194M ILE* 1.3 78.1 - - - +
196M MET* 1.3 64.1 + - + +
198M LEU* 3.0 24.6 + - - +
199M ILE* 3.0 15.3 + - - +
458M ASN 4.9 2.0 - - - +
459M TYR* 4.6 4.5 - - + -
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Residues in contact with MET 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165M SER* 3.4 12.3 - - - +
192M GLY* 2.9 24.5 + - - +
193M SER 3.6 1.1 - - - +
195M ASP* 1.3 77.7 - - + +
197M GLU* 1.3 62.6 + - - +
199M ILE* 4.1 3.8 - - - -
200M TRP* 2.9 39.7 + - + +
217M ASP* 3.3 29.2 - - + +
253M ARG* 3.4 40.6 - - - +
254M SER 4.0 3.1 - - - +
256M VAL* 3.5 16.6 - - + -
257M ALA* 3.5 38.8 - - + +
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Residues in contact with GLU 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M ALA* 3.4 34.7 - - - +
5M ARG* 4.3 16.2 + - - +
193M SER 3.2 11.7 + - - +
194M ILE* 3.7 9.8 - - - +
195M ASP 3.3 0.2 - - - -
196M MET* 1.3 78.6 - - - +
198M LEU* 1.3 64.5 + - - +
201M THR* 2.7 38.5 + - - +
256M VAL* 3.3 14.1 - - + +
260M ALA* 4.7 4.0 - - - -
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Residues in contact with LEU 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138M LEU 4.3 1.3 - - - +
139M ARG* 4.0 40.8 - - + +
143M TYR* 3.5 39.0 - - + +
194M ILE 3.4 6.6 + - - +
195M ASP* 3.0 25.4 + - - +
197M GLU* 1.3 84.7 - - - +
199M ILE* 1.3 62.8 + - + +
201M THR* 3.4 12.9 + - - -
202M ASP* 3.5 14.2 + - - +
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Residues in contact with ILE 199 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130M ARG* 3.5 33.4 - - - +
143M TYR* 3.8 16.6 - - + -
146M PHE* 4.0 18.2 - - + -
147M LEU* 5.4 0.6 - - - +
163M VAL* 4.2 9.2 - - + -
165M SER* 3.4 36.8 - - - +
195M ASP* 3.0 17.3 + - - +
196M MET* 3.6 6.1 - - - +
198M LEU* 1.3 75.1 - - + +
200M TRP* 1.3 84.9 + - + +
202M ASP* 3.2 4.4 + - - +
203M ILE* 2.8 33.2 + - + +
217M ASP* 3.8 0.7 - - - +
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Residues in contact with TRP 200 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161M LEU 3.7 10.8 - - - -
162M SER* 4.1 4.3 - - - -
163M VAL* 3.7 13.2 - - + -
196M MET* 2.9 43.4 + - + +
199M ILE* 1.3 87.5 - - + +
201M THR* 1.3 59.6 + - - +
203M ILE* 3.6 26.9 - - + +
204M SER* 2.6 37.8 + - - -
214M SER* 3.2 26.9 - - - -
216M GLY* 3.4 48.0 - - - -
217M ASP* 2.6 31.2 + - - +
257M ALA* 3.5 26.7 - - + +
260M ALA* 3.3 8.2 - - + +
262M ALA* 4.0 9.2 - - + -
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Residues in contact with THR 201 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3M ALA* 4.9 5.2 - - + +
197M GLU* 2.7 30.4 + - - +
198M LEU* 3.5 5.4 - - - -
200M TRP* 1.3 77.5 - - - +
202M ASP* 1.3 64.7 + - - +
204M SER* 3.9 2.4 - - - -
205M LYS* 3.2 41.2 + - - +
260M ALA* 4.0 17.4 + - - +
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Residues in contact with ASP 202 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M TYR* 2.7 29.1 + - - +
147M LEU* 3.8 26.9 - - + -
198M LEU* 3.5 12.6 + - - +
199M ILE 3.2 8.9 + - - +
201M THR* 1.3 79.2 - - - +
203M ILE* 1.3 63.7 + - - +
205M LYS* 3.3 21.4 + - - +
206M ILE* 3.0 29.2 + - - +
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Residues in contact with ILE 203 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146M PHE* 4.8 1.3 - - + -
147M LEU* 5.1 4.9 - - + -
150M PHE* 3.4 56.5 - - + -
161M LEU* 4.5 12.3 - - + -
163M VAL* 3.9 17.3 - - + -
199M ILE* 2.8 33.0 + - + +
200M TRP* 3.6 36.6 - - + -
202M ASP* 1.3 71.2 - - - +
204M SER* 1.3 58.8 + - - +
206M ILE* 3.2 11.4 + - - +
207M ALA* 2.9 26.0 + - - +
214M SER* 3.9 4.7 - - - +
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Residues in contact with SER 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200M TRP* 2.6 23.8 + - - -
201M THR 3.9 3.4 - - - -
203M ILE* 1.3 77.2 - - - +
205M LYS* 1.3 57.3 + - - +
207M ALA* 3.4 1.4 - - - +
208M LYS* 2.8 30.7 + - - +
214M SER* 3.2 24.9 + - - -
260M ALA 3.1 16.8 + - - -
261M GLY* 3.3 18.4 - - - -
262M ALA 3.5 1.0 + - - -
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Residues in contact with LYS 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201M THR* 3.2 29.2 + - - +
202M ASP* 3.4 25.7 + - - +
203M ILE 3.2 0.4 - - - -
204M SER* 1.3 75.7 - - - +
206M ILE* 1.3 66.6 + - + +
207M ALA 3.2 0.3 + - - -
208M LYS* 3.2 8.1 + - - +
209M LYS* 2.9 26.9 + - + +
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Residues in contact with ILE 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M LEU* 3.7 48.9 - - + +
150M PHE* 4.1 14.1 - - + -
151M GLU* 3.4 45.1 - - + +
154M ALA* 4.5 6.7 - - + -
161M LEU* 4.6 2.7 - - + -
202M ASP* 3.0 16.1 + - + +
203M ILE* 3.4 9.4 - - - +
205M LYS* 1.3 75.6 - - + +
207M ALA* 1.3 56.8 + - - +
209M LYS* 3.4 9.3 + - + +
210M THR* 3.0 30.1 + - - +
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Residues in contact with ALA 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161M LEU* 4.0 7.0 - - + -
203M ILE 2.9 13.6 + - - +
204M SER 3.1 7.8 + - - +
206M ILE* 1.3 73.8 - - - +
208M LYS* 1.3 66.4 + - - +
210M THR* 3.2 1.3 + - - -
211M GLY 3.0 18.7 + - - -
212M THR* 3.1 32.6 + - - +
213M ILE 4.0 0.7 - - - -
214M SER* 3.7 34.1 - - - +
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Residues in contact with LYS 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G GLY* 4.8 21.6 + - - -
204M SER 2.8 18.7 + - - +
205M LYS* 3.7 5.4 - - - +
207M ALA* 1.3 74.2 - - - +
209M LYS* 1.3 64.1 + - - +
210M THR 3.3 0.5 + - - -
211M GLY* 3.4 10.4 + - - -
212M THR 5.0 1.3 - - - -
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Residues in contact with LYS 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M GLU* 3.0 29.0 + - - +
155M GLU* 4.5 6.9 + - - -
205M LYS* 2.9 18.7 + - + +
206M ILE* 3.5 11.0 - - + +
208M LYS* 1.3 79.2 - - - +
210M THR* 1.3 63.6 + - + +
211M GLY 3.7 0.2 + - - -
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Residues in contact with THR 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M GLU* 4.5 5.8 - - + +
154M ALA* 3.2 31.8 - - + +
155M GLU* 3.9 28.0 - - + +
206M ILE* 3.0 20.4 + - + +
207M ALA 3.2 0.4 + - - -
209M LYS* 1.3 84.5 - - + +
211M GLY* 1.3 59.8 + - - +
212M THR* 3.1 28.1 + - - +
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Residues in contact with GLY 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208G LYS* 5.2 17.3 + - - -
207M ALA 3.0 5.6 + - - -
208M LYS* 3.4 9.9 + - - -
209M LYS 3.4 0.6 + - - -
210M THR* 1.3 78.9 - - - +
212M THR* 1.3 63.3 + - - +
213M ILE* 5.5 2.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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