Contacts of the helix formed by residues 190 - 211 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185G LEU* 3.5 10.0 + - - -
186G TYR* 3.0 15.8 + - + +
188G ILE 3.3 0.2 - - - -
189G GLY* 1.3 78.5 - - - +
191G LEU* 1.3 71.9 + - - +
192G GLY 3.3 0.7 - - - -
193G SER* 3.2 3.9 + - - -
194G ILE* 2.9 27.5 + - - +
389G ILE* 4.2 6.2 - - + +
390G TYR* 4.0 37.0 - - - -
439G PHE* 4.2 8.3 - - - -
440G MET* 3.7 33.9 - - + -
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Residues in contact with LEU 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G GLY* 3.8 9.2 - - - -
170G GLU* 4.3 1.1 - - - +
171G VAL* 3.8 22.2 - - + -
186G TYR* 2.8 59.0 + - + +
187G SER* 3.5 21.8 - - - +
190G CYS* 1.3 71.0 - - + +
192G GLY* 1.3 65.5 + - - +
194G ILE* 2.8 18.4 + - + +
195G ASP* 3.0 11.3 + - - +
440G MET* 5.4 0.2 - - + -
454G PHE* 4.0 7.6 - - + -
459G TYR* 3.7 45.1 - - + -
461G PHE* 4.2 10.5 - - + -
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Residues in contact with GLY 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167G GLY* 3.6 23.0 + - - -
187G SER 2.9 11.7 + - - -
188G ILE* 3.2 12.2 + - - -
191G LEU* 1.3 75.2 - - - +
193G SER* 1.3 51.9 + - - +
195G ASP* 3.2 1.7 + - - +
196G MET* 2.7 38.7 + - - +
222G GLN* 5.0 0.4 - - - -
253G ARG* 4.0 13.9 - - - -
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Residues in contact with SER 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ARG* 5.2 0.9 + - - -
188G ILE 3.5 5.9 + - - -
189G GLY 2.6 26.3 + - - -
190G CYS 3.2 4.8 + - - -
192G GLY* 1.3 73.1 - - - +
194G ILE* 1.3 64.1 + - - +
196G MET* 3.3 7.9 + - - +
197G GLU* 3.0 23.6 + - - +
252G PRO* 4.2 3.1 + - - +
253G ARG* 3.9 17.8 + - - +
256G VAL* 3.9 15.5 - - - +
389G ILE* 4.0 27.4 + - - +
392G ARG* 4.8 0.9 + - - -
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Residues in contact with ILE 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G ARG* 3.6 22.2 + - - +
190G CYS 2.9 19.4 + - - +
191G LEU* 2.8 17.5 + - - +
193G SER* 1.3 70.5 - - - +
195G ASP* 1.3 61.7 + - - +
197G GLU* 3.2 20.4 + - - +
198G LEU* 3.2 11.8 + - - +
389G ILE* 4.3 14.8 - - + -
436G MET* 6.0 0.7 - - + -
440G MET* 3.9 26.7 - - + -
459G TYR* 4.0 17.3 - - + +
461G PHE* 3.9 18.2 - - + -
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Residues in contact with ASP 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG* 2.8 45.2 + - - -
138G LEU* 3.8 11.0 - - + +
139G ARG* 5.0 3.3 + - - +
165G SER* 4.3 9.0 + - - -
167G GLY* 3.3 32.0 + - - -
191G LEU 3.0 7.7 + - - +
192G GLY 3.7 6.0 - - - +
194G ILE* 1.3 78.1 - - - +
196G MET* 1.3 64.5 + - - +
198G LEU* 3.2 10.7 + - - +
199G ILE* 3.0 30.3 + - - +
458G ASN 5.1 1.9 - - - +
459G TYR* 4.5 8.7 - - + -
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Residues in contact with MET 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G SER* 3.4 13.2 - - - +
192G GLY* 2.7 23.9 + - - +
193G SER 3.5 5.8 - - - +
194G ILE 3.2 0.2 - - - -
195G ASP* 1.3 73.6 - - - +
197G GLU* 1.3 57.8 + - - +
199G ILE* 4.5 1.8 - - - -
200G TRP* 3.0 52.7 + - + +
217G ASP* 3.3 43.1 - - + +
253G ARG* 3.5 40.6 - - - +
254G SER 4.0 2.7 - - - +
256G VAL* 3.8 14.1 - - + -
257G ALA* 3.7 20.0 - - + +
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Residues in contact with GLU 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ALA* 3.7 36.0 + - - +
5G ARG* 4.3 18.1 + - - +
193G SER 3.0 12.6 + - - +
194G ILE* 3.2 13.8 + - - +
196G MET* 1.3 73.5 - - - +
198G LEU* 1.3 61.6 + - - +
201G THR* 2.5 39.0 + - - +
256G VAL* 3.6 12.1 - - + +
260G ALA* 4.2 3.3 - - + +
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Residues in contact with LEU 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG* 4.7 1.8 - - - +
138G LEU 4.6 2.2 - - - +
139G ARG* 3.4 45.3 - - + +
143G TYR* 3.8 34.8 - - + +
194G ILE 3.2 8.8 + - - +
195G ASP* 3.2 13.2 + - - +
197G GLU* 1.3 82.8 - - - +
199G ILE* 1.3 66.1 + - + +
201G THR* 3.4 10.1 + - - -
202G ASP* 3.5 17.3 + - - +
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Residues in contact with ILE 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G ARG* 3.3 36.3 - - - +
143G TYR* 3.9 13.7 - - + +
146G PHE* 4.2 13.0 - - + -
147G LEU* 5.2 0.8 - - - +
163G VAL* 4.1 10.8 - - + -
165G SER* 3.4 35.2 - - - +
195G ASP* 3.0 17.0 + - - +
196G MET* 3.8 4.3 - - - +
198G LEU* 1.3 77.9 - - + +
200G TRP* 1.3 85.8 + - + +
202G ASP* 3.2 4.3 + - - +
203G ILE* 2.9 38.7 + - + +
217G ASP* 3.9 0.9 - - - +
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Residues in contact with TRP 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161G LEU 3.6 13.5 - - - -
162G SER* 4.1 4.0 - - - -
163G VAL* 3.6 17.9 - - + -
196G MET* 3.0 44.1 + - + +
199G ILE* 1.3 86.2 - - + +
201G THR* 1.3 63.4 + - - +
202G ASP 3.2 0.2 - - - -
203G ILE* 3.6 29.4 - - + -
204G SER* 3.0 30.8 + - - -
214G SER* 3.4 26.9 - - - -
216G GLY 3.4 46.0 - - - -
217G ASP* 2.7 27.4 + - + +
257G ALA* 3.8 15.3 - - + +
260G ALA* 3.3 16.9 - - + +
262G ALA* 4.2 7.0 - - + -
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Residues in contact with THR 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G ALA* 4.9 9.9 - - + +
197G GLU* 2.5 33.5 + - - +
198G LEU* 3.6 5.1 - - - -
199G ILE 3.4 0.2 - - - -
200G TRP* 1.3 75.6 - - - +
202G ASP* 1.3 65.1 + - - +
204G SER* 4.0 2.3 - - - -
205G LYS* 3.4 37.0 + - - +
260G ALA* 3.7 18.4 - - - +
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Residues in contact with ASP 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G TYR* 2.6 30.8 + - - +
147G LEU* 3.9 25.1 - - + -
198G LEU* 3.5 12.3 + - - +
199G ILE 3.2 8.0 + - - +
201G THR* 1.3 81.1 - - - +
203G ILE* 1.3 65.0 - - - +
205G LYS* 3.2 20.8 + - - +
206G ILE* 3.0 28.2 + - + +
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Residues in contact with ILE 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146G PHE* 4.5 1.8 - - + -
147G LEU* 4.8 7.2 - - + -
150G PHE* 3.6 56.8 - - + -
161G LEU* 4.5 9.8 - - + +
163G VAL* 4.0 4.3 - - + -
199G ILE* 2.9 44.2 + - + +
200G TRP* 3.6 40.6 - - + -
202G ASP* 1.3 68.4 - - - +
204G SER* 1.3 65.9 + - - +
206G ILE* 3.1 11.1 + - - +
207G ALA* 2.9 20.6 + - - +
214G SER* 4.5 2.5 - - - +
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Residues in contact with SER 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200G TRP* 3.0 20.9 + - - -
201G THR 4.0 3.1 - - - -
203G ILE* 1.3 78.0 - - - +
205G LYS* 1.3 57.5 + - - +
207G ALA* 3.1 4.3 + - - +
208G LYS* 2.9 30.7 + - - +
214G SER* 3.1 17.6 + - - -
260G ALA 3.2 10.3 + - - -
261G GLY* 3.0 33.6 - - - -
262G ALA 3.4 1.2 + - - -
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Residues in contact with LYS 205 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201G THR* 3.4 29.1 + - - +
202G ASP* 3.2 23.7 + - - +
204G SER* 1.3 77.8 - - - +
206G ILE* 1.3 57.3 + - + +
208G LYS* 3.4 9.8 + - + +
209G LYS* 2.9 30.8 + - + +
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Residues in contact with ILE 206 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G LEU* 3.6 46.7 - - + +
150G PHE* 4.0 16.6 - - + +
151G GLU* 3.7 44.9 - - + +
154G ALA* 4.6 0.2 - - + -
161G LEU* 4.5 5.4 - - + -
202G ASP* 3.0 19.0 + - + +
203G ILE* 3.1 8.9 + - - +
205G LYS* 1.3 74.8 - - + +
207G ALA* 1.3 55.0 + - - +
209G LYS* 3.1 9.2 + - + +
210G THR* 2.7 43.2 + - + +
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Residues in contact with ALA 207 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G LEU* 4.4 5.4 - - + +
203G ILE 2.9 12.4 + - - +
204G SER 3.4 7.4 - - - +
206G ILE* 1.3 74.4 - - - +
208G LYS* 1.3 57.2 + - - +
210G THR* 3.2 6.4 + - - -
211G GLY* 2.9 26.3 + - - -
212G THR* 2.9 26.9 + - - +
213G ILE 4.0 0.7 - - - -
214G SER* 3.4 36.8 - - - +
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Residues in contact with LYS 208 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204G SER 2.9 19.0 + - - +
205G LYS* 3.6 9.4 - - + +
207G ALA* 1.3 74.5 - - - +
209G LYS* 1.3 63.1 + - - +
211G GLY* 3.5 8.2 + - - -
212G THR 5.1 0.4 - - - -
211M GLY* 5.2 16.9 + - - -
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Residues in contact with LYS 209 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G GLU* 3.9 21.0 + - - +
155G GLU* 5.6 3.6 + - - +
205G LYS* 2.9 19.1 + - + +
206G ILE* 3.1 8.9 + - + +
208G LYS* 1.3 76.4 - - - +
210G THR* 1.3 66.2 + - + +
211G GLY 3.7 0.3 + - - -
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Residues in contact with THR 210 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G GLU* 4.4 3.4 - - + +
154G ALA* 3.4 29.0 - - + +
155G GLU* 4.2 28.3 - - + +
206G ILE* 2.7 27.8 + - + +
207G ALA* 3.2 0.9 + - - -
209G LYS* 1.3 83.7 - - + +
211G GLY* 1.3 60.7 + - - +
212G THR* 2.9 29.7 + - - +
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Residues in contact with GLY 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G ALA 2.9 5.4 + - - -
208G LYS* 3.5 6.9 + - - -
209G LYS 3.4 3.8 + - - -
210G THR* 1.3 78.7 - - - +
212G THR* 1.3 61.9 + - - +
213G ILE* 5.9 0.5 - - - +
208M LYS* 4.8 22.6 + - - -
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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
------------------------------------------------------------
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