Contacts of the helix formed by residues 190 - 211 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.6 4.9 + - - -
186E TYR* 3.1 14.4 + - + +
189E GLY* 1.3 78.2 - - - +
191E LEU* 1.3 68.9 + - - +
192E GLY 3.3 0.9 - - - -
193E SER* 3.3 2.9 + - - -
194E ILE* 3.1 29.0 + - - +
389E ILE* 4.5 8.1 - - + -
390E TYR* 3.7 43.1 - - - -
439E PHE* 4.2 10.5 - - - -
440E MET* 3.7 32.1 - - + -
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Residues in contact with LEU 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E GLY* 3.9 4.0 - - - -
171E VAL* 3.6 26.7 - - + -
186E TYR* 2.8 59.8 + - + +
187E SER* 3.2 17.7 - - - +
190E CYS* 1.3 74.5 - - - +
192E GLY* 1.3 62.9 + - - +
194E ILE* 3.3 4.4 + - + +
195E ASP* 3.3 12.0 + - - +
454E PHE* 4.2 8.3 - - + -
459E TYR* 3.3 61.5 - - + -
461E PHE* 4.4 7.9 - - + -
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Residues in contact with GLY 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E GLY* 3.1 23.9 + - - -
187E SER 2.8 13.9 + - - -
188E ILE* 3.5 11.3 + - - -
190E CYS 3.3 0.4 - - - -
191E LEU* 1.3 72.9 - - - +
193E SER* 1.3 55.7 + - - +
195E ASP* 3.6 2.9 + - - +
196E MET* 2.9 37.5 + - - +
222E GLN* 5.0 0.2 - - - -
253E ARG* 3.9 8.5 - - - -
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Residues in contact with SER 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E ILE 3.7 3.8 + - - -
189E GLY 2.6 26.2 + - - -
190E CYS 3.3 4.3 + - - -
192E GLY* 1.3 71.0 - - - +
194E ILE* 1.3 67.5 + - - +
196E MET* 2.9 9.5 + - - +
197E GLU* 2.7 25.8 + - - +
252E PRO* 4.4 1.2 + - - +
253E ARG* 3.6 20.5 + - - +
256E VAL* 3.9 18.4 - - - +
389E ILE* 4.1 19.6 + - - +
392E ARG* 5.0 0.7 + - - -
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Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ARG* 4.1 13.0 + - - +
190E CYS 3.1 18.1 + - - +
191E LEU* 3.3 8.7 + - - +
193E SER* 1.3 77.4 - - - +
195E ASP* 1.3 62.7 + - - +
197E GLU* 3.2 10.4 + - - +
198E LEU* 3.2 18.2 + - - +
389E ILE* 4.1 14.4 - - + -
440E MET* 3.8 28.3 - - + -
459E TYR* 4.0 21.5 - - + +
461E PHE* 3.9 19.7 - - + -
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Residues in contact with ASP 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ARG* 2.9 42.5 + - - -
138E LEU* 3.8 20.4 - - + +
139E ARG* 5.2 4.5 - - - +
165E SER* 4.0 8.3 + - - -
167E GLY* 3.3 26.3 + - - -
191E LEU 3.3 9.8 + - - +
192E GLY 3.9 5.7 - - - +
193E SER 3.2 0.4 - - - -
194E ILE* 1.3 76.9 - - - +
196E MET* 1.3 66.5 + - - +
198E LEU* 3.0 19.1 + - - +
199E ILE* 3.1 13.6 + - - +
458E ASN 5.4 1.3 - - - +
459E TYR* 4.4 3.7 - - + -
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Residues in contact with MET 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E SER* 3.1 26.2 - - - +
192E GLY 2.9 24.4 + - - +
193E SER* 2.9 9.3 + - - +
195E ASP* 1.3 75.8 - - - +
197E GLU* 1.3 63.2 + - - +
199E ILE* 3.4 6.5 - - - +
200E TRP* 3.0 39.7 + - + +
217E ASP* 3.5 21.3 - - + +
253E ARG* 3.2 54.5 - - - +
254E SER* 3.8 5.6 - - - -
256E VAL* 4.1 11.0 - - + -
257E ALA* 3.8 16.8 - - + +
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Residues in contact with GLU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ALA* 3.2 42.3 + - - +
5E ARG* 4.3 8.6 + - - +
193E SER 2.7 14.8 + - - +
194E ILE* 3.4 14.3 - - - +
196E MET* 1.3 74.0 - - - +
198E LEU* 1.3 58.0 + - - +
201E THR* 2.4 37.9 + - - +
256E VAL* 3.6 16.7 - - + +
260E ALA* 4.3 4.1 - - + +
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Residues in contact with LEU 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ARG* 5.0 1.8 - - - +
138E LEU* 4.9 1.3 - - + +
139E ARG* 4.1 40.8 - - + +
143E TYR* 3.4 36.8 - - + +
194E ILE 3.2 8.4 + - - +
195E ASP* 3.0 14.8 + - - +
197E GLU* 1.3 83.8 + - - +
199E ILE* 1.3 65.6 + - + +
200E TRP 3.3 0.3 + - - -
201E THR* 3.7 4.3 - - - -
202E ASP* 3.4 23.8 + - - +
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Residues in contact with ILE 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E ARG* 3.2 37.0 - - - +
143E TYR* 3.7 20.9 - - + +
146E PHE* 4.5 10.3 - - + -
147E LEU* 5.1 0.8 - - - +
163E VAL* 4.4 9.9 - - + -
165E SER* 3.4 35.9 - - - +
195E ASP* 3.6 10.8 - - - +
196E MET* 3.4 12.3 - - - +
198E LEU* 1.3 77.0 - - + +
200E TRP* 1.3 77.2 + - + +
202E ASP* 3.3 3.9 + - - +
203E ILE* 2.8 37.5 + - + +
217E ASP* 4.2 1.3 - - - +
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Residues in contact with TRP 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E LEU 4.1 10.3 - - - -
162E SER* 4.3 6.1 - - - -
163E VAL* 4.0 7.9 - - + -
196E MET* 3.0 33.9 + - + +
199E ILE* 1.3 82.6 - - + +
201E THR* 1.3 65.5 + - - +
202E ASP 3.2 1.6 - - - -
203E ILE* 3.5 28.2 - - + +
204E SER* 3.1 30.8 + - - -
214E SER* 3.5 26.7 - - - -
216E GLY* 3.2 46.2 - - - -
217E ASP* 2.7 37.4 + - - +
257E ALA* 3.7 26.6 - - + +
260E ALA* 3.2 18.6 - - + +
262E ALA* 4.3 7.2 - - + -
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Residues in contact with THR 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ALA* 4.8 13.4 - - + +
197E GLU* 2.4 35.1 + - - +
198E LEU* 3.7 5.1 - - - -
200E TRP* 1.3 76.6 - - - +
202E ASP* 1.3 66.6 + - - +
204E SER* 4.2 1.9 - - - -
205E LYS* 3.3 26.2 + - + +
260E ALA* 3.6 18.2 + - - +
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Residues in contact with ASP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E TYR* 2.7 35.3 + - - +
147E LEU* 3.8 23.4 - - + +
198E LEU* 3.4 14.6 + - - +
199E ILE 3.3 9.1 + - - +
200E TRP 3.2 0.4 - - - -
201E THR* 1.3 79.2 - - - +
203E ILE* 1.3 64.4 + - - +
205E LYS* 3.2 20.9 + - - +
206E ILE* 3.1 26.0 + - - +
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Residues in contact with ILE 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E PHE* 4.7 1.3 - - + -
147E LEU* 4.9 4.5 - - + -
150E PHE* 3.7 52.5 - - + -
161E LEU* 4.7 8.0 - - + +
163E VAL* 4.1 10.3 - - + -
199E ILE* 2.8 33.7 + - + +
200E TRP* 3.5 32.7 + - + +
202E ASP* 1.3 70.8 - - - +
204E SER* 1.3 59.7 + - - +
206E ILE* 3.0 15.8 + - + +
207E ALA* 2.8 23.4 + - - +
214E SER* 3.4 22.0 - - - +
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Residues in contact with SER 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E TRP* 3.1 18.1 + - - -
201E THR 4.2 1.8 - - - -
203E ILE* 1.3 71.1 - - - +
205E LYS* 1.3 56.8 + - - +
206E ILE 3.0 4.7 - - - -
207E ALA* 2.9 2.3 + - - +
208E LYS* 2.9 31.4 + - - +
214E SER* 2.7 28.7 + - - -
260E ALA 3.8 1.8 - - - -
261E GLY* 3.0 36.9 - - - -
262E ALA 3.3 1.0 + - - -
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Residues in contact with LYS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E THR* 3.3 14.5 + - + +
202E ASP* 3.2 23.6 + - - +
204E SER* 1.3 77.4 - - - +
206E ILE* 1.3 59.2 + - - +
208E LYS* 4.3 6.0 - - - +
209E LYS* 3.4 21.8 + - - +
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Residues in contact with ILE 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU* 3.6 48.9 - - + +
150E PHE* 4.2 12.6 - - + -
151E GLU* 3.7 38.1 - - + +
161E LEU* 4.4 9.2 - - + -
202E ASP 3.1 12.3 + - - +
203E ILE* 3.0 16.3 + - - +
204E SER 3.0 0.6 - - - -
205E LYS* 1.3 78.6 - - - +
207E ALA* 1.3 58.7 + - - +
208E LYS 3.3 0.2 - - - -
209E LYS* 3.1 11.1 - - + +
210E THR* 2.9 36.6 + - + +
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Residues in contact with ALA 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161E LEU* 4.8 3.6 - - + +
203E ILE 2.8 12.3 + - - +
204E SER* 2.9 8.0 + - - +
206E ILE* 1.3 75.3 - - - +
208E LYS* 1.3 64.0 + - - +
210E THR 3.5 0.2 + - - -
211E GLY* 3.0 19.4 + - - -
212E THR* 3.0 32.5 + - - +
213E ILE 4.0 0.7 - - - -
214E SER* 3.5 35.7 - - - +
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Residues in contact with LYS 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E SER 2.9 13.8 + - - +
205E LYS* 4.4 6.1 - - - +
207E ALA* 1.3 72.9 - - - +
209E LYS* 1.3 69.1 + - - +
210E THR 2.9 1.6 + - - -
211E GLY* 3.0 13.3 + - - -
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Residues in contact with LYS 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLU* 2.9 31.4 + - - +
155E GLU* 5.0 6.3 - - - -
205E LYS 3.4 16.0 + - - +
206E ILE* 3.1 16.8 - - + +
208E LYS* 1.3 79.0 - - - +
210E THR* 1.3 64.2 + - + +
211E GLY 3.8 0.3 + - - -
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Residues in contact with THR 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E GLU* 4.4 5.4 - - + +
154E ALA* 3.6 26.2 - - + +
155E GLU* 4.1 30.1 - - + +
206E ILE* 2.9 24.3 + - + +
207E ALA* 3.5 0.3 + - - -
209E LYS* 1.3 85.2 - - + +
211E GLY* 1.3 64.3 + - - +
212E THR* 2.7 31.5 + - - +
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Residues in contact with GLY 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ALA 3.0 6.5 + - - -
208E LYS* 3.0 9.1 + - - -
209E LYS 3.5 1.2 + - - -
210E THR* 1.3 78.7 - - - +
212E THR* 1.3 61.8 + - - +
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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