Contacts of the helix formed by residues 180 - 190 (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 ASP 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174E TYR* 5.0 5.2 - - + -
175E ALA* 3.3 24.7 + - + +
178E ARG* 3.1 10.2 - - + +
179E ASN* 1.3 74.4 - - - +
181E ILE* 1.3 58.1 + - - +
182E PRO* 3.1 14.1 - - - +
183E GLY* 3.0 13.5 + - - -
184E LEU* 3.1 26.5 + - - +
446E LYS* 3.1 21.3 + - - -
447E TYR* 2.7 29.2 + - - -
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Residues in contact with ILE 181 (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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179E ASN* 3.1 17.1 + - + +
180E ASP* 1.3 68.4 - - - +
182E PRO* 1.4 71.2 - - + +
183E GLY 3.2 1.3 - - - -
184E LEU* 3.2 15.7 + - + +
185E LEU* 2.8 24.8 + - - +
242E ILE* 3.9 35.9 - - + -
245E ILE* 4.8 12.1 - - + -
249E ILE* 4.8 1.2 - - + +
424E ASP 5.4 0.2 - - - -
425E ALA* 3.8 34.3 - - + +
428E ALA* 4.8 7.0 - - + -
429E LEU* 3.8 35.2 - - + -
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Residues in contact with PRO 182 (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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180E ASP* 3.1 10.8 - - - +
181E ILE* 1.4 95.8 - - + +
183E GLY* 1.3 52.4 + - - +
185E LEU* 3.0 10.7 + - + +
186E TYR* 2.7 36.6 + - - +
428E ALA* 4.6 14.6 - - + +
429E LEU* 5.7 0.2 - - + -
432E LEU* 4.2 33.0 - - + -
439E PHE* 3.8 10.5 - - + -
443E CYS* 5.3 2.5 - - - -
446E LYS* 5.6 4.5 - - - -
447E TYR* 3.7 6.1 - - - +
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Residues in contact with GLY 183 (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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171E VAL* 4.3 2.9 - - - +
175E ALA* 3.8 11.7 - - - -
180E ASP* 3.0 15.6 + - - -
181E ILE 3.2 0.2 - - - -
182E PRO* 1.3 74.2 - - - +
184E LEU* 1.3 51.0 - - - +
186E TYR* 3.9 1.0 - - - +
187E SER* 2.7 39.7 + - - -
447E TYR* 2.8 33.2 + - - -
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Residues in contact with LEU 184 (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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172E PHE* 4.5 8.5 - - + -
175E ALA* 3.8 15.5 - - + +
176E VAL* 3.8 28.0 - - + +
179E ASN* 6.3 0.4 - - - -
180E ASP 3.1 16.0 + - - +
181E ILE* 3.2 23.1 - - + +
183E GLY* 1.3 72.9 - - - +
185E LEU* 1.3 64.3 + - - +
187E SER* 3.2 4.4 + - - -
188E ILE* 3.1 45.6 + - + +
242E ILE* 4.0 28.3 - - + +
245E ILE* 5.5 1.6 - - + -
246E ALA* 4.4 19.1 - - + +
249E ILE* 4.3 9.1 - - + +
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Residues in contact with LEU 185 (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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181E ILE 2.8 16.3 + - - +
182E PRO* 3.0 10.5 + - + +
184E LEU* 1.3 72.6 - - - +
186E TYR* 1.3 57.0 + - - +
189E GLY* 3.1 26.0 + - - -
190E CYS* 3.6 3.4 + - - -
249E ILE* 4.0 16.3 - - + +
390E TYR* 3.5 35.0 - - + +
393E ALA* 3.8 30.5 - - + +
394E LYS* 4.1 15.7 - - + +
397E ALA* 5.5 0.2 - - + -
429E LEU* 4.2 18.4 - - + -
432E LEU* 3.6 24.5 - - + -
439E PHE* 3.8 4.9 - - + -
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Residues in contact with TYR 186 (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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171E VAL* 4.3 3.6 - - + -
182E PRO 2.7 18.9 + - - +
183E GLY 3.9 2.9 - - - +
185E LEU* 1.3 72.2 - - - +
187E SER* 1.3 61.9 + - - +
190E CYS* 3.1 13.3 + - + +
191E LEU* 2.8 66.4 + - + +
439E PHE* 3.9 13.2 - + - -
440E MET* 3.9 29.2 + - + -
443E CYS* 3.5 40.4 - - + -
444E LEU* 4.1 14.0 - - - +
447E TYR* 3.6 26.5 - + + -
454E PHE* 4.1 17.4 - + - -
461E PHE* 4.3 11.4 - - - -
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Residues in contact with SER 187 (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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168E GLY* 3.4 22.6 - - - -
171E VAL* 3.9 7.6 - - - -
172E PHE* 3.4 25.5 - - - +
183E GLY 2.7 22.7 + - - -
184E LEU* 3.2 8.7 + - - -
186E TYR* 1.3 75.8 - - - +
188E ILE* 1.3 65.2 + - - +
191E LEU* 3.2 15.5 - - - +
192E GLY 2.8 24.8 + - - -
222E GLN* 3.4 10.1 + - - -
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Residues in contact with ILE 188 (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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172E PHE* 3.9 22.0 - - + -
184E LEU* 3.1 27.6 + - + +
187E SER* 1.3 80.7 + - - +
189E GLY* 1.3 65.2 + - - +
192E GLY* 3.5 9.0 - - - -
219E ASP* 3.7 5.2 - - - +
222E GLN* 3.2 35.7 - - + +
223E ALA 5.3 0.4 - - - +
246E ALA* 3.9 23.3 - - + +
249E ILE* 3.6 11.9 - - + +
250E SER* 3.6 31.4 - - - -
253E ARG* 3.3 27.4 - - + +
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Residues in contact with GLY 189 (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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185E LEU 3.1 13.3 + - - -
188E ILE* 1.3 78.9 - - - +
190E CYS* 1.3 61.1 + - - +
193E SER* 2.6 26.8 + - - -
249E ILE* 3.5 18.0 - - - +
252E PRO* 6.0 0.5 - - - +
253E ARG* 4.8 3.1 + - - -
389E ILE* 4.1 12.6 - - - +
393E ALA* 4.1 11.9 - - - -
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Residues in contact with CYS 190 (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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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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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