Contacts of the helix formed by residues 180 - 190 (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 ASP 180 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174M TYR* 4.4 7.2 - - + -
175M ALA* 3.2 27.4 + - + +
178M ARG* 3.1 9.2 - - + -
179M ASN* 1.3 74.2 - - - +
181M ILE* 1.3 58.3 + - - +
182M PRO* 3.2 14.0 - - - +
183M GLY* 2.9 26.0 + - - -
184M LEU* 2.9 15.0 + - - +
446M LYS* 3.9 9.8 - - - -
447M TYR* 2.5 36.7 + - - -
450M GLU* 4.9 0.2 - - - +
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Residues in contact with ILE 181 (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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179M ASN* 3.2 20.9 + - + +
180M ASP* 1.3 68.9 - - - +
182M PRO* 1.4 76.9 - - + +
184M LEU* 2.9 27.5 + - + +
185M LEU* 2.9 21.0 + - - +
242M ILE* 4.0 21.8 - - + -
245M ILE* 4.5 14.6 - - + -
249M ILE* 5.4 0.9 - - + -
425M ALA* 3.7 31.0 - - + +
428M ALA* 4.3 7.9 - - + -
429M LEU* 3.7 38.1 - - + -
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Residues in contact with PRO 182 (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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180M ASP* 3.2 12.1 - - - +
181M ILE* 1.4 95.7 - - + +
183M GLY* 1.3 56.7 + - - +
185M LEU* 3.2 10.2 + - + +
186M TYR* 3.0 29.3 + - - +
428M ALA* 4.4 16.8 - - + +
432M LEU* 4.3 33.9 - - + -
439M PHE* 3.7 7.6 - - + -
443M CYS* 5.4 2.9 - - - -
446M LYS* 6.3 1.1 - - + -
447M TYR* 4.1 4.7 - - - +
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Residues in contact with GLY 183 (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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171M VAL* 3.9 3.8 - - - +
175M ALA* 3.9 11.0 - - - -
180M ASP* 2.9 19.6 + - - -
182M PRO* 1.3 74.7 - - - +
184M LEU* 1.3 61.5 + - - +
186M TYR* 3.9 0.4 - - - -
187M SER* 2.8 34.3 + - - -
447M TYR* 3.1 27.6 + - - -
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Residues in contact with LEU 184 (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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172M PHE* 4.2 14.4 - - + -
175M ALA* 3.7 20.4 - - + +
176M VAL* 3.9 23.6 - - + +
179M ASN* 6.1 0.2 - - - -
180M ASP 2.9 7.5 + - - +
181M ILE* 2.9 37.4 + - + +
183M GLY* 1.3 75.1 - - - +
185M LEU* 1.3 64.6 + - - +
187M SER* 3.3 4.2 + - - -
188M ILE* 3.0 41.6 + - + +
242M ILE* 4.1 17.9 - - + +
245M ILE* 5.3 2.7 - - + -
246M ALA* 4.6 16.4 - - + +
249M ILE* 4.2 10.7 - - + +
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Residues in contact with LEU 185 (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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181M ILE 2.9 11.2 + - - +
182M PRO* 3.2 10.5 + - + +
184M LEU* 1.3 77.2 - - - +
186M TYR* 1.3 56.8 + - - +
189M GLY* 2.9 24.9 + - - -
190M CYS* 3.5 3.1 + - - -
249M ILE* 3.9 16.5 - - + +
390M TYR* 3.4 36.1 - - + +
393M ALA* 3.6 31.2 - - + +
394M LYS* 3.9 20.0 - - + +
429M LEU* 4.4 13.2 - - + -
432M LEU* 3.7 23.6 - - + -
439M PHE* 3.7 2.5 - - + -
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Residues in contact with TYR 186 (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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171M VAL* 4.4 4.3 - - + -
182M PRO 3.0 16.7 + - - +
183M GLY* 4.0 3.6 - - - +
185M LEU* 1.3 73.7 - - - +
187M SER* 1.3 64.2 + - - +
190M CYS* 3.0 15.1 + - + +
191M LEU* 2.9 64.1 + - + +
439M PHE* 3.8 22.9 - + + -
440M MET* 3.8 29.0 + - + -
443M CYS* 3.5 35.0 - - + -
444M LEU* 3.8 15.5 + - - +
447M TYR* 3.7 20.4 - + - -
454M PHE* 3.8 18.2 - + - -
461M PHE* 4.1 10.0 - - - -
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Residues in contact with SER 187 (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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168M GLY* 3.6 7.9 - - - -
171M VAL* 3.7 7.9 - - - -
172M PHE* 3.4 40.8 - - - +
183M GLY 2.8 22.9 + - - -
184M LEU* 3.3 6.9 + - - -
186M TYR* 1.3 77.2 - - - +
188M ILE* 1.3 67.7 + - - +
191M LEU* 3.5 15.4 - - - +
192M GLY 3.0 23.2 + - - -
222M GLN* 3.2 10.5 + - - -
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Residues in contact with ILE 188 (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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172M PHE* 3.9 23.3 - - + -
184M LEU* 3.0 20.5 + - + +
187M SER* 1.3 88.8 + - - +
189M GLY* 1.3 62.6 + - - +
192M GLY* 3.5 9.4 - - - -
193M SER 3.7 0.2 + - - -
219M ASP* 3.6 19.3 - - - +
222M GLN* 3.6 28.3 - - + +
223M ALA 4.8 0.4 - - - +
246M ALA* 4.0 29.2 - - + +
249M ILE* 3.8 6.5 - - + +
250M SER* 3.6 26.7 - - - +
253M ARG* 3.5 21.2 - - + +
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Residues in contact with GLY 189 (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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185M LEU 2.9 16.9 + - - -
188M ILE* 1.3 80.2 - - - +
190M CYS* 1.3 59.5 + - - +
193M SER* 2.5 27.1 + - - -
249M ILE* 3.5 17.7 - - - +
253M ARG* 4.9 1.3 - - - -
389M ILE* 3.8 13.4 - - - +
393M ALA* 3.9 12.0 - - - +
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Residues in contact with CYS 190 (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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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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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