Contacts of the helix formed by residues 180 - 190 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C TYR* 4.5 7.4 - - + -
175C ALA* 3.3 25.3 + - + +
178C ARG* 3.1 11.1 - - + +
179C ASN* 1.3 73.8 - - - +
181C ILE* 1.3 62.7 + - - +
182C PRO* 3.4 11.8 - - - +
183C GLY* 2.8 24.7 + - - -
184C LEU* 3.1 19.5 + - - +
446C LYS* 4.1 8.4 - - - -
447C TYR* 2.7 32.9 + - - -
450C GLU* 4.8 0.9 - - - +
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ASN 3.2 16.4 + - - +
180C ASP* 1.3 69.4 - - - +
182C PRO* 1.4 75.4 - - + +
184C LEU* 3.0 18.4 + - + +
185C LEU* 3.0 19.8 + - - +
242C ILE* 3.7 34.8 - - + -
245C ILE* 4.6 13.0 - - + -
249C ILE* 5.4 0.9 - - + -
425C ALA* 3.5 31.9 - - + +
428C ALA* 4.4 7.9 - - + -
429C LEU* 3.8 36.8 - - + -
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Residues in contact with PRO 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C ASP* 3.4 10.5 - - - +
181C ILE* 1.4 93.8 - - + +
183C GLY* 1.3 54.4 + - - +
185C LEU* 3.1 11.5 + - + +
186C TYR* 2.9 29.4 + - - +
428C ALA* 4.4 15.9 - - + +
429C LEU* 5.7 0.2 - - + -
432C LEU* 4.0 34.5 - - + -
439C PHE* 3.7 10.6 - - + -
443C CYS* 5.5 2.7 - - - -
446C LYS* 6.1 2.2 - - + -
447C TYR* 4.1 4.0 - - - +
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Residues in contact with GLY 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 4.4 2.4 - - - +
175C ALA* 3.8 10.4 - - - +
180C ASP* 2.8 23.4 + - - -
181C ILE 3.1 0.2 - - - -
182C PRO* 1.3 69.7 - - - +
184C LEU* 1.3 53.7 + - - +
186C TYR* 4.0 1.0 - - - +
187C SER* 2.6 39.7 + - - -
447C TYR* 3.1 29.3 + - - -
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Residues in contact with LEU 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PHE* 3.9 29.2 - - + -
175C ALA* 4.0 16.8 - - + -
176C VAL* 4.0 16.8 - - + +
179C ASN* 5.8 0.7 - - - -
180C ASP 3.1 7.7 + - - +
181C ILE* 3.0 40.5 + - + +
183C GLY* 1.3 75.1 - - - +
185C LEU* 1.3 56.8 + - - +
187C SER* 3.2 2.6 + - - -
188C ILE* 2.9 46.8 + - + +
242C ILE* 4.0 19.3 - - + +
245C ILE* 5.5 2.5 - - + -
246C ALA* 4.8 11.2 - - + +
249C ILE* 4.3 12.1 - - + +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181C ILE 3.0 11.1 + - - +
182C PRO* 3.3 11.0 - - + +
184C LEU* 1.3 75.6 - - - +
186C TYR* 1.3 59.9 + - - +
189C GLY* 2.9 28.1 + - - -
190C CYS* 3.4 3.5 + - - -
249C ILE* 4.1 17.5 - - + +
390C TYR* 3.6 30.3 - - + +
393C ALA* 3.7 31.4 - - + +
394C LYS* 3.9 18.8 - - + +
429C LEU* 4.2 13.9 - - + -
432C LEU* 3.5 30.3 - - + -
439C PHE* 3.9 3.8 - - + -
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Residues in contact with TYR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 4.4 4.0 - - + -
182C PRO 2.9 15.6 + - - +
183C GLY* 4.0 5.2 - - - +
184C LEU 3.3 0.2 - - - -
185C LEU* 1.3 76.2 - - - +
187C SER* 1.3 59.6 + - - +
190C CYS* 2.8 33.6 + - + +
191C LEU* 2.9 52.1 + - + +
439C PHE* 3.9 17.0 - + + -
440C MET* 4.0 25.9 + - + -
443C CYS* 3.5 39.3 - - + -
444C LEU* 3.7 20.9 - - - +
447C TYR* 3.7 18.8 - + + -
454C PHE* 3.7 15.2 - + - -
461C PHE* 4.1 7.4 - - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C GLY* 3.3 23.4 - - - -
171C VAL* 3.9 8.3 - - - -
172C PHE* 3.4 25.8 - - - +
183C GLY 2.6 24.6 + - - -
184C LEU* 3.2 5.9 + - - -
186C TYR* 1.3 78.5 - - - +
188C ILE* 1.3 59.3 + - - +
191C LEU* 3.6 13.5 - - - +
192C GLY 3.0 23.7 + - - -
222C GLN* 3.1 10.8 + - - -
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Residues in contact with ILE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PHE* 4.1 14.8 - - + -
184C LEU* 2.9 29.9 + - + +
187C SER* 1.3 79.7 + - - +
189C GLY* 1.3 64.1 + - - +
190C CYS 3.4 0.5 + - - -
192C GLY* 3.5 14.7 - - - -
219C ASP* 3.5 20.6 - - - +
222C GLN* 3.6 29.4 - - + +
223C ALA 5.0 0.7 - - - +
246C ALA* 4.0 34.3 - - + +
249C ILE* 3.7 11.0 - - + +
250C SER* 3.6 22.2 - - - -
253C ARG* 3.5 13.3 - - + +
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Residues in contact with GLY 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU 2.9 14.6 + - - -
188C ILE* 1.3 81.1 - - - +
190C CYS* 1.3 61.3 + - - +
193C SER* 2.7 25.6 + - - -
249C ILE* 3.4 19.0 - - - +
252C PRO* 6.0 0.2 - - - +
253C ARG* 4.8 1.8 - - - -
389C ILE* 3.7 13.7 - - - +
393C ALA* 4.0 12.6 - - - -
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Residues in contact with CYS 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU* 3.9 10.1 - - - -
186C TYR* 2.8 21.6 + - + +
188C ILE 3.3 0.4 - - - -
189C GLY* 1.3 78.3 - - - +
191C LEU* 1.3 67.2 + - - +
192C GLY 3.2 0.7 - - - -
193C SER* 3.3 2.7 + - - -
194C ILE* 2.9 31.4 + - - +
389C ILE* 4.2 6.0 - - + +
390C TYR* 4.1 25.1 - - - -
439C PHE* 4.0 18.6 - - - -
440C MET* 3.7 34.1 - - + -
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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