Contacts of the helix formed by residues 180 - 190 (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 ASP 180 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174G TYR* 4.4 6.7 - - + -
175G ALA* 3.0 26.2 + - + +
178G ARG* 3.0 9.9 - - + +
179G ASN* 1.3 74.0 - - - +
181G ILE* 1.3 49.2 + - - +
182G PRO* 3.3 12.1 - - - +
183G GLY* 2.8 18.9 + - - -
184G LEU* 2.8 33.4 + - - +
446G LYS* 4.3 8.7 + - - -
447G TYR* 2.5 39.4 + - - -
450G GLU* 4.9 0.3 - - - +
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Residues in contact with ILE 181 (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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179G ASN 2.8 20.6 + - - +
180G ASP* 1.3 70.1 - - - +
182G PRO* 1.4 71.5 - - + +
184G LEU* 3.0 26.3 + - + +
185G LEU* 2.9 20.1 + - - +
242G ILE* 4.0 26.9 - - + -
245G ILE* 4.6 12.3 - - + -
249G ILE* 5.0 0.8 - - + +
424G ASP 5.5 0.4 - - - -
425G ALA* 3.7 32.3 - - + +
428G ALA* 4.7 6.7 - - + -
429G LEU* 3.7 38.1 - - + -
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Residues in contact with PRO 182 (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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180G ASP* 3.3 13.5 - - - +
181G ILE* 1.4 96.1 - - + +
183G GLY* 1.3 54.0 - - - +
185G LEU* 3.1 11.4 + - + +
186G TYR* 2.8 25.2 + - - +
428G ALA* 4.8 14.8 - - + +
432G LEU* 4.3 33.4 - - + -
439G PHE* 3.6 13.9 - - + -
443G CYS* 5.5 2.2 - - - -
446G LYS* 5.9 2.7 - - - -
447G TYR* 4.1 4.0 - - - +
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Residues in contact with GLY 183 (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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171G VAL* 4.5 2.7 - - - +
175G ALA* 4.0 10.0 - - - +
180G ASP* 2.8 20.3 + - - -
182G PRO* 1.3 72.5 - - - +
184G LEU* 1.3 58.5 + - - +
185G LEU 3.1 0.2 - - - -
186G TYR* 4.0 1.5 - - - +
187G SER* 2.5 38.6 + - - -
447G TYR* 3.2 27.0 + - - -
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Residues in contact with LEU 184 (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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172G PHE* 4.0 19.3 - - + -
175G ALA* 4.2 2.7 - - + -
176G VAL* 3.9 34.8 - - + +
179G ASN* 5.5 1.1 - - - -
180G ASP 2.8 15.6 + - - +
181G ILE* 3.0 41.7 + - + +
183G GLY* 1.3 71.1 - - - +
185G LEU* 1.3 55.1 + - - +
187G SER* 3.1 3.8 + - - -
188G ILE* 3.0 39.7 + - + +
242G ILE* 4.0 22.2 - - + +
245G ILE* 5.4 1.8 - - + -
246G ALA* 4.6 18.4 - - + +
249G ILE* 4.3 11.8 - - + +
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Residues in contact with LEU 185 (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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181G ILE 2.9 12.0 + - - +
182G PRO* 3.1 10.5 + - + +
184G LEU* 1.3 73.8 - - - +
186G TYR* 1.3 64.9 + - - +
189G GLY* 3.1 17.2 + - - -
190G CYS* 3.5 7.1 + - - -
249G ILE* 4.2 15.0 - - + -
390G TYR* 4.1 22.2 - - + +
393G ALA* 3.7 31.2 - - + +
394G LYS* 3.8 25.4 - - + +
429G LEU* 3.8 17.3 - - + -
432G LEU* 3.8 28.3 - - + -
439G PHE* 4.1 4.5 - - + -
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Residues in contact with TYR 186 (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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171G VAL* 4.3 4.5 - - + -
182G PRO 2.8 17.3 + - - +
183G GLY* 3.3 5.6 + - - +
185G LEU* 1.3 71.3 - - - +
187G SER* 1.3 61.7 + - - +
190G CYS* 3.0 14.2 + - + +
191G LEU* 2.8 68.1 + - + +
439G PHE* 3.8 18.8 - + + -
440G MET* 3.8 26.9 + - + -
443G CYS* 3.4 34.3 - - + -
444G LEU* 3.8 14.4 - - - +
447G TYR* 3.8 24.0 - + + -
454G PHE* 3.8 18.2 - + - -
461G PHE* 4.0 11.4 - - - -
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Residues in contact with SER 187 (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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168G GLY* 3.3 25.3 - - - -
171G VAL* 3.9 8.1 - - - -
172G PHE* 3.4 24.8 - - - +
183G GLY 2.5 24.8 + - - -
184G LEU* 3.1 7.8 + - - -
186G TYR* 1.3 77.8 - - - +
188G ILE* 1.3 62.8 + - - +
191G LEU* 3.7 11.9 - - - -
192G GLY 2.9 25.5 + - - -
222G GLN* 3.2 9.7 + - - -
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Residues in contact with ILE 188 (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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172G PHE* 4.0 18.6 - - + -
184G LEU* 3.0 22.7 + - + +
187G SER* 1.3 89.4 + - - +
189G GLY* 1.3 62.9 + - - +
192G GLY* 3.2 18.2 - - - -
193G SER 3.5 2.1 + - - -
219G ASP* 3.6 12.8 - - - +
222G GLN* 3.4 37.9 - - + +
223G ALA 4.9 0.2 - - - +
246G ALA* 4.0 34.3 - - + +
249G ILE* 3.7 10.1 - - + +
250G SER* 3.7 20.6 - - - -
253G ARG* 3.6 9.8 - - + +
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Residues in contact with GLY 189 (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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185G LEU 3.1 12.4 + - - -
188G ILE* 1.3 81.2 - - - +
190G CYS* 1.3 59.6 + - - +
193G SER* 2.6 27.8 + - - -
249G ILE* 3.6 17.3 - - - +
252G PRO* 5.4 0.4 - - - +
253G ARG* 4.7 3.8 - - - -
389G ILE* 4.1 10.8 - - - +
393G ALA* 4.0 13.9 - - - +
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Residues in contact with CYS 190 (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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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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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