Contacts of the helix formed by residues 180 - 190 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174K TYR* 4.8 5.3 - - + -
175K ALA* 3.1 26.4 + - + +
178K ARG* 4.0 10.8 - - + +
179K ASN* 1.3 75.8 - - - +
181K ILE* 1.3 62.1 + - - +
182K PRO* 3.1 14.0 - - - +
183K GLY* 2.9 13.3 + - - -
184K LEU* 3.1 21.1 + - - +
446K LYS* 4.1 7.8 - - - -
447K TYR* 2.5 35.1 + - - -
450K GLU* 5.3 0.3 - - - +
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Residues in contact with ILE 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K ASN* 3.2 17.2 + - + +
180K ASP* 1.3 69.3 - - - +
182K PRO* 1.4 76.2 - - + +
184K LEU* 3.1 22.0 + - + +
185K LEU* 2.9 20.8 + - - +
242K ILE* 4.0 23.3 - - + -
245K ILE* 4.2 20.4 - - + -
249K ILE* 5.0 1.5 - - + +
425K ALA* 3.7 30.5 - - + -
428K ALA* 4.5 9.6 - - + -
429K LEU* 4.0 30.7 - - + -
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Residues in contact with PRO 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K ASP* 3.1 11.9 - - - +
181K ILE* 1.4 92.5 - - + +
183K GLY* 1.3 56.0 + - - +
185K LEU* 3.1 9.8 + - + +
186K TYR* 2.9 29.9 + - - +
428K ALA* 4.4 17.0 - - + +
432K LEU* 4.4 32.1 - - + -
439K PHE* 3.8 9.8 - - + -
443K CYS* 5.5 3.1 - - - -
446K LYS* 6.1 2.0 - - + -
447K TYR* 4.0 6.3 - - + +
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Residues in contact with GLY 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K VAL* 4.1 3.0 - - - +
175K ALA* 3.7 14.8 - - - -
180K ASP* 2.9 16.0 + - - -
182K PRO* 1.3 75.7 - - - +
184K LEU* 1.3 51.2 + - - +
186K TYR* 3.9 0.9 - - - +
187K SER* 2.6 39.8 + - - -
447K TYR* 3.1 27.9 + - - -
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Residues in contact with LEU 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PHE* 3.8 29.4 - - + -
175K ALA* 3.9 19.3 - - + +
176K VAL* 4.0 14.1 - - + +
179K ASN* 5.4 0.7 - - - -
180K ASP 3.1 18.0 + - - +
181K ILE* 3.1 30.9 + - + +
183K GLY* 1.3 72.3 - - - +
185K LEU* 1.3 65.8 + - - +
187K SER* 3.7 3.1 - - - -
188K ILE* 3.0 39.3 + - + +
242K ILE* 4.1 16.6 - - + -
245K ILE* 5.6 1.8 - - + -
246K ALA* 4.6 13.0 - - + +
249K ILE* 4.1 14.3 - - + +
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Residues in contact with LEU 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K ILE 2.9 11.7 + - - +
182K PRO* 3.3 11.0 - - + +
184K LEU* 1.3 76.5 - - - +
186K TYR* 1.3 57.2 + - - +
189K GLY* 3.0 30.0 + - - -
190K CYS* 3.4 3.7 + - - -
249K ILE* 4.0 15.0 - - + +
390K TYR* 3.3 35.2 - - + +
393K ALA* 3.6 41.5 - - + +
394K LYS* 3.8 13.0 - - + +
429K LEU* 4.4 11.9 - - + -
432K LEU* 3.8 23.3 - - + -
439K PHE* 3.9 4.3 - - + -
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Residues in contact with TYR 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K VAL* 4.2 5.8 - - + -
182K PRO 2.9 15.5 + - - +
183K GLY 3.9 3.6 - - - +
185K LEU* 1.3 77.2 - - - +
187K SER* 1.3 58.9 + - - +
190K CYS* 3.0 17.9 + - + +
191K LEU* 2.8 62.0 + - + +
439K PHE* 4.0 11.6 - + + -
440K MET* 4.0 27.7 + - + +
443K CYS* 3.4 39.5 - - + -
444K LEU* 3.6 20.4 - - - +
447K TYR* 3.6 26.0 - + + -
454K PHE* 3.7 14.7 - + - -
461K PHE* 4.3 8.0 - - - -
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Residues in contact with SER 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K GLY* 3.4 25.1 - - - -
171K VAL* 3.8 10.8 - - - -
172K PHE* 3.4 28.4 - - - +
183K GLY 2.6 23.7 + - - -
184K LEU* 3.5 5.7 + - - -
186K TYR* 1.3 77.1 - - - +
188K ILE* 1.3 60.4 + - - +
191K LEU* 4.1 9.2 - - - -
192K GLY 3.0 19.6 + - - -
222K GLN* 3.0 13.1 + - - -
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Residues in contact with ILE 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172K PHE* 4.1 17.9 - - + -
184K LEU* 3.0 23.2 + - + +
187K SER* 1.3 80.3 - - - +
189K GLY* 1.3 64.5 + - - +
190K CYS 3.4 0.2 - - - -
192K GLY* 3.4 13.9 - - - -
219K ASP* 3.5 14.8 - - - +
222K GLN* 3.4 38.8 - - + +
223K ALA 4.9 0.4 - - - +
246K ALA* 4.1 30.1 - - + +
249K ILE* 3.8 8.3 - - + +
250K SER* 3.6 22.4 - - - +
253K ARG* 3.3 18.2 - - + +
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Residues in contact with GLY 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K LEU 3.0 14.8 + - - -
188K ILE* 1.3 77.7 - - - +
190K CYS* 1.3 60.2 + - - +
193K SER* 2.4 28.5 + - - -
249K ILE* 3.6 9.6 - - - +
252K PRO* 5.7 0.2 - - - -
253K ARG* 4.9 1.8 - - - -
389K ILE* 3.8 12.5 - - - +
393K ALA* 3.8 22.4 - - - -
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Residues in contact with CYS 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K LEU* 3.4 7.4 + - - -
186K TYR* 3.0 15.5 + - + +
189K GLY* 1.3 79.7 - - - +
191K LEU* 1.3 68.3 + - - +
192K GLY 3.3 0.7 - - - -
193K SER* 3.2 2.8 + - - -
194K ILE* 3.1 28.4 + - + +
389K ILE* 4.5 7.0 - - + -
390K TYR* 4.0 26.2 - - - -
439K PHE* 4.0 22.0 - - - -
440K MET* 3.6 36.3 - - + -
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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