Contacts of the strand formed by residues 192 - 196 (chain B) in PDB entry 2I6A
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 ILE 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B ARG 3.0 15.3 + - - +
164B VAL* 3.4 12.0 - - + +
165B CYS* 2.7 35.0 + - - +
186B ALA* 4.5 2.0 - - - -
191B ARG* 1.3 73.9 - - - +
193B PHE* 1.3 58.4 + - - +
194B THR* 4.0 16.2 - - + -
218B ASP* 3.8 20.2 - - + -
219B ILE* 4.4 7.6 - - + -
258B ARG* 4.1 29.6 - - - +
310B LEU* 4.1 30.1 - - + +
313B ASP* 6.2 0.2 - - - +
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Residues in contact with PHE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B CYS* 3.9 19.1 - - + -
167B ILE* 3.5 33.2 - - + -
179B VAL* 3.9 10.5 - - + -
182B VAL* 4.4 2.7 - - + -
183B ALA* 3.2 45.3 - - + +
186B ALA* 4.0 14.1 - - + -
191B ARG 3.6 1.0 + - - -
192B ILE* 1.3 69.4 - - - +
194B THR* 1.3 78.9 + - - +
195B LEU* 4.3 8.7 - - + -
213B VAL* 3.8 16.2 - - + -
216B TYR 3.7 20.9 - - - +
217B VAL* 3.8 12.0 - - + -
218B ASP* 2.9 37.2 + - - +
219B ILE 3.2 6.4 + - - -
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B VAL* 4.6 7.0 - - + -
165B CYS 2.6 24.8 + - - +
166B TYR* 3.0 21.3 - - - +
167B ILE 3.1 21.8 + - - +
192B ILE* 4.0 13.9 - - + +
193B PHE* 1.3 91.5 - - - +
195B LEU* 1.3 61.8 + - - +
219B ILE* 3.4 36.3 - - + -
221B PHE* 3.9 14.4 - - + -
307B LEU* 3.9 5.9 - - + +
310B LEU* 4.6 2.9 - - + -
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 4.1 4.3 - - - -
167B ILE* 3.2 26.0 - - + +
168B ALA 4.7 0.4 - - - +
169B GLY* 4.5 7.9 - - - +
172B LEU* 4.8 8.7 - - + -
179B VAL* 4.4 15.7 - - + -
193B PHE* 4.3 17.3 - - + -
194B THR* 1.3 73.7 - - - +
196B ASN* 1.3 72.8 + - - +
210B LEU* 3.6 31.9 - - + -
213B VAL* 4.5 9.0 - - + -
214B MET* 5.1 0.9 - - + -
217B VAL* 4.1 28.0 - - + +
219B ILE 3.1 6.1 + - - -
220B LEU* 3.6 14.8 - - + +
221B PHE* 2.9 27.4 + - - -
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Residues in contact with ASN 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B SER* 5.4 2.1 + - - -
166B TYR* 2.9 28.9 + - + +
167B ILE 3.4 5.1 + - - -
168B ALA* 3.8 4.7 - - + -
169B GLY* 2.9 24.6 + - - -
195B LEU* 1.3 85.3 - - - +
197B LEU* 1.3 62.8 + - - +
198B SER* 2.8 37.0 + - - +
210B LEU* 5.1 0.7 - - - +
220B LEU* 4.6 2.2 - - - -
221B PHE* 3.5 17.1 - - - +
222B GLY* 3.8 9.2 - - - +
226B GLU* 4.0 1.7 - - - +
299B GLY 6.0 0.8 - - - -
300B ASP* 5.4 4.4 + - - -
303B VAL* 3.6 21.4 - - - +
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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
------------------------------------------------------------
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