Contacts of the strand formed by residues 196 - 206 (chain B) in PDB entry 1IS0
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 GLY 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A LYS 3.2 10.5 - - - -
240A ARG* 3.8 9.8 - - - +
191B PHE* 3.5 16.8 - - - -
192B ASP 2.8 23.1 + - - -
194B ALA 3.5 1.4 - - - -
195B LYS* 1.3 76.6 - - - +
197B LEU* 1.3 66.6 + - - -
198B ASN* 3.1 17.2 + - - -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LYS* 2.7 47.1 + - + +
233A HIS* 3.5 25.5 + - - +
163B LEU* 4.0 25.3 - - + +
164B ASN 4.9 0.9 - - - +
165B PRO* 4.1 18.6 - - + +
167B ASN 5.5 7.0 - - - +
169B ARG* 6.6 0.7 - - - -
189B SER* 6.2 3.1 - - - -
190B ASP 3.5 11.0 - - - +
191B PHE* 3.6 21.0 - - + -
195B LYS 4.4 0.3 - - - +
196B GLY* 1.3 72.4 - - - -
198B ASN* 1.3 62.3 + - - +
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Residues in contact with ASN 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 4.1 6.6 - - - +
189B SER* 3.6 2.1 - - - -
190B ASP* 2.7 51.2 + - - +
191B PHE* 3.8 4.8 - - - +
192B ASP* 4.1 10.9 + - - -
195B LYS* 4.2 17.6 - - + +
196B GLY 3.1 20.5 + - - +
197B LEU* 1.3 76.2 - - - +
199B VAL* 1.3 63.0 + - - +
200B LYS* 2.8 38.1 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B GLU* 3.9 27.2 + - + +
162B LEU* 3.8 35.0 - - + -
163B LEU* 3.5 25.3 - - + +
188B VAL 3.4 11.4 - - - +
189B SER* 4.8 1.3 - - - -
198B ASN* 1.3 79.5 - - - +
200B LYS* 1.3 70.3 + - - +
201B HIS* 3.4 42.7 + - + +
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LEU 3.6 2.1 - - - +
187B SER* 3.4 2.4 - - - -
188B VAL* 2.8 33.4 + - - +
190B ASP* 2.7 28.9 + - + +
192B ASP* 5.0 1.8 + - - -
195B LYS* 4.7 12.3 - - - +
198B ASN* 2.8 30.3 + - - +
199B VAL* 1.3 75.6 - - - +
201B HIS* 1.3 60.2 + - - +
202B TYR* 3.8 20.0 - - + -
238B CYS* 3.6 27.4 - - + -
353D GLU* 3.6 35.9 - - + +
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Residues in contact with HIS 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ARG* 3.5 38.6 - - + +
158B SER* 3.2 26.9 - - - -
159B GLU* 2.8 28.6 + - + +
175B ARG* 2.9 22.9 + - - +
185B CYS* 5.2 0.7 - - + -
186B LEU 3.6 2.5 - - - -
187B SER* 2.7 21.4 + - - +
199B VAL* 3.4 26.7 + - + +
200B LYS* 1.3 73.5 - - - +
202B TYR* 1.3 58.7 + - - +
203B LYS 4.0 0.4 - - - -
352D AY0 3.4 14.2 + - + +
353D GLU* 2.7 32.9 + - - +
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Residues in contact with TYR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B CYS* 3.2 4.3 - - - -
186B LEU* 2.8 48.6 + - + +
188B VAL* 4.3 8.7 - - + -
200B LYS* 3.8 20.6 - - + -
201B HIS* 1.3 73.6 - - - +
203B LYS* 1.3 65.3 + - - +
204B ILE* 3.4 1.2 + - - +
214B ILE* 3.7 35.7 - - + -
236B GLY 4.8 0.8 + - - -
237B LEU* 3.4 30.7 - - + -
238B CYS* 2.8 35.9 + - - +
352D AY0 4.5 0.2 - - - -
353D GLU* 3.3 50.0 + - + +
354D GLU 4.2 2.2 - - - -
355D ILE* 4.2 12.6 - - + -
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B SER* 3.6 10.3 - - - -
179B THR* 3.0 19.8 + - - -
180B THR* 2.8 35.4 + - + +
183B ALA* 4.8 2.9 - - + -
184B TYR 3.8 7.9 - - - +
185B CYS* 4.2 1.3 - - - -
202B TYR* 1.3 71.7 - - - +
204B ILE* 1.3 66.9 + - - +
205B ARG* 2.9 43.6 + - + +
213B TYR 4.1 1.7 - - - +
214B ILE* 4.1 7.8 - - - +
352D AY0 3.3 48.4 + - + -
353D GLU 4.7 3.0 + - - -
354D GLU* 5.1 3.3 + - - +
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 4.6 6.3 - - + -
183B ALA* 3.6 11.1 - - - +
184B TYR* 2.7 39.8 + - + +
185B CYS* 4.1 5.8 - - - +
186B LEU* 3.9 24.5 - - + +
202B TYR 3.9 7.9 - - - +
203B LYS* 1.3 74.4 - - - +
205B ARG* 1.3 68.6 + - - +
212B PHE* 4.1 16.6 - - + -
213B TYR 3.4 14.1 - - - +
214B ILE* 4.0 14.1 - - + -
223B LEU* 4.1 17.5 - - + -
226B LEU* 3.7 29.2 - - + -
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Residues in contact with ARG 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B ALA* 5.3 2.7 - - - -
203B LYS* 2.9 44.2 + - + +
204B ILE* 1.3 77.3 - - - +
206B LYS* 1.3 62.5 + - - +
212B PHE* 3.4 4.0 - - - -
213B TYR* 2.9 73.3 + - + +
214B ILE* 3.4 20.7 + - - +
354D GLU* 2.9 33.9 + - - -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLY 4.8 17.3 - - - +
183B ALA* 5.8 2.8 - - - +
184B TYR* 5.3 2.7 - - + -
204B ILE 4.2 0.4 + - - -
205B ARG* 1.3 77.3 - - - +
207B LEU* 1.3 80.9 + - - +
208B ASP 5.5 0.8 + - - -
210B GLY* 4.2 12.9 - - - +
211B GLY 3.1 18.2 - - - +
212B PHE* 3.4 31.9 - - + -
213B TYR* 4.9 1.0 - - - -
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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