Contacts of the strand formed by residues 190 - 195 (chain B) in PDB entry 1O6V
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 GLN 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B ASN 3.1 8.6 + - - +
168B ARG* 3.4 20.2 - - + +
169B LEU 3.0 24.0 + - - -
170B GLU* 3.5 29.8 + - + -
188B LEU* 4.0 3.2 - - - +
189B GLN* 1.6 62.5 - - + +
191B LEU* 1.3 66.7 + - - +
209B LEU* 4.2 0.4 - - - -
211B ARG* 3.3 33.4 + - + +
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Residues in contact with LEU 191 (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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169B LEU* 3.2 37.0 - - + +
171B LEU* 5.1 0.9 - - + -
182B LEU* 3.9 14.8 - - + -
188B LEU* 4.1 7.6 - - + -
190B GLN* 1.3 79.1 - - - +
192B SER* 1.3 74.5 + - - +
193B PHE* 3.9 15.7 - - + -
203B LEU* 3.6 31.6 - - + -
206B LEU* 4.2 12.1 - - + -
209B LEU* 3.6 17.2 - - + +
211B ARG 3.0 7.1 + - - +
212B LEU* 3.3 13.9 - - + +
213B ASP* 3.0 22.7 + - - +
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Residues in contact with SER 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PHE* 5.8 0.2 - - - +
169B LEU 3.0 6.6 + - - +
170B GLU* 3.4 24.3 + - - +
171B LEU* 2.8 23.4 + - - +
172B SER* 3.3 17.7 + - - -
191B LEU* 1.3 79.8 - - - +
193B PHE* 1.3 68.0 + - - +
213B ASP* 3.1 27.6 - - - -
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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
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171B LEU* 3.6 25.1 - - + -
172B SER* 3.7 9.8 + - - -
176B ILE* 4.6 5.8 - - + -
179B ILE* 3.8 24.0 - - + -
182B LEU* 3.9 14.6 - - + -
191B LEU* 3.9 23.8 - - + -
192B SER* 1.3 82.2 - - - +
194B GLY* 1.3 58.1 + - - +
197B VAL* 3.7 39.5 - - + -
200B LEU* 3.7 16.4 - - + -
203B LEU* 4.1 4.9 - - + -
212B LEU* 4.3 1.6 - - + -
213B ASP 3.4 7.6 + - - +
214B ILE* 3.5 29.8 - - + -
215B SER 4.1 5.0 - - - +
217B ASN* 2.9 23.3 + - - -
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU 3.4 6.3 + - - +
172B SER* 3.9 0.6 - - - +
174B ASN* 3.2 27.1 + - - +
176B ILE* 3.2 18.5 + - - +
193B PHE* 1.3 79.0 - - - +
195B ASN* 1.3 72.5 + - - -
196B GLN 3.8 1.6 - - - -
215B SER 4.9 0.2 - - - -
217B ASN* 3.2 11.9 - - - -
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Residues in contact with ASN 195 (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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172B SER* 5.2 0.2 - - - -
173B SER* 3.0 40.7 + - - +
174B ASN 3.0 17.2 + - - +
175B THR* 4.2 0.6 - - + +
176B ILE 3.7 2.4 + - - +
194B GLY* 1.3 73.1 + - - -
196B GLN* 1.7 63.8 + - + +
215B SER 4.8 1.8 + - - -
216B SER* 3.1 37.5 + - - +
217B ASN* 3.3 15.7 - - - -
218B LYS* 4.4 2.6 - - - +
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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