Contacts of the strand formed by residues 168 - 176 (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 ARG 168 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124B ASP* 2.8 40.0 + - - -
125B ILE 3.8 1.8 + - - -
126B LEU* 3.5 10.4 - - - +
145B THR 3.2 3.3 + - - +
146B GLY* 3.5 26.2 - - - -
147B LEU 2.9 26.9 + - - +
148B THR* 3.0 17.8 + - - -
166B LEU* 3.7 5.6 - - - +
167B ASN* 1.4 90.4 + - - +
169B LEU* 1.3 62.9 + - - +
170B GLU* 3.0 28.5 + - + +
188B LEU* 4.0 1.3 - - - -
190B GLN* 3.4 30.5 - - + +
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Residues in contact with LEU 169 (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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147B LEU* 3.4 39.0 - - + +
160B LEU* 3.9 7.6 - - + -
166B LEU* 4.3 6.3 - - + -
168B ARG* 1.3 75.9 - - - +
170B GLU* 1.3 63.2 + - - +
171B LEU* 3.8 26.5 - - + -
182B LEU* 3.5 31.4 - - + -
185B LEU* 3.9 17.5 - - + -
188B LEU* 3.7 15.2 - - + +
190B GLN 3.0 7.1 + - - +
191B LEU* 3.2 16.9 - - + +
192B SER* 3.0 22.9 + - - -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 5.3 0.3 - - - +
147B LEU 3.0 7.1 + - - +
148B THR* 2.7 33.3 + - - +
149B LEU* 2.8 31.4 + - - +
150B PHE* 3.0 26.4 + - + -
168B ARG* 3.0 20.0 + - + -
169B LEU* 1.3 77.3 - - - +
171B LEU* 1.3 61.3 + - - +
172B SER 3.8 1.3 - - - -
190B GLN* 3.5 24.9 + - + +
192B SER* 3.4 12.9 + - - +
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Residues in contact with LEU 171 (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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135B ILE* 5.4 0.2 - - + -
149B LEU* 3.8 34.5 - - + -
150B PHE* 4.3 0.2 - - - +
154B ILE* 4.4 6.5 - - + -
157B ILE* 4.4 12.8 - - + -
160B LEU* 3.8 18.2 - - + -
169B LEU* 3.8 32.3 - - + -
170B GLU* 1.3 75.4 - - - +
172B SER* 1.3 68.5 + - - +
174B ASN* 3.0 23.8 + - - +
176B ILE* 3.8 24.9 - - + -
182B LEU* 4.5 3.1 - - + -
191B LEU* 5.1 0.4 - - + -
192B SER 2.8 16.4 + - - +
193B PHE* 3.6 10.1 - - + -
194B GLY 3.4 10.2 + - - +
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Residues in contact with SER 172 (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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150B PHE* 3.1 14.4 - - - +
151B ASN 3.0 18.7 + - - -
171B LEU* 1.3 81.1 - - - +
173B SER* 1.3 70.9 + - - +
174B ASN* 3.4 0.2 + - - -
192B SER* 3.3 25.3 + - - -
193B PHE* 3.7 6.4 + - - +
194B GLY 3.9 9.0 - - - +
195B ASN* 5.2 0.4 - - - -
213B ASP* 4.5 8.0 + - - -
215B SER 5.4 4.0 + - - -
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Residues in contact with SER 173 (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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150B PHE* 5.3 0.4 - - - -
151B ASN* 3.0 43.9 + - - -
152B ASN 3.4 7.8 + - - +
172B SER* 1.3 78.8 - - - +
174B ASN* 1.3 58.1 + - - +
195B ASN* 3.0 28.8 + - - +
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Residues in contact with ASN 174 (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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149B LEU 3.0 22.6 + - - -
150B PHE* 3.8 0.6 - - - +
152B ASN* 3.0 39.5 - - - +
154B ILE* 3.0 27.3 + - - +
171B LEU* 3.0 27.4 + - - +
172B SER 3.3 7.9 + - - -
173B SER* 1.3 80.1 - - - +
175B THR* 1.3 68.4 + - - +
176B ILE* 4.0 6.3 - - + -
194B GLY 3.2 14.7 + - - +
195B ASN* 3.0 22.0 + - - +
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Residues in contact with THR 175 (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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153B GLN* 4.2 11.8 + - + +
154B ILE 2.8 15.3 + - - +
155B THR* 2.8 39.7 + - - +
174B ASN* 1.3 76.0 - - - +
176B ILE* 1.3 61.9 + - - +
177B SER* 3.6 1.7 + - - -
195B ASN* 4.2 2.2 - - + +
196B GLN* 4.4 20.0 - - + +
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Residues in contact with ILE 176 (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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154B ILE* 3.5 14.8 - - + +
155B THR 3.9 15.3 - - - +
157B ILE* 3.6 28.3 - - + -
171B LEU* 3.8 31.9 - - + +
174B ASN* 4.0 7.9 - - + -
175B THR* 1.3 77.9 - - - +
177B SER* 1.3 61.5 + - - +
178B ASP 3.7 22.0 - - - +
179B ILE* 4.0 18.4 - - + -
193B PHE* 4.6 3.8 - - + -
194B GLY 3.2 18.3 + - - +
195B ASN 3.7 1.1 + - - +
196B GLN* 2.8 27.3 + - - -
197B VAL* 3.4 7.5 + - + +
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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