Contacts of the strand formed by residues 168 - 176 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ASP* 2.8 40.0 + - - -
125A ILE 3.9 1.6 + - - -
126A LEU* 3.6 10.8 - - - +
145A THR 3.2 4.6 + - - +
146A GLY* 3.4 25.3 - - - -
147A LEU 2.9 28.2 + - - +
148A THR* 3.0 28.9 + - - -
166A LEU* 3.7 4.7 - - - +
167A ASN* 1.3 88.4 + - - +
169A LEU* 1.3 63.3 + - - +
170A GLU* 3.3 23.7 + - + +
188A LEU* 4.1 1.1 - - - -
190A GLN* 3.6 27.4 - - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 3.4 37.7 - - + +
160A LEU* 4.0 8.1 - - + -
166A LEU* 4.2 6.5 - - + -
168A ARG* 1.3 76.6 - - - +
170A GLU* 1.3 64.3 + - - +
171A LEU* 3.8 27.4 - - + -
182A LEU* 3.6 31.4 - - + -
185A LEU* 3.9 17.9 - - + -
188A LEU* 3.7 14.8 - - + -
190A GLN 3.2 6.5 + - - +
191A LEU* 3.3 16.7 - - + +
192A SER 3.1 22.2 + - - -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU 3.0 8.7 + - - +
148A THR* 3.2 34.5 + - - +
149A LEU* 2.8 32.2 + - - +
150A PHE* 3.1 26.1 + - + -
168A ARG* 3.3 27.3 - - + +
169A LEU* 1.3 76.8 - - - +
171A LEU* 1.3 61.1 + - - +
172A SER 3.7 1.3 - - - -
190A GLN* 4.4 6.5 - - + +
191A LEU 6.0 0.2 - - - -
192A SER* 3.4 15.7 - - - +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 5.5 0.2 - - + -
149A LEU* 3.9 34.8 - - + -
150A PHE* 4.3 0.2 - - - +
154A ILE* 4.5 6.3 - - + -
157A ILE* 4.4 12.6 - - + -
160A LEU* 3.8 19.3 - - + -
169A LEU* 3.8 31.2 - - + -
170A GLU* 1.3 73.9 - - - +
172A SER* 1.3 67.0 + - - +
174A ASN* 3.0 23.0 + - - +
176A ILE* 3.7 24.9 - - + -
182A LEU* 4.6 2.7 - - + -
191A LEU* 5.1 0.4 - - + -
192A SER 2.7 16.9 + - - +
193A PHE* 3.6 10.8 - - + -
194A GLY 3.3 10.4 + - - +
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Residues in contact with SER 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.0 14.4 - - - +
151A ASN 3.0 18.7 + - - -
170A GLU 3.7 0.4 - - - -
171A LEU* 1.3 81.4 - - - +
173A SER* 1.3 71.3 + - - +
174A ASN* 3.4 0.3 + - - -
192A SER* 3.3 24.8 + - - -
193A PHE* 3.7 7.4 + - - +
194A GLY 3.8 8.3 - - - +
213A ASP* 4.3 9.7 + - - -
215A SER 5.3 3.3 + - - -
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 5.2 0.4 - - - -
151A ASN* 3.0 46.2 + - - -
152A ASN 3.3 8.3 + - - +
171A LEU 3.6 0.2 + - - -
172A SER* 1.3 76.6 - - - +
174A ASN* 1.3 58.3 + - - +
195A ASN* 3.0 28.2 + - - +
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Residues in contact with ASN 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU 3.0 23.0 + - - -
152A ASN* 2.9 38.9 - - - +
154A ILE* 3.0 28.5 + - - +
171A LEU* 3.0 26.2 + - - +
172A SER 3.3 9.3 + - - -
173A SER* 1.3 78.7 + - - +
175A THR* 1.3 67.8 + - - +
176A ILE* 4.0 6.5 - - + -
194A GLY 3.1 15.2 + - - +
195A ASN* 3.0 23.0 + - - +
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASN 5.8 0.7 - - - +
153A GLN* 4.2 11.3 + - + -
154A ILE 2.8 14.9 + - - +
155A THR* 2.8 37.5 + - - +
174A ASN* 1.3 76.2 - - - +
176A ILE* 1.3 62.3 + - - +
177A SER* 3.5 3.6 + - - -
195A ASN 4.1 1.6 - - - +
196A GLN* 3.5 29.1 - - - +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.5 14.1 - - + +
155A THR 3.8 15.5 - - - +
157A ILE* 3.8 25.6 - - + -
171A LEU* 3.7 34.3 - - + +
174A ASN* 4.0 8.3 - - + -
175A THR* 1.3 77.1 - - - +
177A SER* 1.3 55.7 + - - +
178A ASP 3.6 24.7 - - - +
179A ILE* 4.0 17.5 - - + -
193A PHE* 4.6 4.3 - - + -
194A GLY 3.1 19.7 + - - +
195A ASN 3.6 1.1 + - - +
196A GLN* 2.8 29.3 + - - -
197A VAL* 3.4 8.8 + - + +
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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