Contacts of the strand formed by residues 160 - 166 (chain W) in PDB entry 1O18
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 THR 160 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153W LEU* 4.4 6.3 - - + -
154W ASP 3.2 9.4 - - - +
155W SER* 2.6 24.8 + - - +
159W VAL* 1.4 71.4 - - - +
161W HIS* 1.3 74.4 + - - +
162W ASN* 5.0 2.7 - - - +
177W ARG* 3.3 6.6 - - - +
178W LEU* 2.9 46.8 + - + -
180W LEU 3.1 16.5 + - - -
181W ALA* 4.3 0.2 - - - +
261W LEU* 5.1 0.2 - - - +
274W ILE* 3.6 31.4 - - + +
277W THR* 6.1 0.4 - - + -
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Residues in contact with HIS 161 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73W HIS 5.2 0.7 - - - -
108W ALA* 4.9 7.9 - - + -
109W PRO* 3.6 42.2 - - + +
110W LEU* 5.2 4.0 + - - +
152W VAL 4.1 0.4 - - - -
153W LEU* 3.4 5.0 - - - -
154W ASP* 2.7 41.7 + - + +
159W VAL* 4.0 31.8 - - + +
160W THR* 1.3 80.6 + - - +
162W ASN* 1.3 66.4 + - - +
163W VAL* 4.2 11.7 - - + -
175W ILE* 4.0 8.7 - - + +
176W MET 3.0 17.5 - - - -
177W ARG* 3.7 28.4 + - + +
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Residues in contact with ASN 162 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151W ILE* 4.5 6.0 - - + +
152W VAL 3.2 6.9 - - - +
153W LEU* 3.6 21.5 - - - +
160W THR* 5.0 2.3 - - - +
161W HIS* 1.3 73.6 - - - +
163W VAL* 1.3 62.3 + - - +
164W PRO* 3.5 2.0 - - - +
175W ILE* 3.2 24.8 - - - +
176W MET* 2.9 15.2 + - + +
178W LEU* 5.8 0.3 + - - +
277W THR* 2.9 30.6 - - - +
278W THR* 3.4 34.4 + - - +
281W SER* 3.6 19.7 - - - +
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Residues in contact with VAL 163 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109W PRO* 3.5 33.7 - - + -
136W ILE* 5.1 2.5 - - + -
138W ALA* 3.4 22.2 - - + -
139W VAL* 5.0 1.1 - - + -
151W ILE* 4.2 0.6 - - - +
152W VAL 2.9 28.9 + - - +
154W ASP* 5.8 0.2 - - + -
161W HIS* 4.2 9.2 - - + -
162W ASN* 1.3 78.2 - - - +
164W PRO* 1.3 62.1 - - - +
165W ILE* 3.5 17.8 + - + +
170W ALA* 3.6 30.7 - - + -
175W ILE* 3.9 16.2 - - + -
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Residues in contact with PRO 164 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150W GLY 3.7 7.2 - - - +
151W ILE* 3.9 16.4 - - + -
162W ASN 3.5 7.2 - - - +
163W VAL* 1.3 84.0 - - - +
165W ILE* 1.4 58.6 + - - +
170W ALA* 3.6 0.3 - - - -
171W LEU* 2.8 37.4 + - + +
174W ALA* 3.7 15.5 - - + -
175W ILE* 4.0 17.5 - - + +
281W SER* 3.4 20.6 - - - +
285W CYS* 3.8 20.6 - - - -
293W LEU* 4.4 8.7 - - + -
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Residues in contact with ILE 165 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138W ALA* 3.7 9.9 - - + +
139W VAL* 3.5 40.6 - - + +
142W LEU* 3.9 18.2 - - + -
148W THR 3.4 16.8 - - - +
149W THR* 3.1 24.3 - - - +
150W GLY 2.9 12.8 + - - +
152W VAL* 4.5 2.7 - - + -
163W VAL* 3.5 21.3 + - + +
164W PRO* 1.4 74.3 - - - +
166W TYR* 1.3 62.9 + - - +
168W GLY* 3.6 25.8 - - - +
169W TYR 3.7 3.1 - - - -
170W ALA* 3.6 15.7 - - + -
171W LEU* 4.7 1.3 - - - -
293W LEU* 4.3 2.1 - - - +
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Residues in contact with TYR 166 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149W THR* 3.6 17.9 - - + -
164W PRO 4.4 0.2 - - - -
165W ILE* 1.3 72.3 - - - +
167W GLU* 1.3 91.6 + - + +
168W GLY 2.9 4.4 + - - -
169W TYR* 3.1 26.8 + - + +
171W LEU* 4.3 20.8 - - + +
289W ILE* 3.7 36.1 - - + -
292W ASP* 4.0 16.8 + - - -
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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