Contacts of the helix formed by residues 158 - 170 (chain W) in PDB entry 5JPQ
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 ASP 158 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156W GLN* 3.2 4.5 - - + +
157W PRO* 1.3 77.8 - - + +
159W GLN* 1.3 62.2 + - - +
160W THR 3.2 3.1 - - - -
161W ASP* 3.2 15.7 + - + +
162W ILE* 3.0 22.2 + - - +
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Residues in contact with GLN 159 (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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154W ILE* 3.6 27.0 - - + +
156W GLN* 3.1 26.9 + - + +
157W PRO 3.2 2.0 + - - +
158W ASP* 1.3 77.4 - - - +
160W THR* 1.3 57.9 + - - +
162W ILE* 3.6 7.5 - - - +
163W ALA* 3.0 27.2 + - - +
180W VAL 5.4 6.1 - - - +
182W LYS 6.4 0.4 - - - +
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Residues in contact with THR 160 (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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157W PRO 5.1 0.8 + - - -
158W ASP 3.2 1.2 - - - -
159W GLN* 1.3 75.7 - - - +
161W ASP* 1.3 65.6 + - - +
163W ALA* 3.1 9.3 + - - +
164W ILE* 3.0 22.3 + - - +
199W GLU* 4.5 28.7 - - - -
202W LYS* 4.9 11.2 - - - -
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Residues in contact with ASP 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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158W ASP* 3.2 18.7 + - + +
160W THR* 1.3 74.1 - - - +
162W ILE* 1.3 65.2 + - - +
164W ILE* 3.1 10.4 + - - +
165W TYR* 3.0 24.1 + - - +
202W LYS* 6.1 0.6 - - - +
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Residues in contact with ILE 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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134W ALA* 4.7 21.2 - - + +
135W ARG* 5.1 10.8 - - + +
156W GLN* 5.9 2.7 - - + -
158W ASP 3.0 13.7 + - - +
159W GLN* 3.6 12.3 - - - +
161W ASP* 1.3 73.6 - - - +
163W ALA* 1.3 64.2 + - - +
165W TYR* 3.2 8.5 + - - +
166W ASN* 3.1 22.6 + - - +
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Residues in contact with ALA 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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152W VAL* 4.3 23.3 - - + -
159W GLN 3.0 14.7 + - - +
160W THR* 3.1 11.9 + - - +
162W ILE* 1.3 77.2 - - - +
164W ILE* 1.3 57.3 + - - +
166W ASN* 3.2 8.9 + - - +
167W ALA* 2.9 28.3 + - - +
179W LEU* 5.5 8.5 - - + -
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Residues in contact with ILE 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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160W THR 3.0 11.5 + - - +
161W ASP* 3.1 10.7 + - - +
163W ALA* 1.3 74.8 - - - +
165W TYR* 1.3 58.8 - - - +
167W ALA* 2.9 22.6 + - - +
168W LYS* 3.0 15.6 + - - +
202W LYS 6.2 0.2 - - - +
203W LEU* 6.5 0.9 - - - -
206W SER* 5.3 13.9 - - - -
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Residues in contact with TYR 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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86S TYR* 5.5 1.7 - - - +
135W ARG* 5.7 6.1 - - - +
137W PRO* 5.7 2.0 - - - -
161W ASP 3.0 11.8 + - - +
162W ILE* 3.4 13.0 - - - +
163W ALA 3.2 0.2 - - - -
164W ILE* 1.3 77.5 - - - +
166W ASN* 1.3 62.2 + - - +
167W ALA 3.3 0.5 + - - -
168W LYS* 3.5 4.8 + - - +
169W PHE* 3.4 17.3 + - - +
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Residues in contact with ASN 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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134W ALA* 5.2 8.7 + - + +
137W PRO* 4.9 10.7 - - + +
162W ILE 3.1 12.0 + - - +
163W ALA* 3.5 9.9 - - - +
165W TYR* 1.3 76.0 - - - +
167W ALA* 1.3 57.3 - - - +
169W PHE* 3.2 7.4 + - - +
170W PHE* 2.8 33.6 + - + +
171W LEU 4.0 0.2 + - - -
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Residues in contact with ALA 167 (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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163W ALA 2.9 13.5 + - - +
164W ILE* 2.9 16.1 + - - +
166W ASN* 1.3 75.8 - - - +
168W LYS* 1.3 61.1 + - - +
169W PHE 3.1 0.2 + - - -
171W LEU* 2.7 50.1 + - + +
230W TYR* 5.6 7.0 - - + -
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Residues in contact with LYS 168 (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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86S TYR* 3.5 27.9 - - + +
91S ARG* 5.4 5.2 - - - +
164W ILE 3.0 12.4 + - - +
165W TYR* 4.3 4.3 - - - +
167W ALA* 1.3 74.9 - - - +
169W PHE* 1.3 60.2 + - - +
171W LEU 5.6 0.4 - - - -
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Residues in contact with PHE 169 (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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86S TYR* 4.3 11.4 - - + +
90S SER 5.8 0.3 - - - -
91S ARG* 4.8 15.2 - - - +
94S ARG* 5.7 3.1 - - - +
137W PRO* 4.5 17.0 - - + -
146W ASN* 5.4 2.4 - - - +
165W TYR 3.4 10.9 + - - +
166W ASN* 3.2 11.8 + - - +
167W ALA 3.1 0.6 - - - -
168W LYS* 1.3 80.7 - - - +
170W PHE* 1.3 62.9 + - + +
171W LEU 3.8 0.2 - - - -
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Residues in contact with PHE 170 (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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81W LEU* 5.1 15.3 - - + -
144W VAL* 6.0 2.7 - - + -
145W GLU 4.1 14.6 - - - +
146W ASN* 3.3 11.1 - - - +
147W VAL* 2.8 31.0 + - + +
166W ASN* 2.8 17.8 + - + +
169W PHE* 1.3 77.5 - - + +
171W LEU* 1.3 59.7 + - - +
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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