Contacts of the helix formed by residues 159 - 171 (chain E) in PDB entry 3HB8
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 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139E TRP 4.1 0.3 - - - +
140E ARG* 2.8 54.1 + - - +
157E GLY 3.9 2.8 + - - -
158E VAL* 1.3 71.6 - - - +
160E GLN* 1.3 60.6 + - - +
161E LEU 3.3 3.5 + - - -
162E GLN* 2.7 38.3 + - + +
163E LYS* 3.0 20.1 + - - +
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Residues in contact with GLN 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TRP* 4.7 0.3 + - - -
184D PRO* 3.5 25.0 - - + +
138E GLN 3.0 22.8 + - - +
139E TRP* 3.0 8.2 + - - +
142E PHE* 3.1 13.7 - - + -
158E VAL* 2.9 24.9 + - + +
159E ASP* 1.3 71.9 - - - +
161E LEU* 1.3 63.0 + - - +
163E LYS* 3.7 10.9 - - - +
164E VAL* 3.0 29.8 + - - +
178E ILE 4.0 5.3 - - - +
179E MET* 3.3 18.7 - - + +
180E CYS* 2.5 49.8 + - - +
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Residues in contact with LEU 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ILE* 3.8 25.8 - - + -
139E TRP* 3.2 17.8 + - + +
140E ARG* 3.9 27.1 - - - +
159E ASP* 3.2 5.8 - - - +
160E GLN* 1.3 74.0 - - - +
162E GLN* 1.3 67.2 + - - +
164E VAL* 3.0 13.5 + - + +
165E ILE* 3.0 24.6 + - + +
179E MET* 3.6 32.9 - - + -
233E LEU* 4.6 4.9 - - + -
237E ILE* 4.3 13.0 - - + -
288E ILE* 3.8 28.7 - - + -
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Residues in contact with GLN 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E ARG* 3.9 11.3 + - - +
159E ASP* 2.7 35.5 + - + +
161E LEU* 1.3 74.0 - - - +
163E LYS* 1.3 63.0 + - - +
165E ILE* 3.3 26.4 + - - +
166E ASP* 3.0 48.2 + - - +
287E LYS* 5.5 12.7 - - - +
288E ILE* 4.6 7.3 + - - +
289E ASP* 4.7 3.6 - - - +
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Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TRP* 5.9 1.2 - - - +
184D PRO* 4.2 18.0 + - - +
187D LEU* 4.3 18.7 - - - +
158E VAL* 3.7 28.5 - - + +
159E ASP 3.0 16.6 + - - +
160E GLN* 3.7 9.5 - - - +
162E GLN* 1.3 78.8 - - - +
164E VAL* 1.3 54.4 + - - +
166E ASP* 3.6 7.3 + - - +
167E THR* 2.8 43.1 + - - +
178E ILE 5.5 6.9 + - - -
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Residues in contact with VAL 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E GLN 3.0 22.4 + - - +
161E LEU* 3.3 9.9 - - + +
163E LYS* 1.3 75.6 - - + +
165E ILE* 1.3 68.4 + - + +
167E THR* 3.2 4.3 + - - -
168E ILE* 2.9 32.5 + - + +
177E ILE* 3.6 19.9 - - + +
178E ILE 3.9 24.2 - - - +
179E MET* 4.0 12.1 - - + -
201E PHE* 3.5 33.0 - - + -
237E ILE* 4.8 10.1 - - + -
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Residues in contact with ILE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LEU* 3.0 18.5 + - + +
162E GLN* 3.6 23.3 - - - +
164E VAL* 1.3 77.4 - - + +
166E ASP* 1.3 66.4 + - - +
168E ILE* 3.0 19.0 + - - +
169E LYS* 3.2 26.8 + - + +
237E ILE* 4.2 19.5 - - + -
240E ILE* 3.7 31.9 - - + -
241E THR* 4.1 2.9 - - + -
288E ILE* 4.0 37.5 - - + +
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Residues in contact with ASP 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E GLN* 3.0 45.2 + - - +
163E LYS* 3.7 7.8 - - - +
165E ILE* 1.3 76.2 - - - +
167E THR* 1.3 63.1 + - - +
169E LYS* 3.0 16.2 + - - +
170E THR* 2.8 29.6 + - + +
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Residues in contact with THR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E LYS* 2.8 29.7 + - - +
164E VAL* 3.5 7.1 - - - -
166E ASP* 1.3 77.5 - - - +
168E ILE* 1.3 62.8 + - - +
170E THR* 3.6 5.4 - - - -
171E ASN* 3.1 34.2 + - - +
174E ASP* 3.9 33.2 - - + +
177E ILE* 4.0 15.5 - - + -
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E VAL* 2.9 28.7 + - + +
165E ILE* 3.0 9.6 + - - +
167E THR* 1.3 76.1 - - - +
169E LYS* 1.3 60.1 + - - +
172E PRO* 3.5 24.5 - - - +
177E ILE* 3.4 36.8 - - + -
201E PHE* 4.1 10.5 - - + -
203E VAL* 3.8 17.5 - - + -
208E LEU* 4.2 5.6 - - + -
237E ILE* 4.7 6.3 - - + -
241E THR* 3.9 18.4 - - + +
243E LEU* 3.4 32.5 - - + +
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Residues in contact with LYS 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E ILE* 3.4 30.9 - - + +
166E ASP* 3.0 13.5 + - - +
168E ILE* 1.3 78.2 - - - +
170E THR* 1.3 65.6 + - + +
172E PRO* 4.1 4.7 - - - +
240E ILE* 4.5 11.1 + - - +
241E THR* 3.9 28.3 - - + +
286E GLU* 5.8 3.0 + - - -
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Residues in contact with THR 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ASP* 2.8 22.2 + - + +
167E THR* 3.6 4.9 + - - -
169E LYS* 1.3 78.3 - - + +
171E ASN* 1.3 75.9 + - - +
172E PRO* 3.8 2.0 - - - +
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Residues in contact with ASN 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A LYS* 6.0 4.3 - - - +
50D ARG* 4.9 7.3 - - - +
167E THR* 3.1 17.5 + - - +
170E THR* 1.3 98.1 + - - +
172E PRO* 1.3 66.8 - - - +
173E ASP* 3.3 4.0 - - + +
174E ASP* 3.2 41.1 + - + +
177E ILE* 5.0 0.2 - - - +
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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