Contacts of the helix formed by residues 154 - 163 (chain C) in PDB entry 4HRE
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 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C TYR* 4.3 1.1 - - - -
148C LYS* 3.6 31.9 + - - +
153C THR* 1.3 89.1 + - - +
155C LEU* 1.3 63.2 + - - +
156C GLU* 3.2 12.9 - - + +
157C LYS* 3.3 31.2 + - + +
158C ASP* 3.5 6.4 + - - +
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LEU* 4.2 14.8 - - + -
118C MET* 4.1 11.9 - - + -
132C ILE* 5.3 2.9 - - + -
140C LEU* 5.4 2.2 - - + -
143C ILE* 3.9 27.1 - - + -
144C ASN* 3.8 28.9 + - - +
147C TYR* 3.6 48.5 - - + +
148C LYS* 5.1 2.0 - - - +
153C THR 3.7 2.6 + - - -
154C ASP* 1.3 69.7 - - - +
156C GLU* 1.3 66.6 + - - +
158C ASP* 3.1 3.5 + - - +
159C ILE* 3.0 40.1 + - + +
175C ALA* 4.8 13.9 - - + -
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Residues in contact with GLU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASN* 5.0 4.1 + - - +
154C ASP* 4.6 11.5 - - + +
155C LEU* 1.3 78.4 - - - +
157C LYS* 1.3 60.0 - - + +
159C ILE* 3.3 12.7 + - - +
160C ILE* 2.9 49.9 + - + +
172C VAL* 3.6 20.0 - - + +
175C ALA* 6.2 1.1 - - - -
176C LYS* 3.0 39.1 + - - +
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Residues in contact with LYS 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C THR* 4.3 8.7 - - - +
154C ASP* 3.3 30.9 + - + +
155C LEU 3.2 0.6 - - - -
156C GLU* 1.3 78.2 - - + +
158C ASP* 1.3 61.9 + - - +
160C ILE* 3.5 18.9 + - + +
161C SER* 3.1 27.4 + - - -
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Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LYS* 4.2 10.2 - - - +
118C MET* 3.6 15.4 - - + +
147C TYR* 2.4 43.3 + - - +
153C THR* 3.5 14.9 + - - +
154C ASP 3.5 4.2 + - - -
155C LEU 3.1 8.8 + - - +
157C LYS* 1.3 75.6 - - - +
159C ILE* 1.3 65.6 + - - +
161C SER* 2.8 24.0 + - - -
162C ASP* 3.0 13.5 + - - +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C MET* 4.0 15.3 - - - -
128C LEU* 4.9 9.6 - - + -
132C ILE* 4.8 8.1 - - + -
155C LEU* 3.0 30.7 + - + +
156C GLU* 3.5 10.5 - - - +
158C ASP* 1.3 75.9 - - - +
160C ILE* 1.3 54.2 + - - +
162C ASP* 3.2 0.6 + - - -
163C THR* 2.3 57.2 + - + +
168C ARG 4.8 0.4 - - - +
171C MET* 3.7 31.0 - - + +
172C VAL* 4.1 14.6 - - + +
175C ALA* 3.9 28.0 - - + -
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Residues in contact with ILE 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLU* 2.9 41.2 + - + +
157C LYS* 3.7 19.5 - - + +
158C ASP 3.4 0.2 - - - -
159C ILE* 1.3 74.5 - - - +
161C SER* 1.3 59.9 + - - +
163C THR 3.1 18.5 - - - +
168C ARG* 3.9 35.6 + - - +
172C VAL* 4.1 16.4 - - + -
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Residues in contact with SER 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C LYS 3.1 14.4 + - - -
158C ASP* 2.8 25.2 + - - -
159C ILE 3.2 0.2 - - - -
160C ILE* 1.3 77.8 - - - +
162C ASP* 1.3 69.2 + - - +
163C THR 3.4 2.0 + - - +
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Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C MET* 2.7 47.3 - - + +
120C GLY 3.3 18.6 - - - +
121C LEU 4.0 7.3 - - - +
123C THR* 2.3 39.7 + - - +
158C ASP 3.0 12.5 + - - +
159C ILE 3.2 1.3 + - - +
161C SER* 1.3 87.0 + - - +
163C THR* 1.3 65.6 + - + +
167C PHE* 5.6 0.5 - - - -
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Residues in contact with THR 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C THR* 5.3 0.7 - - - +
128C LEU* 4.1 15.7 - - + -
159C ILE* 2.3 40.4 + - + +
160C ILE 3.1 10.6 - - - +
161C SER 4.5 1.4 - - - +
162C ASP* 1.3 86.1 - - + +
164C SER* 1.3 62.4 + - - +
167C PHE* 3.8 29.4 - - + -
168C ARG* 2.9 47.8 + - - +
171C MET* 4.7 2.5 - - + -
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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