Contacts of the helix formed by residues 158 - 169 (chain C) in PDB entry 1APL
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C TRP* 5.3 1.8 + - - -
156C TYR 3.8 4.1 + - - +
157C LEU* 1.3 73.7 - - - +
159C THR* 1.3 73.1 + - - +
160C LYS* 3.1 23.4 + - - +
161C GLY* 2.9 27.8 + - - -
162C LEU* 2.8 21.6 + - - -
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Residues in contact with THR 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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158C ASP* 1.3 80.1 + - - +
160C LYS* 1.3 65.0 + - - +
162C LEU* 3.3 5.9 + - - +
163C GLU* 3.0 29.0 + - - +
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Residues in contact with LYS 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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158C ASP* 3.1 9.3 + - - +
159C THR* 1.3 76.9 + - - +
161C GLY* 1.4 67.8 + - - +
163C GLU* 3.0 11.0 + - - +
164C ASN* 3.0 22.8 + - - +
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Residues in contact with GLY 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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147C TRP* 5.0 12.9 + - - -
157C LEU* 5.4 1.8 - - - -
158C ASP* 2.9 28.5 + - - -
160C LYS* 1.4 76.2 - - - +
162C LEU* 1.3 61.6 + - - +
164C ASN* 3.0 16.6 + - - +
165C LEU* 3.3 16.9 + - - +
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Residues in contact with LEU 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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23B G 5.6 0.4 - - - +
157C LEU* 4.7 20.8 - - + +
158C ASP 2.8 15.9 + - - +
159C THR* 3.8 8.5 - - - +
161C GLY* 1.3 70.1 - - - +
163C GLU* 1.3 59.9 + - + +
165C LEU* 3.2 9.2 + - - +
166C MET* 2.8 32.3 + - + +
173C ARG* 3.7 34.3 - - + +
176C ILE* 4.0 28.0 - - + -
177C LYS* 3.7 32.1 - - + +
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Residues in contact with GLU 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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159C THR 3.0 19.1 - - - +
160C LYS* 3.0 10.6 + - - +
162C LEU* 1.3 77.7 - - + +
164C ASN* 1.3 58.3 + - - +
166C MET* 3.6 27.6 - - + +
167C LYS* 2.7 28.8 + - - +
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Residues in contact with ASN 164 (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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160C LYS 3.0 9.3 + - - +
161C GLY* 3.0 10.0 + - - +
163C GLU* 1.3 75.3 - - - +
165C LEU* 1.3 60.9 + - - +
167C LYS* 3.2 11.3 + - - +
168C ASN* 2.8 62.6 + - - +
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Residues in contact with LEU 165 (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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143C ILE* 4.4 16.6 - - + +
144C LEU* 3.6 30.7 - - + +
147C TRP* 4.1 34.5 - - + -
157C LEU* 3.8 29.4 - - + -
161C GLY 3.3 9.5 + - - +
162C LEU* 3.2 5.5 + - - +
164C ASN* 1.3 77.3 - - - +
166C MET* 1.3 54.3 + - - +
168C ASN* 2.7 23.0 + - - +
169C THR* 2.9 23.4 + - + +
176C ILE* 3.5 23.6 - - + -
180C VAL* 5.2 0.4 - - + -
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Residues in contact with MET 166 (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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162C LEU* 2.8 20.4 + - + +
163C GLU* 3.6 33.4 - - + +
165C LEU* 1.3 76.0 - - - +
167C LYS* 1.3 63.1 + - - +
168C ASN 3.3 0.5 + - - -
169C THR* 3.4 17.8 - - - +
171C LEU 4.6 13.0 - - - +
173C ARG* 3.2 45.5 - - + +
176C ILE* 3.8 8.0 - - + +
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Residues in contact with LYS 167 (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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163C GLU 2.7 17.8 + - - +
164C ASN* 3.5 17.9 - - - +
166C MET* 1.3 78.2 - - - +
168C ASN* 1.3 63.4 + - - +
169C THR 3.8 0.5 + - - -
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Residues in contact with ASN 168 (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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139C GLU* 4.7 3.8 - - - +
140C ASN* 4.2 1.6 + - - -
143C ILE* 3.1 34.3 - - + +
164C ASN* 2.8 42.7 + - - +
165C LEU* 2.7 17.0 + - - +
167C LYS* 1.3 77.0 - - - +
169C THR* 1.3 65.2 + - + +
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Residues in contact with THR 169 (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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140C ASN* 3.2 26.5 - - + +
143C ILE* 3.8 16.8 - - + -
144C LEU* 4.9 8.3 - - + -
165C LEU* 2.9 21.4 + - + +
166C MET* 3.4 12.3 - - - +
167C LYS 3.6 2.6 + - - -
168C ASN* 1.3 88.5 - - + +
170C SER* 1.3 60.0 + - - +
171C LEU* 2.9 33.0 + - + +
176C ILE* 3.9 12.6 - - - +
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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