Contacts of the helix formed by residues 166 - 176 (chain C) in PDB entry 3IKH
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 ASN 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137C GLY 5.8 0.2 - - - +
139C PHE 4.8 1.0 + - - -
140C SER* 4.8 5.7 - - - +
141C LEU* 4.3 19.2 - - - +
165C VAL* 1.3 79.4 - - - +
167C PRO* 1.3 75.5 - - - +
168C ASP* 2.9 29.8 + - - +
169C PHE* 2.8 51.0 + - + +
189C LEU* 3.5 4.3 - - - +
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Residues in contact with PRO 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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165C VAL* 4.6 5.7 - - + +
166C ASN* 1.3 91.5 - - - +
168C ASP* 1.3 65.1 + - - +
169C PHE 3.2 1.2 + - - -
170C CYS* 3.4 23.7 + - - +
188C LEU* 4.6 13.8 - - + +
189C LEU* 3.8 9.3 - - + +
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Residues in contact with ASP 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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141C LEU* 3.5 43.6 - - + +
166C ASN* 2.9 19.2 + - - +
167C PRO* 1.3 76.9 - - - +
169C PHE* 1.3 60.2 + - - +
170C CYS* 3.0 8.0 + - - -
171C HIS* 3.3 30.1 + - - +
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Residues in contact with PHE 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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137C GLY* 3.6 21.1 - - - -
139C PHE 3.5 25.6 - - - -
141C LEU* 4.3 9.2 - - + -
144C THR* 4.0 13.9 - - - -
160C PHE* 3.8 16.3 - + + -
162C PRO* 3.8 18.2 - - + -
164C PRO 3.5 22.0 - - - -
166C ASN* 2.8 43.6 + - + +
168C ASP* 1.3 73.2 - - - +
170C CYS* 1.3 61.2 + - - +
171C HIS 2.9 7.2 + - - -
172C LEU* 3.0 39.7 + - + +
173C TRP* 4.4 7.9 + - - -
189C LEU* 4.0 13.2 - - + -
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Residues in contact with CYS 170 (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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167C PRO 3.4 18.6 + - - +
168C ASP 3.0 1.2 - - - -
169C PHE* 1.3 78.1 - - - +
171C HIS* 1.3 83.3 + - - +
172C LEU 3.3 1.6 - - - -
173C TRP* 3.3 28.6 - - - +
188C LEU 5.2 1.3 - - - +
189C LEU* 3.7 27.2 - - - +
192C TYR* 4.3 9.7 + - - -
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Residues in contact with HIS 171 (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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141C LEU* 4.8 7.6 - - + +
145C ARG* 5.7 6.1 - - - +
168C ASP* 3.6 31.2 + - - +
169C PHE 2.9 1.2 + - - -
170C CYS* 1.3 96.5 - - - +
172C LEU* 1.3 68.5 + - + +
173C TRP 3.7 0.9 - - - -
174C PRO* 3.9 13.5 - - - +
175C LEU* 5.8 0.9 - - - +
192C TYR* 5.7 1.3 - - - -
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Residues in contact with LEU 172 (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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141C LEU* 3.1 30.7 - - + -
144C THR* 4.0 16.6 - - + -
145C ARG* 4.5 24.0 - - + +
148C PHE* 4.9 5.2 - - + -
160C PHE* 3.9 23.8 - - + -
168C ASP 4.1 0.9 - - - +
169C PHE* 3.0 39.7 + - + +
171C HIS* 1.3 85.9 - - + +
173C TRP* 1.3 65.5 + - - +
174C PRO* 3.2 5.4 - - - -
175C LEU* 2.9 24.6 + - + +
176C ILE* 3.4 14.4 - - + +
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Residues in contact with TRP 173 (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 PHE* 3.8 20.0 - + - -
162C PRO* 4.0 22.0 - - + -
169C PHE 4.5 6.5 - - - -
170C CYS* 3.3 26.4 + - - +
171C HIS 3.7 0.2 - - - -
172C LEU* 1.3 77.3 - - - +
174C PRO* 1.3 67.4 - - + +
175C LEU 3.0 0.2 - - - -
176C ILE* 2.9 33.6 + - + +
179C ALA* 3.4 25.4 - - + -
181C VAL* 4.2 2.0 - - + -
189C LEU* 2.9 42.6 + - + -
190C GLN 3.8 0.4 - - - -
191C PRO* 3.4 39.6 - - + +
192C TYR* 3.7 35.2 - + + +
193C GLY 5.2 2.6 - - - +
194C VAL* 4.0 18.5 - - + +
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Residues in contact with PRO 174 (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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152C ARG* 2.7 33.6 + - - -
171C HIS 3.9 14.4 - - - +
172C LEU 3.2 4.5 - - - +
173C TRP* 1.3 92.2 - - + +
175C LEU* 1.3 58.0 + - + +
176C ILE 3.4 1.3 - - - +
192C TYR* 3.8 22.2 - - + +
193C GLY 6.0 1.1 - - - +
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Residues in contact with LEU 175 (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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145C ARG* 3.9 23.8 - - + +
148C PHE* 4.2 16.3 - - + -
149C GLN* 3.8 35.0 - - + +
152C ARG* 3.3 46.4 + - + +
158C THR* 2.6 29.5 + - - +
171C HIS 5.8 0.7 - - - +
172C LEU* 2.9 18.8 + - + +
174C PRO* 1.3 85.0 - - + +
176C ILE* 1.3 55.5 + - + +
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Residues in contact with ILE 176 (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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148C PHE* 3.6 42.2 - - + -
152C ARG* 5.0 1.6 + - - -
158C THR* 3.4 2.2 - - - +
160C PHE* 3.6 22.0 - - + +
172C LEU* 3.4 19.1 - - + +
173C TRP* 2.9 31.6 + - + +
174C PRO 3.4 1.6 - - - +
175C LEU* 1.3 86.6 - - + +
177C ASP* 1.3 67.0 + - - +
178C ILE 3.2 29.8 - - - +
179C ALA* 4.0 10.5 - - + +
193C GLY 5.0 1.2 - - - +
194C VAL* 3.7 14.5 - - + +
195C LYS* 4.4 3.1 + - - -
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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