Contacts of the helix formed by residues 166 - 176 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A PHE 5.2 1.2 + - - -
140A SER* 5.3 2.4 - - - +
141A LEU* 4.5 14.6 - - - +
164A PRO 4.9 0.2 - - - +
165A VAL* 1.3 78.7 - - - +
167A PRO* 1.3 74.8 - - - +
168A ASP* 2.8 27.5 + - - +
169A PHE* 2.8 62.5 + - + +
189A LEU* 3.7 3.8 - - - +
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Residues in contact with PRO 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A VAL* 4.4 6.0 - - + +
166A ASN* 1.3 89.4 - - - +
168A ASP* 1.3 59.5 + - - +
169A PHE 3.1 4.9 + - - -
170A CYS* 3.1 27.9 + - - +
188A LEU* 4.8 18.1 - - + +
189A LEU* 4.2 10.3 - - + +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.4 34.4 - - + +
166A ASN* 2.8 22.6 + - - +
167A PRO* 1.3 72.5 - - - +
169A PHE* 1.3 65.2 + - - +
170A CYS 3.0 3.2 + - - -
171A HIS* 3.3 40.9 + - - +
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 3.8 19.7 - - - -
139A PHE 3.7 23.3 - - - -
141A LEU* 4.1 17.9 - - + -
144A THR* 4.2 11.7 - - - -
160A PHE* 3.8 19.0 - + + -
162A PRO* 3.7 18.8 - - + -
164A PRO 3.6 18.6 - - - -
166A ASN* 2.8 49.7 + - + +
168A ASP* 1.3 75.0 - - - +
170A CYS* 1.3 56.9 + - - +
171A HIS 2.9 12.1 + - - -
172A LEU* 3.1 33.3 + - + +
173A TRP* 4.3 9.0 + - - -
189A LEU* 4.3 11.4 - - + -
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Residues in contact with CYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A PRO 3.1 23.5 + - - +
168A ASP 3.0 1.0 - - - -
169A PHE* 1.3 77.4 - - - +
171A HIS* 1.3 81.1 + - - +
172A LEU 3.5 0.2 - - - -
173A TRP* 3.4 26.8 - - - +
188A LEU 5.1 1.6 - - - +
189A LEU* 3.5 29.6 - - - +
192A TYR* 4.3 10.9 + - - -
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Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 4.7 6.8 - - + +
145A ARG* 5.0 13.8 + - - +
168A ASP* 3.4 38.5 + - - +
169A PHE 2.9 1.4 + - - -
170A CYS* 1.3 100.5 - - - +
172A LEU* 1.3 61.1 + - + +
173A TRP 3.4 1.3 - - - -
174A PRO* 3.4 16.2 - - - +
192A TYR* 5.1 2.2 + - - -
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU* 3.7 27.1 - - + -
144A THR* 3.9 28.3 - - + -
145A ARG* 3.4 47.6 - - + +
148A PHE* 4.7 4.0 - - + -
160A PHE* 4.4 7.0 - - + -
169A PHE* 3.1 21.3 + - + +
171A HIS* 1.3 78.0 - - - +
173A TRP* 1.3 53.5 + - - +
174A PRO* 3.1 4.9 - - - -
175A LEU* 2.7 42.9 + - + +
176A ILE* 3.2 19.2 - - + +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 4.0 15.7 - + - -
162A PRO* 4.2 13.5 - - + -
169A PHE 4.4 6.7 - - - -
170A CYS* 3.4 26.2 - - - +
171A HIS 3.4 0.4 - - - -
172A LEU* 1.3 75.4 - - - +
174A PRO* 1.3 69.1 - - + +
176A ILE* 3.0 42.7 + - + +
179A ALA* 3.5 26.9 - - + -
181A VAL* 4.3 4.0 - - + -
189A LEU* 3.1 44.9 + - + -
191A PRO* 3.4 35.7 - - + +
192A TYR* 3.8 35.8 - + + +
193A GLY 5.6 1.2 - - - +
194A VAL* 3.6 19.8 - - + +
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Residues in contact with PRO 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 3.0 20.4 + - - -
171A HIS 3.4 13.5 - - - +
172A LEU 3.2 6.1 - - - -
173A TRP* 1.3 95.2 - - + +
175A LEU* 1.3 60.5 + - + +
176A ILE 3.3 1.2 - - - +
192A TYR* 4.0 21.8 - - + +
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 3.8 34.5 - - + +
148A PHE* 4.1 15.3 - - + +
149A GLN* 3.9 26.9 - - + +
152A ARG* 3.2 38.0 + - + +
158A THR* 2.7 31.2 + - - +
172A LEU* 2.7 28.7 + - + +
174A PRO* 1.3 75.4 - - + +
176A ILE* 1.3 52.9 + - + +
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A PHE* 4.4 11.0 - - + -
152A ARG* 3.8 6.2 + - - -
158A THR* 3.3 4.7 - - - +
160A PHE* 3.4 39.7 - - + -
172A LEU* 3.2 30.7 - - + +
173A TRP* 3.0 38.9 + - + +
174A PRO 3.3 1.1 - - - +
175A LEU* 1.3 83.4 - - - +
177A ASP* 1.3 61.9 + - - +
178A ILE 3.2 33.7 - - - +
179A ALA* 4.1 5.6 - - + +
193A GLY 5.4 0.2 - - - +
194A VAL* 3.7 17.1 - - + +
195A LYS* 4.7 1.4 + - - +
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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