Contacts of the helix formed by residues 166 - 176 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D GLY 5.5 0.9 - - - +
139D PHE 4.8 3.2 + - - -
140D SER* 5.0 2.2 - - - +
141D LEU* 4.4 13.1 - - - +
164D PRO 4.9 0.2 - - - +
165D VAL* 1.3 78.1 - - - +
167D PRO* 1.3 74.7 - - - +
168D ASP* 2.9 32.4 + - - +
169D PHE* 2.8 57.8 + - + +
189D LEU* 3.6 3.8 - - - +
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Residues in contact with PRO 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D VAL* 4.2 7.5 - - + +
166D ASN* 1.3 89.3 - - - +
168D ASP* 1.3 69.5 + - - +
169D PHE 3.1 1.1 + - - -
170D CYS* 3.3 24.9 + - - +
188D LEU* 5.1 13.2 - - + +
189D LEU* 4.0 10.0 - - + +
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Residues in contact with ASP 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.6 41.2 - - + +
166D ASN* 2.9 21.2 + - - +
167D PRO* 1.3 81.2 - - - +
169D PHE* 1.3 60.7 + - - +
170D CYS* 3.0 10.5 + - - -
171D HIS* 3.3 24.4 + - - +
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D GLY* 3.7 30.3 - - - -
139D PHE 3.7 20.0 - - - -
141D LEU* 4.2 16.6 - - + -
144D THR* 3.9 20.2 - - - -
160D PHE* 3.8 23.2 - + + -
162D PRO* 3.8 11.2 - - + -
164D PRO 3.7 8.3 - - - -
166D ASN* 2.8 43.7 + - + +
168D ASP* 1.3 75.5 - - - +
170D CYS* 1.3 55.6 + - - +
171D HIS 2.9 12.5 + - - -
172D LEU* 3.0 35.1 + - + +
173D TRP* 4.4 9.0 - - - -
189D LEU* 4.2 10.8 - - + -
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Residues in contact with CYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D PRO 3.3 20.2 + - - +
168D ASP* 3.0 2.8 - - - -
169D PHE* 1.3 77.0 - - - +
171D HIS* 1.3 82.9 + - - +
172D LEU 3.4 0.4 - - - -
173D TRP* 3.3 28.5 - - - +
188D LEU 5.1 1.6 - - - +
189D LEU* 3.7 27.4 - - + +
192D TYR* 4.2 8.7 + - - -
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Residues in contact with HIS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 5.1 10.2 - - + +
145D ARG* 5.6 5.9 - - - +
168D ASP* 3.7 20.3 + - + +
169D PHE 2.9 1.4 + - - -
170D CYS* 1.3 101.7 - - - +
172D LEU* 1.3 65.3 + - + +
173D TRP 3.5 1.6 - - - -
174D PRO* 3.6 13.4 - - - +
175D LEU* 6.1 0.3 - - - +
192D TYR* 5.7 1.3 - - - -
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.2 29.2 - - + -
144D THR* 3.7 32.1 - - + -
145D ARG* 4.0 25.4 - - + +
148D PHE* 4.6 6.1 - - + -
160D PHE* 3.7 26.9 - - + -
168D ASP 4.4 0.2 - - - +
169D PHE* 3.0 22.9 + - + +
171D HIS* 1.3 82.4 - - + +
173D TRP* 1.3 67.1 + - + +
174D PRO* 3.2 4.9 - - - -
175D LEU* 2.8 24.7 + - + +
176D ILE* 3.4 13.5 - - + +
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Residues in contact with TRP 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D PHE* 4.0 20.0 - + - -
162D PRO* 4.2 20.9 - - + -
169D PHE 4.4 7.6 - - - -
170D CYS* 3.3 25.7 - - - +
171D HIS 3.5 0.2 - - - -
172D LEU* 1.3 76.5 - - - +
174D PRO* 1.3 68.8 - - + +
176D ILE* 3.1 30.6 + - + +
179D ALA* 3.6 25.8 - - + -
181D VAL* 4.5 3.8 - - + -
189D LEU* 3.0 45.2 + - + -
190D GLN 3.9 1.1 - - - -
191D PRO* 3.3 28.1 - - + +
192D TYR* 3.6 43.0 - + + +
193D GLY 5.6 0.7 - - - +
194D VAL* 3.9 18.2 - - + +
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Residues in contact with PRO 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ARG* 3.4 19.1 + - - -
171D HIS 3.6 13.9 - - - +
172D LEU 3.2 5.8 - - - -
173D TRP* 1.3 94.3 - - + +
175D LEU* 1.3 61.9 + - + +
176D ILE 3.6 1.0 + - - +
192D TYR* 3.9 21.5 - - + +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ARG* 3.8 38.8 - - + +
148D PHE* 4.1 15.9 - - + -
149D GLN* 3.9 24.2 - - + +
152D ARG* 3.1 39.3 + - + +
158D THR* 2.7 31.0 + - - +
172D LEU* 2.8 17.6 + - + +
174D PRO* 1.3 79.8 - - + +
176D ILE* 1.3 53.9 + - + +
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Residues in contact with ILE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D PHE* 3.4 43.5 - - + -
152D ARG* 3.9 4.5 + - - -
158D THR* 3.4 2.5 - - - +
160D PHE* 3.7 19.3 - - + +
172D LEU* 3.4 19.1 - - + +
173D TRP* 3.1 31.2 + - + +
174D PRO 3.3 1.7 - - - +
175D LEU* 1.3 86.7 - - + +
177D ASP* 1.3 64.5 + - - +
178D ILE 3.3 30.1 - - - +
179D ALA* 4.0 10.1 - - + +
194D VAL* 3.7 13.5 - - + +
195D LYS* 4.8 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