Contacts of the helix formed by residues 166 - 173 (chain D) in PDB entry 2IK8
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 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179C VAL* 3.5 15.3 - - + +
180C LYS 3.2 22.9 - - - +
181C THR* 3.3 10.9 + - - +
182C THR* 2.9 30.7 + - + +
162D LEU 3.2 14.6 + - - +
165D LYS* 1.3 79.7 - - + +
167D SER* 1.3 66.2 + - - +
168D TYR 3.6 0.4 - - - -
169D PRO* 3.4 10.7 - - - +
170D ARG* 3.1 50.8 + - - +
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C THR* 4.3 11.6 - - - +
79D PHE* 4.5 3.8 - - - -
82D PHE* 3.9 4.2 - - - -
83D LEU* 3.8 29.5 - - - +
86D GLU* 4.4 7.4 - - - -
88D SER* 4.6 2.9 + - - -
91D ASN* 5.4 0.3 + - - -
162D LEU 4.2 1.6 + - - -
163D MET* 3.2 21.9 + - - +
166D ASP* 1.3 75.1 - - - +
168D TYR* 1.3 65.7 + - - +
170D ARG* 3.0 23.3 + - - +
171D PHE* 2.9 19.8 + - - +
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Residues in contact with TYR 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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62D TRP 2.6 29.6 + - - -
63D ARG 3.3 15.6 + - - -
64D GLU 4.5 0.2 - - - -
65D SER* 3.6 10.1 + - - -
66D PHE* 3.6 34.8 - + + -
69D LEU* 3.6 27.1 - - + -
79D PHE* 4.0 10.6 - - + -
163D MET 2.9 19.3 + - - +
164D GLU* 3.6 20.6 - - + +
167D SER* 1.3 76.0 - - - +
169D PRO* 1.3 67.8 - - + +
171D PHE* 2.9 20.3 + + - +
172D LEU* 3.2 30.3 + - + +
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Residues in contact with PRO 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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164D GLU 3.5 14.4 - - - +
165D LYS 3.7 15.7 - - - +
166D ASP 3.4 14.8 - - - +
168D TYR* 1.3 100.1 - - + +
170D ARG* 1.3 60.6 + - + +
172D LEU* 3.4 11.6 + - + +
173D LYS* 3.4 25.9 + - - +
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Residues in contact with ARG 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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181C THR* 5.2 1.0 - - - +
182C THR 4.5 3.0 + - - -
185C VAL* 3.7 38.5 - - - +
82D PHE* 3.4 17.3 - - + -
86D GLU* 3.3 29.5 + - - -
166D ASP* 3.1 54.0 + - - +
167D SER* 3.0 14.7 + - - +
169D PRO* 1.3 77.2 - - + +
171D PHE* 1.3 65.0 + - - +
173D LYS* 3.8 8.9 - - + +
174D SER* 3.2 17.7 + - - -
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Residues in contact with PHE 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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62D TRP* 4.6 5.8 - + - -
69D LEU* 4.0 27.6 - - + -
78D ALA* 3.7 28.9 - - + -
79D PHE* 3.5 41.3 - + + -
82D PHE* 3.7 31.8 - + + -
167D SER 2.9 6.7 + - - +
168D TYR 2.9 10.1 + - - +
170D ARG* 1.3 77.6 - - - +
172D LEU* 1.3 73.0 + - + +
174D SER* 2.5 31.8 + - - -
176D ALA* 5.5 4.3 - - + -
177D TYR* 3.3 34.4 - + + +
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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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62D TRP 3.7 10.5 - - - +
63D ARG* 3.8 25.1 - - + +
168D TYR* 3.2 54.8 + - + +
169D PRO* 3.8 10.8 - - + +
170D ARG 3.3 0.4 - - - -
171D PHE* 1.3 89.3 - - + +
173D LYS* 1.3 61.0 + - + +
174D SER 3.4 0.8 - - - +
177D TYR* 3.2 39.4 - - + -
178D ARG* 5.1 1.7 + - - +
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Residues in contact with LYS 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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169D PRO 3.4 16.7 + - - +
170D ARG* 3.6 9.4 + - + +
171D PHE 3.2 0.8 - - - -
172D LEU* 1.3 80.1 - - + +
174D SER* 1.3 61.6 + - - +
175D PRO* 4.6 0.9 - - - +
178D ARG* 5.4 1.8 - - - +
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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