Contacts of the helix formed by residues 166 - 173 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.6 13.5 - - + +
180A LYS 3.2 24.2 - - - +
181A THR* 3.5 7.2 - - - +
182A THR* 2.9 33.9 + - + +
162B LEU 3.2 16.9 + - - +
165B LYS* 1.3 79.2 - - - +
167B SER* 1.3 61.4 + - - +
169B PRO* 3.3 13.0 - - - +
170B ARG* 2.8 40.4 + - - +
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A THR* 4.2 12.5 - - - +
79B PHE* 4.5 2.8 - - - -
82B PHE* 3.5 10.5 - - - -
83B LEU* 3.5 25.4 - - - +
86B GLU* 3.8 9.2 - - - -
88B SER* 4.8 0.7 - - - -
163B MET* 3.4 17.7 + - - +
166B ASP* 1.3 78.2 - - - +
168B TYR* 1.3 66.0 + - - +
169B PRO* 3.4 2.0 - - - -
170B ARG* 3.5 23.2 + - - +
171B PHE* 3.1 18.4 + - - +
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Residues in contact with TYR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B SER* 2.9 26.7 + - - -
66B PHE* 3.5 44.2 - + + -
69B LEU* 3.5 28.7 - - + +
79B PHE* 4.2 5.3 - + + -
163B MET 2.8 19.6 + - - +
164B GLU* 3.5 17.9 - - + +
167B SER* 1.3 72.2 + - - +
169B PRO* 1.3 72.9 - - + +
171B PHE* 3.2 8.7 + + - +
172B LEU* 3.1 57.4 + - + +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLU 3.6 6.7 - - - +
165B LYS* 3.3 19.7 - - - +
166B ASP 3.3 21.5 - - - +
167B SER 3.4 0.2 - - - -
168B TYR* 1.3 94.8 - - + +
170B ARG* 1.3 63.6 + - + +
172B LEU* 3.4 14.4 + - + +
173B LYS* 3.3 26.2 + - - +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 4.3 3.2 - - - +
182A THR 5.1 1.6 + - - -
185A VAL* 3.5 40.1 - - - +
82B PHE* 3.7 12.6 - - + -
86B GLU* 2.7 41.4 + - - -
166B ASP* 2.8 45.9 + - - +
167B SER* 3.5 21.9 + - - +
169B PRO* 1.3 80.5 - - + +
171B PHE* 1.3 57.2 + - - +
173B LYS* 3.1 9.7 + - - +
174B SER* 3.0 25.6 + - - -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 4.0 30.7 - - + -
78B ALA* 3.6 31.2 - - + -
79B PHE* 3.7 31.4 - + + -
82B PHE* 3.5 35.4 - + + -
167B SER 3.1 14.1 + - - +
168B TYR* 3.2 15.5 + + - +
170B ARG* 1.3 76.8 - - - +
172B LEU* 1.3 61.7 + - + +
174B SER* 2.8 29.9 + - - -
176B ALA* 5.0 2.7 - - + -
177B TYR* 3.5 44.5 - + + +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B TYR* 3.1 58.2 + - + +
169B PRO* 3.6 13.5 - - + +
170B ARG 3.3 0.2 - - - -
171B PHE* 1.3 79.8 - - + +
173B LYS* 1.3 62.0 + - + +
174B SER 3.3 1.1 - - - +
177B TYR* 3.4 49.6 - - + +
178B ARG* 5.1 2.4 + - - +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B PRO 3.3 14.6 + - - +
170B ARG* 3.1 13.0 + - - +
172B LEU* 1.3 79.2 - - + +
174B SER* 1.3 61.3 + - - +
175B PRO* 4.1 2.1 - - - +
178B ARG* 5.3 2.1 - - - +
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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