Contacts of the helix formed by residues 166 - 176 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B PHE 5.2 1.8 + - - -
140B SER* 5.2 2.0 - - - +
141B LEU* 4.4 17.0 - - - +
164B PRO 4.7 0.2 - - - +
165B VAL* 1.3 76.4 - - - +
167B PRO* 1.3 66.1 - - - +
168B ASP* 3.0 30.2 + - - +
169B PHE* 2.8 65.0 + - + +
189B LEU* 3.4 3.3 - - - +
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Residues in contact with PRO 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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165B VAL* 4.3 8.9 - - + +
166B ASN* 1.3 87.4 - - - +
168B ASP* 1.3 65.6 + - - +
169B PHE 3.1 1.6 + - - -
170B CYS* 3.4 24.6 + - - +
188B LEU* 5.2 18.0 - - + +
189B LEU* 3.9 9.9 - - + +
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Residues in contact with ASP 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.8 36.8 - - + +
166B ASN* 2.9 19.6 + - - +
167B PRO* 1.3 77.7 - - - +
169B PHE* 1.3 60.9 + - - +
170B CYS 3.0 6.6 + - - -
171B HIS* 3.3 36.0 + - - +
172B LEU* 4.5 0.3 - - - +
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Residues in contact with PHE 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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137B GLY* 3.8 24.2 - - - -
139B PHE 4.0 13.2 - - - -
141B LEU* 4.1 18.2 - - + -
144B THR* 4.1 20.2 - - - -
160B PHE* 3.7 22.2 - + + -
162B PRO* 3.7 18.6 - - + -
164B PRO 3.5 18.2 - - - -
165B VAL* 4.7 0.2 - - - -
166B ASN* 2.8 44.1 + - + +
168B ASP* 1.3 72.7 - - - +
170B CYS* 1.3 57.2 + - - +
171B HIS 3.0 5.8 - - - -
172B LEU* 2.9 42.0 + - + +
173B TRP* 4.2 8.3 + - + -
189B LEU* 4.0 11.2 - - + -
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Residues in contact with CYS 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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167B PRO 3.4 18.8 + - - +
168B ASP 3.0 1.2 - - - -
169B PHE* 1.3 78.3 - - - +
171B HIS* 1.3 89.3 + - - +
172B LEU 3.2 0.9 - - - -
173B TRP* 3.1 31.7 + - - +
174B PRO* 5.2 0.2 - - - +
188B LEU 5.2 1.8 - - - +
189B LEU* 3.7 25.2 - - + +
192B TYR* 4.4 7.6 + - - -
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Residues in contact with HIS 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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141B LEU* 5.7 2.4 - - + +
145B ARG* 5.9 3.6 - - - +
168B ASP* 3.5 33.8 + - - +
169B PHE 3.0 1.0 + - - -
170B CYS* 1.3 99.4 - - - +
172B LEU* 1.3 68.0 + - + +
173B TRP 3.5 1.1 - - - -
174B PRO* 3.6 12.3 - - - +
175B LEU* 5.6 0.9 - - - +
192B TYR* 6.2 0.2 - - - -
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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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141B LEU* 3.8 24.5 - - + -
144B THR* 4.0 20.2 - - + -
145B ARG* 4.1 30.7 - - + +
148B PHE* 4.7 3.8 - - + -
160B PHE* 4.3 14.6 - - + -
168B ASP 4.5 1.8 - - - +
169B PHE* 2.9 38.6 + - + +
171B HIS* 1.3 85.0 - - + +
173B TRP* 1.3 66.4 + - - +
174B PRO* 3.2 4.0 - - - -
175B LEU* 2.9 35.5 + - + +
176B ILE* 3.5 8.8 - - + +
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Residues in contact with TRP 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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160B PHE* 4.0 18.8 - + + -
162B PRO* 3.9 22.9 - - + -
169B PHE 4.5 7.0 - - - -
170B CYS* 3.1 26.9 + - - +
171B HIS 3.5 0.4 - - - -
172B LEU* 1.3 75.9 - - - +
174B PRO* 1.3 68.5 - - + +
176B ILE* 2.9 32.4 + - + +
179B ALA* 3.5 26.9 - - + -
181B VAL* 4.2 4.5 - - + -
189B LEU* 2.9 46.7 + - + -
191B PRO* 3.4 33.3 - - + +
192B TYR* 3.8 33.4 - + + +
193B GLY 5.5 1.2 - - - +
194B VAL* 3.8 18.8 - - + +
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Residues in contact with PRO 174 (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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152B ARG* 4.2 9.4 + - - -
171B HIS 3.6 13.5 - - - +
172B LEU 3.3 4.9 - - - +
173B TRP* 1.3 95.2 - - + +
175B LEU* 1.3 62.6 + - + +
176B ILE 3.3 2.0 + - - +
192B TYR* 3.7 22.7 - - + +
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Residues in contact with LEU 175 (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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145B ARG* 4.0 28.3 - - + -
148B PHE* 4.3 24.0 - - + +
149B GLN* 4.3 21.1 - - + +
152B ARG* 3.5 30.3 + - + +
158B THR* 2.6 30.1 + - - +
171B HIS 5.6 0.4 - - - +
172B LEU* 2.9 27.3 + - + +
174B PRO* 1.3 84.0 - - + +
176B ILE* 1.3 54.2 + - + +
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Residues in contact with ILE 176 (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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148B PHE* 3.5 47.1 - - + -
152B ARG* 4.3 2.1 + - - -
158B THR* 3.3 4.7 - - - +
160B PHE* 3.6 16.8 - - + -
172B LEU 3.5 17.5 - - - +
173B TRP* 2.9 31.8 + - + +
174B PRO 3.3 1.8 - - - +
175B LEU* 1.3 86.5 - - - +
177B ASP* 1.3 67.0 + - - +
178B ILE 3.2 31.0 - - - +
179B ALA* 4.1 6.3 - - + +
193B GLY 5.1 0.9 - - - +
194B VAL* 3.6 17.8 - - + +
195B LYS* 4.4 3.8 + - - -
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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