Contacts of the helix formed by residues 167 - 183 (chain F) in PDB entry 1TKK
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 167 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166F ASP* 1.3 90.1 + - - +
168F ILE* 1.3 66.5 + - - +
169F ALA* 3.2 9.0 - - + +
170F THR* 2.6 46.6 + - - -
171F ASP* 3.3 13.8 + - - -
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Residues in contact with ILE 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ASP 4.0 1.2 + - - -
167F ASP* 1.3 72.5 - - - +
169F ALA* 1.3 64.4 + - - +
171F ASP* 3.0 19.2 + - + +
172F ILE* 3.1 30.5 + - + +
196F TRP* 3.3 42.5 - - + +
200F GLU* 3.3 41.5 + - + +
204F ALA* 3.5 24.7 - - + -
207F LYS* 5.2 6.5 - - - +
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Residues in contact with ALA 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ASP* 3.2 10.6 + - + +
168F ILE* 1.3 82.1 - - + +
170F THR* 1.3 61.4 + - - +
172F ILE* 3.4 10.9 + - - +
173F ALA* 3.1 22.0 + - - +
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Residues in contact with THR 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PRO* 4.5 13.5 - - + -
166F ASP* 3.8 4.9 - - - +
167F ASP* 2.6 31.6 + - - -
169F ALA* 1.3 75.9 - - - +
171F ASP* 1.3 59.4 + - - +
173F ALA* 3.5 7.1 + - + +
174F ARG* 2.8 61.1 + - - +
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Residues in contact with ASP 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F VAL* 3.5 25.7 - - + +
164F GLY* 3.1 23.7 + - - -
165F LYS 4.8 1.1 + - - -
166F ASP* 4.5 1.4 + - - +
167F ASP 3.3 10.9 + - - +
168F ILE* 3.0 10.4 + - + +
170F THR* 1.3 75.2 - - - +
172F ILE* 1.3 64.8 + - + +
174F ARG* 2.8 30.8 + - - +
175F ILE* 3.0 31.0 + - + +
196F TRP* 3.3 28.0 + - + -
208F MET* 5.7 0.7 - - - -
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Residues in contact with ILE 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ILE* 3.1 34.2 + - + +
169F ALA* 3.7 10.8 - - - +
170F THR 3.4 0.2 - - - -
171F ASP* 1.3 75.7 - - + +
173F ALA* 1.3 57.1 + - - +
175F ILE* 3.1 8.9 + - - +
176F GLN* 2.9 46.0 + - + +
204F ALA* 4.4 14.8 - - + +
207F LYS* 3.8 36.6 - - + +
208F MET* 4.4 24.5 - - + +
213F LEU* 4.8 0.8 - - + +
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Residues in contact with ALA 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PRO* 4.1 14.7 - - + +
169F ALA 3.1 14.5 + - - +
170F THR* 3.6 9.0 - - + +
172F ILE* 1.3 79.6 - - - +
174F ARG* 1.3 62.8 + - - +
176F GLN* 3.8 7.8 - - - +
177F GLU* 3.2 24.4 + - - +
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F VAL* 4.5 13.6 - - - +
139F ASN* 2.8 28.8 + - - +
140F SER* 4.8 2.0 - - - +
141F PRO* 3.9 23.1 - - + +
144F MET* 3.5 29.0 - - + -
163F VAL* 5.0 2.7 - - + -
166F ASP* 2.8 39.6 + - - +
170F THR* 2.8 35.6 + - - +
171F ASP* 2.8 41.6 + - - +
172F ILE 3.2 0.4 - - - -
173F ALA* 1.3 77.6 - - - +
175F ILE* 1.3 60.3 + - + +
177F GLU* 3.3 2.1 + - - +
178F ILE* 3.1 37.7 + - + +
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Residues in contact with ILE 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F ILE* 3.4 27.1 - - + -
163F VAL* 3.9 10.5 - - + -
171F ASP 3.0 15.3 + - - +
172F ILE 3.1 5.6 + - - +
174F ARG* 1.3 75.0 - - + +
176F GLN* 1.3 59.0 + - - +
178F ILE* 4.0 4.6 - - + +
179F ARG* 3.1 27.0 + - - +
188F LEU* 4.5 9.4 - - + -
190F LEU* 3.4 27.6 - - + -
208F MET* 4.0 18.8 - - - -
213F LEU* 4.0 15.6 - - + +
215F ILE* 3.6 27.1 - - + -
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Residues in contact with GLN 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F ILE* 2.9 31.8 + - + +
173F ALA* 3.8 9.0 - - - +
174F ARG 3.2 0.4 - - - -
175F ILE* 1.3 78.7 - - - +
177F GLU* 1.3 58.7 + - - +
179F ARG* 3.9 1.6 - - - +
180F LYS* 3.2 28.6 + - - +
211F ALA* 4.2 19.0 - - - +
213F LEU* 3.6 29.4 - - + +
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Residues in contact with GLU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F PRO* 4.0 18.8 - - + +
142F GLU* 4.3 13.0 - - - +
145F ALA* 3.8 16.6 - - + -
173F ALA 3.2 17.3 + - - +
174F ARG 3.3 3.1 + - - +
176F GLN* 1.3 75.4 - - - +
178F ILE* 1.3 60.4 + - - +
180F LYS* 4.5 18.6 - - - +
181F ARG* 3.1 52.5 + - - +
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Residues in contact with ILE 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F VAL* 4.8 0.4 - - + -
141F PRO 4.9 0.4 - - - +
144F MET* 3.8 26.9 - - + +
145F ALA* 3.9 26.7 - - - +
148F ALA* 4.1 17.2 - - + +
161F ILE* 3.9 36.3 - - + -
174F ARG 3.1 26.0 + - - +
175F ILE* 4.2 4.5 - - - +
177F GLU* 1.3 75.0 - - - +
179F ARG* 1.3 64.6 + - - +
181F ARG* 3.3 2.2 + - - +
182F VAL* 3.0 31.1 + - + +
188F LEU* 4.0 29.2 - - + -
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Residues in contact with ARG 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F ILE 3.1 17.3 + - - +
176F GLN 3.9 4.0 - - - +
178F ILE* 1.3 77.8 - - - +
180F LYS* 1.3 63.1 + - - +
182F VAL* 4.5 1.1 - - - -
183F GLY* 3.0 54.2 + - - +
184F SER* 3.7 21.8 + - - +
186F VAL* 2.4 34.8 + - - +
188F LEU* 3.5 31.4 - - + +
212F GLY 5.2 1.8 - - - -
213F LEU* 2.4 63.7 + - + +
214F GLY* 3.5 14.8 + - - -
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Residues in contact with LYS 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F GLN 3.2 16.2 + - - +
177F GLU* 4.3 20.0 - - - +
179F ARG* 1.3 80.3 - - - +
181F ARG* 1.3 64.1 + - - +
182F VAL 3.6 0.3 + - - -
183F GLY* 4.0 5.0 + - - -
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Residues in contact with ARG 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F GLU* 3.0 33.0 + - - +
145F ALA* 3.4 32.9 + - + +
146F ALA* 3.9 24.4 - - - +
149F GLU* 3.2 37.4 + - + +
177F GLU* 3.1 45.3 + - - +
178F ILE* 3.7 3.8 - - - +
179F ARG 3.2 0.2 - - - -
180F LYS* 1.3 81.6 - - - +
182F VAL* 1.3 59.2 + - + +
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Residues in contact with VAL 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F ALA* 4.2 22.9 - - + +
149F GLU* 4.6 2.2 - - - +
152F LEU* 3.5 35.9 - - + +
159F LEU* 4.3 10.8 - - + -
178F ILE* 3.0 19.5 + - + +
179F ARG* 4.0 6.7 - - - +
181F ARG* 1.3 79.1 - - + +
183F GLY* 1.3 73.4 + - - +
186F VAL* 3.3 38.4 - - + +
188F LEU* 4.8 5.4 - - + -
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Residues in contact with GLY 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179F ARG* 3.0 29.2 + - - -
180F LYS* 4.0 4.5 + - - -
181F ARG 3.6 2.0 - - - -
182F VAL* 1.3 90.1 - - - +
184F SER* 1.3 59.7 + - - -
185F ALA 3.5 3.4 + - - -
186F VAL 4.3 0.9 + - - -
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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