Contacts of the helix formed by residues 167 - 183 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP* 1.3 89.6 + - - +
168A ILE* 1.3 66.0 + - - +
169A ALA* 4.2 7.3 + - + +
170A THR* 2.6 46.5 + - - -
171A ASP* 3.4 14.2 + - - +
200A GLU* 5.9 0.7 - - - -
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ASP 4.3 0.4 + - - -
167A ASP* 1.3 74.8 - - - +
169A ALA* 1.3 67.9 + - + +
171A ASP* 3.3 10.3 + - + +
172A ILE* 3.3 29.5 + - + +
196A TRP* 3.4 35.2 - - + +
200A GLU* 3.7 39.6 + - + +
204A ALA* 3.4 32.5 - - + -
207A LYS* 5.9 1.6 - - - +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASP* 3.3 8.0 - - + +
168A ILE* 1.3 83.5 - - + +
170A THR* 1.3 64.2 + - - +
172A ILE* 3.2 13.4 + - - +
173A ALA* 3.1 21.4 + - - +
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PRO* 4.6 15.3 - - + -
166A ASP* 4.0 5.5 + - - +
167A ASP* 2.6 28.5 + - - -
169A ALA* 1.3 75.7 - - - +
171A ASP* 1.3 60.6 + - - +
173A ALA* 3.3 7.6 + - + +
174A ARG* 2.8 69.0 + - - +
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Residues in contact with ASP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 5.1 0.3 - - - +
163A VAL* 3.4 34.8 - - + +
164A GLY* 3.3 19.9 + - - -
165A LYS 4.4 2.6 + - - -
166A ASP 5.0 0.3 - - - -
167A ASP 3.4 17.7 + - - +
168A ILE* 3.3 9.0 + - + +
170A THR* 1.3 75.5 - - - +
172A ILE* 1.3 66.4 + - + +
174A ARG* 3.1 25.5 + - - +
175A ILE* 3.0 28.6 + - - +
190A LEU* 6.3 0.2 - - + -
196A TRP* 3.6 22.2 + - + -
208A MET* 5.6 1.3 - - - -
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Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 3.3 17.4 + - + +
169A ALA* 3.2 15.1 + - - +
171A ASP* 1.3 77.4 - - + +
173A ALA* 1.3 58.6 + - - +
175A ILE* 3.1 7.7 + - - +
176A GLN* 2.9 51.4 + - + +
204A ALA* 4.4 19.7 - - + +
207A LYS* 3.7 41.5 - - + +
208A MET* 4.3 25.8 - - + -
213A LEU* 5.0 1.0 - - + +
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PRO* 4.0 13.4 - - + +
169A ALA 3.1 12.9 + - - +
170A THR* 3.5 12.6 - - + +
171A ASP 3.3 0.2 - - - -
172A ILE* 1.3 76.3 - - - +
174A ARG* 1.3 62.3 + - - +
176A GLN* 3.8 9.5 - - - +
177A GLU* 3.1 25.5 + - - +
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 5.0 10.6 - - - +
139A ASN* 2.9 30.1 + - - +
140A SER* 5.1 1.0 - - - +
141A PRO* 3.8 23.7 - - + +
144A MET* 3.5 29.9 - - + -
162A LYS 5.2 0.4 - - - -
163A VAL* 4.9 3.1 - - + -
165A LYS* 5.6 0.6 - - - +
166A ASP* 3.1 34.1 + - - +
170A THR* 2.8 45.6 + - - +
171A ASP* 3.1 33.3 + - - +
173A ALA* 1.3 77.0 - - - +
175A ILE* 1.3 60.8 + - + +
177A GLU* 3.8 1.6 - - - +
178A ILE* 3.0 38.2 + - + +
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Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ILE* 3.4 35.7 - - + -
163A VAL* 4.0 5.6 - - + -
171A ASP 3.0 15.1 + - - +
172A ILE 3.7 4.7 - - - +
174A ARG* 1.3 73.9 - - + +
176A GLN* 1.3 59.7 + - - +
178A ILE* 4.1 3.5 - - + +
179A ARG* 2.9 28.9 + - - +
188A LEU* 4.2 11.2 - - + -
190A LEU* 3.5 31.4 - - + -
208A MET* 4.0 11.4 - - - -
213A LEU* 4.0 15.0 - - + -
215A ILE* 3.6 28.3 - - + -
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ILE* 2.9 39.8 + - + +
173A ALA* 3.8 8.3 - - - +
175A ILE* 1.3 76.1 - - - +
177A GLU* 1.3 62.4 + - - +
179A ARG* 3.6 2.4 - - - +
180A LYS* 3.2 27.2 + - - +
211A ALA* 4.5 15.8 - - - +
213A LEU* 3.6 29.3 - - + +
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A PRO* 3.9 29.8 - - + +
142A GLU* 4.4 9.0 - - - +
145A ALA* 4.0 5.8 - - + -
173A ALA 3.1 15.4 + - - +
174A ARG 3.8 3.6 - - - +
176A GLN* 1.3 78.6 - - - +
178A ILE* 1.3 64.5 + - - +
180A LYS* 3.3 31.3 + - - +
181A ARG* 3.0 51.4 + - - +
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Residues in contact with ILE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A VAL* 4.6 0.2 - - + -
141A PRO 4.7 0.7 - - - +
144A MET* 3.7 26.5 - - + +
145A ALA* 3.8 27.4 - - + +
148A ALA* 4.0 21.1 - - + -
161A ILE* 3.9 43.5 - - + -
174A ARG 3.0 27.4 + - - +
175A ILE* 4.1 4.9 - - - +
177A GLU* 1.3 75.5 - - - +
179A ARG* 1.3 64.5 + - - +
181A ARG* 3.3 1.7 + - - +
182A VAL* 3.0 31.0 + - + +
188A LEU* 4.3 17.7 - - + -
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Residues in contact with ARG 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE 2.9 20.1 + - - +
176A GLN 3.6 5.4 - - - +
177A GLU 3.3 0.2 - - - -
178A ILE* 1.3 77.7 - - - +
180A LYS* 1.3 64.0 + - - +
182A VAL* 4.0 2.0 - - - +
183A GLY 2.9 56.8 + - - +
184A SER* 4.1 15.6 + - - +
186A VAL* 2.7 46.1 + - - +
188A LEU* 3.6 28.4 - - + +
212A GLY 4.9 2.7 - - - -
213A LEU* 2.7 63.8 + - + +
214A GLY* 3.6 12.3 + - - -
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Residues in contact with LYS 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLN 3.2 13.7 + - - +
177A GLU* 3.3 38.9 + - - +
179A ARG* 1.3 80.0 - - + +
181A ARG* 1.3 69.4 + - - +
182A VAL 3.6 0.2 + - - -
183A GLY* 4.1 5.4 + - - -
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 3.0 50.6 + - - +
145A ALA* 3.7 22.6 - - + +
146A ALA* 4.1 10.7 - - - +
149A GLU* 3.6 46.1 + - + +
177A GLU* 3.0 45.5 + - - +
178A ILE 3.8 2.9 - - - +
179A ARG 3.2 0.6 - - - -
180A LYS* 1.3 86.2 - - - +
182A VAL* 1.3 60.8 + - + +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ALA* 3.9 36.6 - - + +
149A GLU* 4.5 3.4 - - + +
152A LEU* 3.6 36.4 - - + +
159A LEU* 4.2 9.0 - - + -
178A ILE* 3.0 18.5 + - + +
179A ARG* 4.0 4.9 - - - +
181A ARG* 1.3 79.3 - - + +
183A GLY* 1.3 68.7 + - - +
186A VAL* 3.4 36.9 - - + +
188A LEU* 4.9 4.3 - - + -
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Residues in contact with GLY 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ARG* 2.9 39.0 + - - +
180A LYS* 4.1 4.8 + - - -
181A ARG 3.6 1.6 - - - -
182A VAL* 1.3 80.3 - - - +
184A SER* 1.3 60.6 + - - -
185A ALA 3.4 3.4 - - - -
186A VAL* 4.8 1.3 - - - -
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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