Contacts of the helix formed by residues 167 - 183 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D ASP* 1.3 85.8 + - + +
168D ILE* 1.3 65.6 + - - +
169D ALA* 3.3 22.9 + - - +
170D THR* 2.9 30.5 + - - -
171D ASP* 3.4 18.2 + - - +
196D TRP* 5.5 1.3 - - - +
200D GLU* 4.9 6.3 - - - +
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Residues in contact with ILE 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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167D ASP* 1.3 74.1 - - - +
169D ALA* 1.3 67.8 + - - +
171D ASP* 3.0 16.6 + - + +
172D ILE* 3.1 29.9 + - + +
196D TRP* 3.5 32.3 - - + +
200D GLU* 3.5 37.7 + - + +
203D THR* 5.8 3.1 - - + -
204D ALA* 3.5 31.0 - - + +
207D LYS* 5.3 9.0 - - - +
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Residues in contact with ALA 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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167D ASP* 3.3 16.4 + - - +
168D ILE* 1.3 82.4 - - - +
170D THR* 1.3 62.4 + - - +
172D ILE* 3.5 7.0 + - - +
173D ALA* 3.3 18.7 + - - +
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Residues in contact with THR 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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141D PRO* 4.3 18.6 - - + -
166D ASP* 4.1 4.6 + - - -
167D ASP* 2.9 23.9 + - - -
168D ILE 3.2 0.6 - - - -
169D ALA* 1.3 74.1 - - - +
171D ASP* 1.3 66.6 + - - +
173D ALA* 3.1 7.5 + - + +
174D ARG* 3.0 56.2 + - - +
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Residues in contact with ASP 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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163D VAL* 3.4 19.5 - - + +
164D GLY* 3.0 33.5 + - - -
165D LYS 4.5 1.0 + - - -
166D ASP* 4.6 0.6 - - - +
167D ASP 3.4 15.0 + - - +
168D ILE* 3.0 10.5 + - + +
170D THR* 1.3 78.0 - - - +
172D ILE* 1.3 64.5 + - + +
174D ARG* 3.0 37.9 + - - +
175D ILE* 3.3 18.4 + - - +
196D TRP* 3.3 24.8 + - + -
208D MET* 4.9 3.8 - - + -
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 3.1 29.2 + - + +
169D ALA* 3.7 7.9 - - - +
171D ASP* 1.3 74.8 - - + +
173D ALA* 1.3 63.7 + - - +
175D ILE* 3.2 6.0 + - - +
176D GLN* 3.1 47.3 + - + +
204D ALA* 3.9 13.7 - - + +
207D LYS* 3.6 45.1 - - + +
208D MET* 4.1 18.6 - - + +
213D LEU* 5.0 8.7 - - + -
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Residues in contact with ALA 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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141D PRO* 4.2 15.3 - - + +
169D ALA 3.3 10.3 + - - +
170D THR* 3.1 13.8 + - + +
172D ILE* 1.3 78.8 - - - +
174D ARG* 1.3 57.2 + - - +
176D GLN* 3.9 11.1 - - - +
177D GLU* 3.1 29.6 + - - +
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Residues in contact with ARG 174 (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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138D VAL* 3.9 20.1 - - - +
139D ASN 3.1 25.7 + - - -
140D SER* 4.9 2.0 - - - +
141D PRO* 3.8 24.4 - - + +
144D MET* 3.5 30.1 - - + -
162D LYS 5.4 2.2 - - - -
163D VAL* 5.4 1.1 - - + -
165D LYS* 5.3 0.8 - - - +
166D ASP* 3.0 36.8 + - - +
170D THR* 3.0 39.0 + - - +
171D ASP* 3.0 32.1 + - - +
173D ALA* 1.3 75.2 - - - +
175D ILE* 1.3 65.1 + - + +
177D GLU* 3.3 2.6 + - - +
178D ILE* 2.9 37.2 + - + +
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Residues in contact with ILE 175 (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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161D ILE* 3.4 34.5 - - + -
163D VAL* 4.1 9.0 - - + -
171D ASP 3.5 15.7 - - - +
172D ILE* 3.2 6.1 + - - +
174D ARG* 1.3 77.5 - - + +
176D GLN* 1.3 59.0 + - - +
178D ILE* 3.5 5.2 + - - +
179D ARG* 2.9 27.9 + - - +
188D LEU* 4.2 14.5 - - + +
190D LEU* 4.0 12.8 - - + -
208D MET* 4.4 20.6 - - + -
213D LEU* 4.2 19.5 - - + -
215D ILE* 3.9 25.8 - - + -
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Residues in contact with GLN 176 (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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172D ILE* 3.1 35.5 + - + +
173D ALA* 3.9 9.6 - - - +
175D ILE* 1.3 77.1 - - - +
177D GLU* 1.3 57.0 + - - +
179D ARG* 3.4 7.0 + - - +
180D LYS* 3.0 27.5 + - - +
211D ALA* 5.3 7.2 - - - +
213D LEU* 4.1 26.3 - - + +
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Residues in contact with GLU 177 (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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141D PRO* 3.7 29.8 - - + +
142D GLU* 4.8 6.1 - - - +
145D ALA* 3.7 9.7 - - + +
173D ALA 3.1 16.9 + - - +
174D ARG 3.8 2.9 - - - +
176D GLN* 1.3 75.7 - - - +
178D ILE* 1.3 65.0 + - - +
180D LYS* 3.6 30.7 + - - +
181D ARG* 3.2 41.1 + - - +
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Residues in contact with ILE 178 (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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136D VAL* 4.7 0.4 - - + -
144D MET* 3.9 34.8 - - + +
145D ALA* 4.0 12.1 - - + +
148D ALA* 4.0 17.0 - - + +
159D LEU* 4.7 0.7 - - + -
161D ILE* 3.9 38.4 - - + -
174D ARG 2.9 25.5 + - - +
175D ILE* 3.7 6.3 - - - +
177D GLU* 1.3 74.5 - - - +
179D ARG* 1.3 65.1 + - - +
181D ARG* 3.2 2.3 + - - +
182D VAL* 3.0 35.4 + - + +
188D LEU* 4.1 27.1 - - + -
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Residues in contact with ARG 179 (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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175D ILE 2.9 19.4 + - - +
176D GLN 3.4 6.0 + - - +
178D ILE* 1.3 76.7 - - - +
180D LYS* 1.3 62.9 + - - +
182D VAL* 4.1 2.6 - - - +
183D GLY* 3.0 43.9 + - - +
184D SER* 3.9 28.6 + - - +
186D VAL* 2.6 34.6 + - - +
188D LEU* 3.5 26.8 - - + +
212D GLY 4.8 3.6 + - - -
213D LEU* 2.6 61.3 + - + +
214D GLY* 3.7 10.1 + - - -
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Residues in contact with LYS 180 (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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176D GLN 3.0 16.3 + - - +
177D GLU* 3.6 29.6 + - - +
178D ILE 3.3 0.2 - - - -
179D ARG* 1.3 79.6 - - - +
181D ARG* 1.3 66.0 + - + +
182D VAL 3.2 0.7 + - - -
183D GLY* 3.8 4.9 + - - -
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Residues in contact with ARG 181 (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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142D GLU* 3.1 49.8 + - - -
145D ALA* 3.5 33.9 + - + +
146D ALA* 4.1 13.3 - - - +
148D ALA* 6.3 0.2 - - + -
149D GLU* 3.3 40.0 + - + +
152D LEU* 5.7 0.2 - - - +
177D GLU* 3.2 33.3 + - - +
178D ILE 3.2 3.1 + - - +
180D LYS* 1.3 81.8 - - - +
182D VAL* 1.3 57.8 + - + +
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Residues in contact with VAL 182 (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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148D ALA* 4.4 14.4 - - + +
149D GLU* 4.9 1.8 - - - +
152D LEU* 3.5 41.6 - - + +
159D LEU* 4.7 8.3 - - + -
178D ILE* 3.0 36.1 + - + +
179D ARG* 3.9 5.2 - - - +
181D ARG* 1.3 79.1 - - + +
183D GLY* 1.3 75.1 + - - +
185D ALA* 5.1 1.0 + - - +
186D VAL* 3.4 30.3 - - + +
188D LEU* 5.3 0.4 - - + -
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Residues in contact with GLY 183 (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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179D ARG* 3.0 23.7 + - - +
180D LYS 3.8 4.7 + - - -
181D ARG 3.8 0.2 - - - -
182D VAL* 1.3 95.9 - - - +
184D SER* 1.3 61.7 + - - -
185D ALA* 3.4 3.3 + - - -
186D VAL* 4.0 2.4 - - - +
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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