Contacts of the helix formed by residues 167 - 183 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ASP* 1.3 90.4 - - - +
168B ILE* 1.3 65.3 + - - +
169B ALA* 3.7 8.2 + - - +
170B THR* 2.7 42.6 + - - -
171B ASP* 3.2 27.8 + - - -
174B ARG* 4.5 0.2 + - - -
196B TRP* 5.7 0.2 - - - -
200B GLU* 5.6 1.1 - - - -
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Residues in contact with ILE 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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167B ASP* 1.3 75.5 - - - +
169B ALA* 1.3 58.9 + - + +
171B ASP* 3.2 6.0 + - - +
172B ILE* 3.0 38.3 + - + +
196B TRP* 3.2 44.9 - - + +
200B GLU* 3.3 35.2 + - + +
203B THR* 5.2 5.2 - - + -
204B ALA* 3.6 30.1 - - + +
207B LYS* 4.8 9.6 - - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ASP* 3.4 7.6 + - - +
168B ILE* 1.3 79.0 - - + +
170B THR* 1.3 60.8 + - - +
172B ILE* 3.4 9.4 + - - +
173B ALA* 3.0 26.7 + - - +
207B LYS* 5.8 4.9 - - - +
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Residues in contact with THR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B PRO* 4.7 15.0 - - + -
166B ASP* 3.8 8.9 + - - +
167B ASP* 2.7 31.6 + - - -
169B ALA* 1.3 73.4 - - - +
171B ASP* 1.3 59.7 + - - +
173B ALA* 3.4 7.4 - - - +
174B ARG* 3.0 61.7 + - - +
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 5.5 0.3 - - - +
163B VAL* 3.7 16.7 - - + +
164B GLY* 3.2 30.7 + - - -
165B LYS 4.7 1.8 + - - -
166B ASP 5.4 0.3 + - - -
167B ASP 3.2 18.2 + - - +
168B ILE* 3.2 13.1 + - + +
170B THR* 1.3 73.9 - - - +
172B ILE* 1.3 65.4 + - + +
174B ARG* 3.1 26.5 + - - +
175B ILE* 3.2 29.7 + - - +
196B TRP* 3.2 26.3 + - + -
208B MET* 5.0 3.4 - - + -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ILE* 3.0 32.3 + - + +
169B ALA* 3.8 7.6 - - - +
170B THR 3.3 0.2 - - - -
171B ASP* 1.3 75.4 - - - +
173B ALA* 1.3 54.6 + - - +
175B ILE* 3.3 3.4 + - - +
176B GLN* 2.7 45.3 + - + +
204B ALA* 4.1 6.1 - - - +
207B LYS* 3.6 44.0 - - + +
208B MET* 3.8 33.9 - - + +
211B ALA* 5.9 1.6 - - + -
213B LEU* 4.4 6.7 - - + +
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Residues in contact with ALA 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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141B PRO* 4.3 14.6 - - + -
169B ALA 3.0 17.7 + - - +
170B THR* 3.4 10.8 - - + +
171B ASP 3.2 0.4 - - - -
172B ILE* 1.3 78.6 - - - +
174B ARG* 1.3 52.6 + - - +
176B GLN* 3.3 6.9 + - - +
177B GLU* 2.8 36.7 + - - +
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Residues in contact with ARG 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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138B VAL* 3.7 17.3 - - - +
139B ASN* 2.9 27.3 + - - +
140B SER* 5.1 1.0 - - - +
141B PRO* 3.9 26.1 - - + +
144B MET* 3.4 32.4 - - + -
162B LYS 5.1 2.0 - - - -
163B VAL* 5.4 1.6 - - - -
166B ASP* 3.3 31.7 + - - -
170B THR* 3.0 42.6 + - - +
171B ASP* 3.1 32.9 + - - +
173B ALA* 1.3 76.1 - - - +
175B ILE* 1.3 59.7 + - + +
177B GLU* 3.4 1.6 + - - +
178B ILE* 3.0 36.6 + - + +
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 3.8 23.8 - - + -
163B VAL* 3.9 12.6 - - + -
171B ASP 3.2 17.1 + - - +
172B ILE 3.8 2.9 - - - +
174B ARG* 1.3 73.2 - - + +
176B GLN* 1.3 67.8 + - - +
178B ILE* 3.2 6.4 + - + +
179B ARG* 2.9 27.2 + - - +
188B LEU* 4.7 9.6 - - + +
190B LEU* 3.3 26.9 - - + -
208B MET* 4.0 17.9 - - + -
213B LEU* 3.7 17.9 - - + -
215B ILE* 3.5 29.4 - - + -
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Residues in contact with GLN 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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172B ILE* 2.7 29.6 + - + +
173B ALA* 3.4 8.3 - - - +
175B ILE* 1.3 73.1 - - - +
177B GLU* 1.3 61.7 + - - +
179B ARG* 3.6 1.2 + - - +
180B LYS* 3.2 26.7 + - + +
211B ALA* 3.7 19.8 + - - +
213B LEU* 3.6 34.3 - - + +
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Residues in contact with GLU 177 (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 PRO* 4.0 18.6 - - + +
142B GLU* 3.9 9.4 - - - +
145B ALA* 3.7 20.2 - - + -
173B ALA 2.8 18.9 + - - +
174B ARG 3.9 4.0 - - - +
175B ILE 3.2 0.2 - - - -
176B GLN* 1.3 71.2 - - - +
178B ILE* 1.3 66.0 + - - +
180B LYS* 3.4 22.6 + - - +
181B ARG* 3.0 45.8 + - - +
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Residues in contact with ILE 178 (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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136B VAL* 5.1 0.7 - - + -
141B PRO 5.1 0.4 - - - +
144B MET* 4.1 16.2 - - + +
145B ALA* 3.9 27.1 - - + +
148B ALA* 3.9 24.2 - - + -
161B ILE* 3.5 37.2 - - + -
174B ARG 3.0 33.2 + - - +
175B ILE* 3.2 6.5 + - + +
177B GLU* 1.3 74.5 - - - +
179B ARG* 1.3 56.7 + - - +
181B ARG* 3.2 4.4 + - - +
182B VAL* 2.9 38.9 + - + +
188B LEU* 4.3 24.5 - - + -
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Residues in contact with ARG 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 2.9 15.9 + - + +
176B GLN 3.8 0.7 - - - +
178B ILE* 1.3 74.4 - - - +
180B LYS* 1.3 64.3 + - - +
182B VAL* 4.1 4.5 - - - -
183B GLY* 3.1 51.8 + - - +
184B SER* 3.7 18.3 + - - +
186B VAL* 2.4 31.9 + - - +
187B LYS* 4.6 0.4 - - - +
188B LEU* 3.6 31.2 - - + +
212B GLY 4.8 3.6 - - - -
213B LEU* 2.8 64.4 + - + +
214B GLY* 3.6 16.3 + - - -
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Residues in contact with LYS 180 (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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176B GLN* 3.2 18.8 + - + +
177B GLU* 3.4 25.5 + - - +
179B ARG* 1.3 79.3 - - - +
181B ARG* 1.3 72.3 + - - +
182B VAL 3.6 0.5 + - - -
183B GLY* 4.3 4.3 + - - -
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Residues in contact with ARG 181 (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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142B GLU* 3.0 41.2 + - - -
145B ALA* 3.7 23.3 + - + +
146B ALA* 3.9 21.0 - - - +
149B GLU* 3.0 39.5 + - - +
177B GLU* 3.0 36.2 + - - +
178B ILE* 3.6 6.1 - - - +
180B LYS* 1.3 91.6 - - + +
182B VAL* 1.3 58.7 + - + +
183B GLY 3.8 0.2 - - - -
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Residues in contact with VAL 182 (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 ALA* 5.1 4.3 - - + -
149B GLU* 5.6 2.7 - - + +
152B LEU* 3.0 37.5 - - + -
159B LEU* 4.7 5.4 - - + -
178B ILE* 2.9 24.4 + - + +
179B ARG* 3.9 9.4 - - - +
181B ARG* 1.3 79.2 - - + +
183B GLY* 1.3 74.9 + - - +
185B ALA* 5.6 1.2 - - - +
186B VAL* 3.3 33.4 + - + +
188B LEU* 4.7 6.1 - - + -
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Residues in contact with GLY 183 (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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179B ARG* 3.1 34.6 + - - +
180B LYS 4.3 3.7 + - - -
181B ARG 3.8 0.6 - - - -
182B VAL* 1.3 86.3 - - - +
184B SER* 1.3 59.6 - - - -
185B ALA* 3.1 9.3 + - - -
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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
------------------------------------------------------------
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