Contacts of the helix formed by residues 167 - 183 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ASP* 1.3 89.8 + - - +
168H ILE* 1.3 64.8 + - - +
169H ALA* 3.5 12.8 + - - +
170H THR* 2.5 43.1 + - - -
171H ASP* 3.5 12.7 + - - -
200H GLU* 5.7 0.4 - - - -
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Residues in contact with ILE 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ASP 4.2 0.6 + - - -
167H ASP* 1.3 70.5 - - - +
169H ALA* 1.3 70.8 + - + +
171H ASP* 3.0 20.4 + - + +
172H ILE* 3.2 15.9 + - + +
196H TRP* 3.2 53.1 - - + +
200H GLU* 3.7 34.4 + - + +
204H ALA* 3.3 33.9 - - + -
207H LYS* 6.1 3.1 - - - +
208H MET* 4.9 2.0 - - + -
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Residues in contact with ALA 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H ASP* 3.4 10.8 + - - +
168H ILE* 1.3 83.5 - - + +
170H THR* 1.3 61.5 + - - +
172H ILE* 3.4 11.2 + - - +
173H ALA* 3.1 19.8 + - - +
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Residues in contact with THR 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 4.6 16.6 - - + -
166H ASP* 4.0 2.5 - - - +
167H ASP* 2.5 34.6 + - - -
168H ILE 3.1 0.8 - - - -
169H ALA* 1.3 77.0 - - - +
171H ASP* 1.3 59.5 + - - +
173H ALA* 3.2 7.3 + - + +
174H ARG* 2.9 54.6 + - - +
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Residues in contact with ASP 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163H VAL* 3.5 19.9 - - + +
164H GLY* 2.9 34.2 + - - -
165H LYS 4.5 1.5 + - - -
166H ASP 5.4 0.3 + - - -
167H ASP 3.5 10.9 + - - +
168H ILE* 3.0 18.7 + - + +
170H THR* 1.3 77.0 - - - +
172H ILE* 1.3 62.4 + - + +
174H ARG* 3.0 37.1 + - - +
175H ILE* 3.1 19.3 + - - +
196H TRP* 3.0 22.4 + - + -
208H MET* 5.5 2.5 - - + -
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Residues in contact with ILE 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 3.2 13.3 + - + +
169H ALA* 3.7 13.0 - - - +
170H THR 3.2 0.2 - - - -
171H ASP* 1.3 74.4 - - + +
173H ALA* 1.3 66.1 + - - +
175H ILE* 3.1 9.2 + - - +
176H GLN* 2.8 50.7 + - + +
204H ALA* 4.3 14.1 - - + +
207H LYS* 4.0 39.3 - - + +
208H MET* 4.1 23.3 - - + -
213H LEU* 4.9 7.0 - - + -
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Residues in contact with ALA 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 4.0 16.5 - - + +
169H ALA 3.1 13.8 + - - +
170H THR* 3.4 13.7 - - + +
172H ILE* 1.3 76.5 - - - +
174H ARG* 1.3 61.5 + - - +
176H GLN* 3.5 12.4 + - - +
177H GLU* 3.1 26.3 + - - +
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Residues in contact with ARG 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H VAL* 3.6 22.0 - - - +
139H ASN 3.0 23.7 + - - +
140H SER* 4.9 1.6 - - - +
141H PRO* 4.1 20.3 - - + +
144H MET* 3.5 33.0 - - + -
163H VAL* 5.0 3.4 - - + -
166H ASP* 2.8 41.6 + - - +
170H THR* 2.9 36.9 + - - +
171H ASP* 3.0 32.8 + - - +
173H ALA* 1.3 77.7 - - - +
175H ILE* 1.3 66.3 + - + +
177H GLU* 3.4 2.8 + - - +
178H ILE* 3.0 27.9 + - - +
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Residues in contact with ILE 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H ILE* 3.6 24.2 - - + -
163H VAL* 4.0 7.6 - - + -
171H ASP 3.1 16.0 + - - +
172H ILE* 3.1 5.4 + - - +
174H ARG* 1.3 75.8 - - + +
176H GLN* 1.3 58.1 + - - +
178H ILE* 3.2 6.8 + - + +
179H ARG* 2.8 28.3 + - + +
188H LEU* 4.0 13.9 - - + -
190H LEU* 3.4 30.5 - - + -
208H MET* 4.2 15.7 - - + -
213H LEU* 3.8 24.9 - - + -
215H ILE* 4.0 20.0 - - + -
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Residues in contact with GLN 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H ILE* 2.8 44.5 + - + +
173H ALA* 3.9 10.3 - - - +
175H ILE* 1.3 71.9 - - - +
177H GLU* 1.3 62.1 + - - +
179H ARG* 3.8 5.9 - - - +
180H LYS* 2.8 34.0 + - - +
211H ALA* 4.6 9.5 - - - +
213H LEU* 4.2 22.9 - - + +
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Residues in contact with GLU 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141H PRO* 3.6 33.9 - - + +
142H GLU* 4.3 5.3 - - - +
145H ALA* 3.5 10.2 - - + +
173H ALA 3.1 17.6 + - - +
174H ARG 3.7 4.5 - - - +
175H ILE 3.3 0.2 - - - -
176H GLN* 1.3 79.0 - - - +
178H ILE* 1.3 59.6 + - - +
180H LYS* 4.0 26.0 + - - +
181H ARG* 3.3 44.5 + - - +
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Residues in contact with ILE 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H VAL* 4.9 0.2 - - + -
144H MET* 3.9 37.9 - - + +
145H ALA* 4.0 11.2 - - + +
148H ALA* 4.0 17.4 - - + +
161H ILE* 3.7 37.7 - - + -
174H ARG 3.0 21.9 + - - +
175H ILE* 3.6 9.0 - - + +
177H GLU* 1.3 75.8 - - - +
179H ARG* 1.3 57.6 + - - +
181H ARG* 3.3 2.3 + - - +
182H VAL* 3.0 37.7 + - + +
188H LEU* 4.0 28.5 - - + -
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Residues in contact with ARG 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H ILE* 2.8 22.7 + - + +
176H GLN* 3.8 6.3 - - - +
178H ILE* 1.3 71.4 - - - +
180H LYS* 1.3 64.1 + - - +
182H VAL* 4.1 2.2 - - - +
183H GLY* 3.1 51.6 + - - -
184H SER* 4.0 18.8 + - - +
186H VAL* 2.6 42.0 + - - +
188H LEU* 3.7 22.1 - - + +
212H GLY 4.6 3.6 - - - -
213H LEU* 2.8 59.1 + - + +
214H GLY* 3.5 17.8 + - - -
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Residues in contact with LYS 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176H GLN 2.8 23.8 + - - +
177H GLU* 4.0 28.6 + - - +
179H ARG* 1.3 73.5 - - - +
181H ARG* 1.3 58.2 + - - +
183H GLY 4.8 1.0 + - - -
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Residues in contact with ARG 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142H GLU* 3.1 40.8 + - - -
145H ALA* 3.5 34.1 + - + +
146H ALA* 3.6 22.2 - - - +
149H GLU* 3.1 48.9 + - + +
177H GLU* 3.3 32.6 + - - +
178H ILE 3.8 2.7 - - - +
179H ARG 3.1 0.4 - - - -
180H LYS* 1.3 80.8 - - - +
182H VAL* 1.3 59.7 + - + +
183H GLY 3.6 0.4 - - - -
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Residues in contact with VAL 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H ALA 6.0 0.4 - - - +
148H ALA* 4.4 14.6 - - + +
149H GLU* 5.0 5.2 - - + +
152H LEU* 3.5 42.1 - - + +
159H LEU* 4.6 5.8 - - + -
178H ILE* 3.0 37.9 + - + +
179H ARG* 4.1 6.3 - - - +
181H ARG* 1.3 77.7 - - + +
183H GLY* 1.3 73.7 + - - +
185H ALA* 5.3 1.0 + - - +
186H VAL* 3.6 27.7 - - + +
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Residues in contact with GLY 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179H ARG* 3.1 35.3 + - - -
180H LYS 4.8 0.8 + - - -
181H ARG 3.6 1.4 - - - -
182H VAL* 1.3 87.9 - - - +
184H SER* 1.3 58.5 + - - -
185H ALA* 3.3 7.5 + - - -
186H VAL* 4.0 1.6 - - - +
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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