Contacts of the helix formed by residues 197 - 211 (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 ARG 197 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D TRP* 1.3 75.9 - - - +
198D PRO* 1.3 69.8 - - + +
199D LYS* 4.5 7.5 - - + +
200D GLU* 3.0 65.4 + - + +
201D ALA* 2.8 26.3 + - - +
222D VAL* 3.9 0.2 - - - -
240F PRO* 5.5 8.9 - - - +
263F ASP* 5.9 4.3 - - - -
264F LEU* 6.4 1.8 - - - -
289F GLY 4.6 17.3 - - - +
291F GLU* 6.0 6.8 + - - +
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Residues in contact with PRO 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ARG* 1.3 87.7 - - + +
199D LYS* 1.3 56.9 + - - +
201D ALA* 3.2 2.4 + - - +
202D VAL* 3.0 34.8 + - - +
222D VAL* 3.6 17.9 - - + -
226D ASP* 3.6 23.3 - - - +
229D GLY* 3.7 26.0 - - - +
232D LYS* 4.0 23.3 - - + +
233D VAL* 3.8 4.2 - - + +
260F ARG* 4.9 2.0 - - - +
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Residues in contact with LYS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D ARG* 3.4 7.8 - - + +
198D PRO* 1.3 75.5 - - - +
200D GLU* 1.3 64.9 + - - +
202D VAL* 3.5 6.3 + - - +
203D THR* 2.9 30.8 + - - +
232D LYS* 5.0 6.6 - - - +
234F THR* 2.7 33.9 + - + +
237F THR* 3.4 25.6 + - - +
238F ASP 3.8 9.2 - - - +
239F THR 2.5 35.9 + - - -
240F PRO* 4.7 3.4 - - + -
241F ILE* 3.7 1.2 - - - +
263F ASP* 2.8 39.9 + - - +
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Residues in contact with GLU 200 (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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166D ASP 5.3 1.4 - - - +
167D ASP* 4.9 5.0 - - - +
168D ILE* 3.5 43.0 + - + +
195D GLY 4.2 3.2 - - - +
196D TRP* 3.5 12.8 - - + -
197D ARG* 3.0 69.7 + - - +
199D LYS* 1.3 79.8 - - - +
201D ALA* 1.3 61.5 + - - +
203D THR* 3.5 6.1 - - - -
204D ALA* 3.1 24.4 + - - +
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Residues in contact with ALA 201 (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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196D TRP* 3.6 32.1 - - + -
197D ARG 2.8 16.7 + - - +
198D PRO* 3.4 5.8 - - + +
200D GLU* 1.3 76.2 - - - +
202D VAL* 1.3 65.7 + - - +
204D ALA* 3.4 1.0 + - - +
205D ILE* 3.1 31.4 + - - +
221D PRO* 4.1 8.3 - - + -
222D VAL* 4.6 0.7 - - + -
233D VAL* 3.8 19.5 - - + -
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Residues in contact with VAL 202 (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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198D PRO 3.0 21.9 + - - +
199D LYS* 3.9 6.3 - - - +
200D GLU 3.4 0.2 - - - -
201D ALA* 1.3 74.6 - - - +
203D THR* 1.3 64.9 + - - +
205D ILE* 3.8 1.5 - - - +
206D ARG* 2.9 68.0 + - + +
232D LYS* 4.1 8.7 - - + +
233D VAL* 3.8 26.0 - - + +
236D ALA* 4.0 18.4 - - + +
237D THR* 4.1 9.0 - - + -
238F ASP* 5.3 1.3 - - - +
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Residues in contact with THR 203 (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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168D ILE* 5.8 3.8 - - + -
199D LYS* 2.9 17.2 + - - +
200D GLU* 3.5 7.3 - - - -
202D VAL* 1.3 78.5 - - - +
204D ALA* 1.3 57.5 + - + +
206D ARG* 3.4 6.8 + - - +
207D LYS* 3.0 54.6 + - - +
238F ASP* 2.6 49.7 + - + +
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Residues in contact with ALA 204 (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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168D ILE* 3.5 40.2 - - + -
171D ASP* 6.3 0.2 - - + -
172D ILE* 3.9 8.7 - - + +
196D TRP* 4.5 9.9 - - + -
200D GLU 3.1 6.1 + - - +
201D ALA 4.1 2.5 - - - +
202D VAL 3.3 0.2 - - - -
203D THR* 1.3 76.9 - - - +
205D ILE* 1.3 65.8 + - - +
207D LYS* 3.4 2.8 + - - +
208D MET* 3.2 43.3 + - + +
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Residues in contact with ILE 205 (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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190D LEU* 6.0 0.2 - - + -
196D TRP* 4.2 17.9 - - + -
201D ALA* 3.1 20.1 + - + +
202D VAL 3.8 2.2 - - - +
204D ALA* 1.3 75.7 - - - +
206D ARG* 1.3 58.8 + - - +
208D MET* 3.2 11.6 + - + +
209D GLU* 3.0 26.9 + - - +
215D ILE* 6.2 1.6 - - + -
218D VAL* 4.1 20.9 - - + -
221D PRO* 5.0 0.7 - - + -
233D VAL* 3.6 28.7 - - + -
237D THR* 3.8 16.4 - - + -
239D THR* 3.4 33.9 - - + +
241D ILE* 4.0 12.8 - - + -
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Residues in contact with ARG 206 (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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202D VAL* 2.9 38.2 + - + +
203D THR* 3.6 7.0 - - - +
205D ILE* 1.3 76.2 - - - +
207D LYS* 1.3 61.4 + - - +
209D GLU* 3.6 18.5 + - - +
210D ASP* 3.2 36.6 + - - +
236D ALA* 2.9 41.3 + - - +
237D THR* 4.5 3.8 - - + +
238F ASP* 4.5 14.1 + - - -
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Residues in contact with LYS 207 (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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168D ILE* 5.3 8.4 - - + +
172D ILE* 3.6 34.4 - - + +
203D THR* 3.0 40.4 + - - +
204D ALA* 3.6 1.3 - - - +
205D ILE 3.3 0.2 - - - -
206D ARG* 1.3 77.4 - - - +
208D MET* 1.3 57.9 + - - +
210D ASP* 4.0 5.0 - - - +
211D ALA* 3.1 29.5 + - - +
238F ASP* 6.1 0.4 - - - +
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Residues in contact with MET 208 (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* 6.2 0.2 - - + -
171D ASP* 4.9 2.7 - - + -
172D ILE* 4.1 29.4 - - + +
175D ILE* 4.4 16.8 - - + -
190D LEU* 3.6 32.5 - - + -
196D TRP* 4.7 10.5 - - + -
204D ALA* 3.2 28.0 - - + +
205D ILE* 3.2 11.8 + - - +
206D ARG 3.2 0.2 - - - -
207D LYS* 1.3 76.4 - - - +
209D GLU* 1.3 62.9 + - - +
210D ASP 3.3 0.2 - - - -
211D ALA 3.8 0.2 - - - -
212D GLY 3.3 2.9 + - - -
213D LEU* 3.1 51.8 + - + +
214D GLY 4.5 1.2 + - - -
215D ILE* 4.1 20.0 - - + -
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Residues in contact with GLU 209 (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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205D ILE* 3.0 17.4 + - - +
206D ARG* 3.7 22.8 - - - +
208D MET* 1.3 77.4 - - - +
210D ASP* 1.3 67.4 + - - +
212D GLY* 3.3 12.8 + - - -
214D GLY 6.0 0.4 - - - +
237D THR* 3.8 4.9 - - - -
238D ASP* 2.9 41.1 + - + +
239D THR* 2.6 30.8 + - - +
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Residues in contact with ASP 210 (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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206D ARG* 3.2 24.1 + - - +
207D LYS* 4.1 4.2 - - - +
209D GLU* 1.3 79.1 - - - +
211D ALA* 1.3 59.5 - - - +
212D GLY* 3.2 5.9 + - - -
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Residues in contact with ALA 211 (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* 6.4 1.3 - - + -
176D GLN* 5.3 7.9 - - - +
207D LYS 3.1 19.4 + - - +
208D MET 3.6 0.4 + - - +
209D GLU 3.4 0.2 - - - -
210D ASP* 1.3 75.8 - - - +
212D GLY* 1.3 62.6 + - - +
213D LEU* 3.4 27.8 + - + +
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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