Contacts of the helix formed by residues 199 - 215 (chain B) in PDB entry 1TKI
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 THR 199 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B HIS* 3.2 69.7 - - + +
139B ASN* 4.8 5.2 - - - +
140B ILE 4.0 9.9 - - - +
141B GLY* 5.2 0.9 - - - -
171B LEU* 3.7 18.4 - - + +
198B SER* 1.3 75.1 - - - +
200B ALA* 1.3 56.6 + - - +
201B THR 3.1 0.2 - - - -
202B ASP* 3.1 20.3 + - - +
203B MET* 3.6 3.3 + - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER* 3.0 14.2 + - - +
199B THR* 1.3 79.4 + - - +
201B THR* 1.3 58.3 + - - +
202B ASP 3.2 0.4 - - - -
203B MET* 3.4 17.2 + - + +
204B TRP 3.4 0.5 + - - -
263B ARG* 3.5 35.0 - - + +
266B ARG* 2.8 36.5 + - + +
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Residues in contact with THR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 3.9 22.9 - - + -
186B TYR 4.8 1.3 - - - +
187B TYR* 5.7 3.1 - - + -
188B ALA* 4.1 6.1 - - + +
190B GLU* 2.9 21.5 + - - +
191B VAL* 3.7 30.7 - - + -
197B VAL* 3.4 7.0 - - + -
198B SER 2.8 28.9 + - - -
200B ALA* 1.3 77.9 - - - +
202B ASP* 1.3 62.0 + - - +
204B TRP* 3.3 13.5 + - - +
205B SER* 3.3 10.9 + - - -
266B ARG* 3.8 1.6 - - - +
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Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 4.1 13.0 - - + +
136B HIS* 2.9 28.6 + - + +
141B GLY* 3.6 5.3 - - - -
142B HIS* 2.8 31.7 + - - +
143B PHE* 2.8 32.7 + - - -
145B ILE* 4.4 6.9 - - + +
198B SER 5.3 0.4 - - - -
199B THR* 3.1 11.0 + - - +
201B THR* 1.3 76.8 - - - +
203B MET* 1.3 61.1 + - - +
205B SER* 3.1 10.2 + - - -
206B LEU* 2.9 26.7 + - - +
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Residues in contact with MET 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B CYS* 4.9 0.9 - - - -
132B LEU* 4.2 8.3 - - + -
136B HIS* 3.9 14.4 - - + +
199B THR 3.9 10.8 - - - +
200B ALA* 3.4 13.7 + - - +
201B THR 3.3 0.6 - - - -
202B ASP* 1.3 75.8 - - - +
204B TRP* 1.3 64.5 + - - +
206B LEU* 3.2 32.2 + - + +
207B GLY 3.0 17.2 + - - -
258B LEU* 3.6 24.6 - - + +
266B ARG* 4.2 6.1 - - - -
267B MET 3.1 22.7 - - - +
268B THR* 3.8 9.9 - - - +
269B ALA* 3.4 41.7 - - + +
272B ALA* 4.2 5.4 - - + -
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Residues in contact with TRP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU 3.2 19.1 + - - -
186B TYR 3.6 9.9 - - - -
187B TYR 3.7 1.4 - - - -
188B ALA* 3.4 35.2 - - + +
189B PRO* 3.7 15.7 - - + -
200B ALA 3.4 3.4 + - - -
201B THR 3.3 10.7 + - - +
202B ASP 3.2 0.2 - - - -
203B MET* 1.3 76.1 - - - +
205B SER* 1.3 59.0 + - - +
207B GLY* 2.8 21.7 + - - -
208B THR* 3.0 12.0 + - - -
220B PHE* 3.4 35.0 - + - -
232B ILE* 3.8 29.8 - - + +
235B ALA* 4.0 10.1 - - + -
258B LEU 3.8 11.0 - - - -
259B LEU* 3.5 17.7 - - + +
260B VAL 3.6 45.5 - - - -
266B ARG* 3.7 9.1 - - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PHE* 5.6 2.6 - - - -
144B ASP* 5.5 0.3 + - - -
145B ILE* 2.8 39.4 + - - +
146B ARG* 4.9 0.2 - - - +
186B TYR* 3.1 35.8 + - - +
187B TYR* 5.7 1.7 - - - -
201B THR 3.3 5.2 + - - -
202B ASP* 3.1 17.0 + - - -
204B TRP* 1.3 80.5 - - - +
206B LEU* 1.3 61.0 + - - +
208B THR* 3.3 4.0 + - - -
209B LEU* 3.0 21.8 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 4.2 16.6 - - + -
128B VAL* 4.0 28.0 - - + -
129B CYS* 3.5 27.8 - - - -
132B LEU* 4.6 7.9 - - + -
145B ILE* 4.4 7.1 - - + +
202B ASP 2.9 12.7 + - - +
203B MET* 3.4 29.6 - - + +
204B TRP 3.1 0.2 - - - -
205B SER* 1.3 74.1 - - - +
207B GLY* 1.3 64.8 + - - +
209B LEU* 3.1 12.6 + - + +
210B VAL* 2.9 34.9 + - + +
254B PHE* 4.3 5.4 - - + -
258B LEU* 3.9 13.5 - - + -
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Residues in contact with GLY 207 (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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203B MET 3.0 7.3 + - - -
204B TRP 2.8 9.8 + - - -
206B LEU* 1.3 77.4 - - - +
208B THR* 1.3 60.5 + - - -
210B VAL* 3.3 4.4 + - - +
211B TYR* 3.0 23.7 + - - +
255B VAL* 3.9 7.0 - - - +
258B LEU* 3.7 28.7 - - - +
259B LEU* 3.7 12.1 - - - -
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLU* 2.8 53.2 + - + +
186B TYR* 3.8 15.0 - - + -
204B TRP* 3.0 16.9 + - - -
205B SER 3.6 7.9 - - - -
207B GLY* 1.3 73.5 - - - +
209B LEU* 1.3 64.0 + - - +
211B TYR* 3.2 6.6 + - - +
212B VAL* 3.0 26.7 + - + +
219B PRO* 4.3 11.7 - - + -
220B PHE* 4.0 4.2 - - - -
259B LEU* 3.5 11.0 - - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR* 3.7 12.6 - - + +
125B VAL* 4.6 3.4 - - + -
128B VAL* 5.6 0.7 - - + -
145B ILE* 4.1 15.5 - - + -
146B ARG* 3.9 4.9 - - - -
147B PRO* 3.9 27.8 - - + -
150B ILE* 3.8 27.4 - - + -
186B TYR* 3.8 12.5 - - + -
205B SER 3.0 13.7 + - - +
206B LEU* 3.1 13.9 + - + +
208B THR* 1.3 77.3 - - - +
210B VAL* 1.3 66.5 + - + +
212B VAL* 3.0 7.1 - - - +
213B LEU* 3.0 54.9 + - + +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 5.0 0.4 - - + -
125B VAL* 3.9 25.8 - - + -
206B LEU* 2.9 26.0 + - + +
207B GLY* 3.7 5.2 - - - +
209B LEU* 1.3 75.0 - - + +
211B TYR* 1.3 66.6 + - - +
213B LEU* 3.2 6.2 + - - +
214B LEU* 2.9 36.2 + - + +
254B PHE* 4.0 20.4 - - + -
255B VAL* 3.5 22.9 - - + -
277B TRP* 3.6 29.2 - - + -
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Residues in contact with TYR 211 (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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207B GLY 3.0 14.1 + - - +
208B THR* 3.5 9.4 - - - +
210B VAL* 1.3 77.0 - - - +
212B VAL* 1.3 55.8 + - - +
214B LEU* 3.3 4.5 + - - +
215B SER* 2.9 43.5 + - - -
217B ILE* 3.2 31.9 - - + +
219B PRO* 3.6 33.3 - - + +
237B TYR* 3.9 13.2 - + - -
238B THR 2.7 26.1 + - - -
239B PHE* 3.8 11.7 - + - -
240B ASP* 3.4 15.8 + - - +
244B PHE* 3.5 23.6 - + - -
255B VAL* 4.1 25.0 - - + +
259B LEU* 4.6 1.1 - - + -
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Residues in contact with VAL 212 (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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106B PHE* 4.2 12.3 - - + -
147B PRO* 4.4 4.0 - - + -
185B GLU* 5.5 0.2 - - + -
186B TYR* 3.5 19.3 - - - +
208B THR* 3.0 16.8 + - + +
209B LEU* 3.0 21.1 - - - +
211B TYR* 1.3 75.1 - - - +
213B LEU* 1.3 59.1 + - + +
216B GLY* 2.6 29.8 + - - +
217B ILE 3.6 22.0 - - - +
219B PRO* 3.9 11.9 - - + -
295B HIS* 3.4 4.2 + - - -
298B TYR* 3.8 38.6 - - + +
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Residues in contact with LEU 213 (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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105B ILE* 3.5 40.6 - - + -
106B PHE* 4.0 18.2 - - + -
109B ILE* 5.9 2.0 - - + -
116B LEU* 3.6 6.4 - - + +
121B ILE* 3.5 38.3 - - + +
124B TYR* 3.7 22.2 - - + +
125B VAL* 4.5 1.3 - - + -
147B PRO* 5.2 2.2 - - + -
209B LEU* 3.0 46.3 + - + +
210B VAL 3.2 3.8 + - - +
212B VAL* 1.3 78.5 - - + +
214B LEU* 1.3 58.3 - - - +
295B HIS* 2.8 24.3 - - - +
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Residues in contact with LEU 214 (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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118B GLU* 4.1 13.0 - - + -
121B ILE* 3.7 22.7 - - + -
210B VAL* 2.9 37.0 + - + +
211B TYR* 3.8 2.7 - - - +
213B LEU* 1.3 79.6 - - - +
215B SER* 1.3 57.0 + - - +
243B ALA 4.4 2.9 - - - +
244B PHE* 4.0 24.5 - - + -
247B ILE* 3.9 30.3 - - + +
251B ALA* 4.0 18.4 - - + +
255B VAL* 4.1 10.8 - - + -
277B TRP* 4.1 19.1 - - + -
290B ILE* 3.7 19.4 - - - +
295B HIS* 4.2 0.2 - - - -
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 2.9 31.4 + - - -
214B LEU* 1.3 78.0 - - - +
216B GLY* 1.3 61.7 + - - +
217B ILE* 3.2 21.8 + - - +
243B ALA* 3.6 29.8 - - - +
244B PHE* 3.7 18.4 - - - -
291B ARG 4.9 1.4 - - - +
294B LYS* 4.1 7.3 - - - +
295B HIS* 3.5 13.7 + - - -
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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
------------------------------------------------------------
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