Contacts of the helix formed by residues 213 - 227 (chain B) in PDB entry 1TF4
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 GLN 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ARG* 4.6 4.5 + - - -
210B SER 5.0 4.0 + - - +
211B GLY* 3.7 1.8 - - - -
212B TYR* 1.3 88.2 - - + +
214B ASP* 1.3 63.8 + - - +
216B LEU* 3.2 24.2 + - - +
217B VAL* 3.4 13.3 + - - +
239B GLU* 3.0 52.0 + - - +
242B PHE* 3.4 38.4 - - - +
243B LEU* 4.1 8.3 - - + -
244B SER* 5.8 2.2 - - - +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 3.1 15.1 + - - +
211B GLY 3.3 4.7 - - - +
213B GLN* 1.3 77.9 - - - +
215B GLU* 1.3 71.0 + - - +
217B VAL* 3.3 3.6 + - - +
218B TRP* 3.0 29.7 + - - +
243B LEU* 3.8 11.4 - - + +
261B ASP 3.0 6.4 - - - +
262B ASP* 3.5 21.5 - - - +
263B LYS* 3.0 12.5 + - - +
264B SER* 3.6 20.6 - - - +
267B THR* 4.6 1.4 - - - +
3003B CA 2.3 29.6 - - - -
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.5 2.8 - - - -
150B SER 4.4 0.2 - - - +
151B ASP* 3.4 30.5 - - - +
154B ALA* 3.4 28.3 - - + +
155B GLU* 4.2 7.2 - - + +
211B GLY 2.8 12.2 - - - +
212B TYR* 3.0 9.5 + - - +
214B ASP* 1.3 88.8 - - - +
216B LEU* 1.3 58.5 + - - +
217B VAL 3.3 0.2 - - - -
218B TRP* 3.9 6.9 - - - -
219B GLY* 2.8 23.7 + - - -
261B ASP 2.9 2.8 - - - +
263B LYS* 2.7 32.0 + - + +
3003B CA 2.3 32.6 - - - -
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Residues in contact with LEU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER* 5.0 2.2 - - - -
154B ALA* 4.7 3.4 - - + -
186B TYR* 2.8 42.9 + - + +
189B ALA* 4.3 13.0 - - + +
190B ASP* 4.2 22.7 - - - +
193B ARG* 3.6 36.6 - - - +
212B TYR* 3.1 32.1 + - + +
213B GLN* 3.2 18.1 + - - +
215B GLU* 1.3 75.4 - - - +
217B VAL* 1.3 63.3 + - - +
220B ALA* 3.3 13.0 + - - +
239B GLU* 4.4 17.6 - - + +
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Residues in contact with VAL 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLN 3.6 13.7 - - - +
214B ASP 3.3 5.5 + - - +
216B LEU* 1.3 73.6 - - - +
218B TRP* 1.3 65.4 + - - +
220B ALA* 3.4 2.1 + - - +
221B TYR* 3.1 24.6 + - + +
236B ALA* 3.7 25.2 - - + +
239B GLU* 3.8 34.1 - - + +
240B TYR* 3.8 12.6 - - + +
243B LEU* 3.9 15.0 - - + -
267B THR* 3.7 26.9 - - + +
271B LEU* 4.3 5.6 - - + -
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Residues in contact with TRP 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.2 13.9 - + - -
71B THR* 3.4 26.7 - - + +
72B MET* 4.6 2.9 - - - -
75B TRP* 3.7 30.5 - + - -
155B GLU* 3.0 35.4 + - - -
158B ALA* 3.8 13.0 - - + +
214B ASP 3.0 17.9 + - - +
215B GLU* 3.9 6.1 - - - +
217B VAL* 1.3 77.4 - - - +
219B GLY* 1.3 62.5 + - - +
221B TYR* 3.4 4.4 + - - +
222B TRP* 3.2 45.9 + - - -
258B ILE* 3.9 16.4 - - + -
263B LYS* 3.7 26.7 - - + -
266B GLY* 4.2 3.8 - - - -
267B THR* 3.8 16.5 - - + +
270B LEU* 3.6 26.7 - - + -
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Residues in contact with GLY 219 (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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154B ALA 4.0 8.3 - - - -
157B ALA* 5.6 0.2 - - - -
158B ALA* 4.0 19.6 + - - -
186B TYR* 3.9 13.5 - - - -
215B GLU 2.8 21.4 + - - -
218B TRP* 1.3 74.4 - - - +
220B ALA* 1.3 62.0 + - - +
222B TRP* 3.4 2.3 + - - +
223B LEU* 3.0 27.2 + - - +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 3.6 16.6 - - + +
216B LEU 3.3 20.5 + - - +
217B VAL 3.8 3.8 - - - +
218B TRP 3.3 0.2 - - - -
219B GLY* 1.3 75.4 - - - +
221B TYR* 1.3 64.2 + - - +
223B LEU* 3.2 5.5 + - - +
224B TYR* 3.0 18.9 + - - +
232B TYR* 3.6 33.8 - - + +
235B LYS* 3.9 6.7 - - + -
236B ALA* 3.9 13.2 - - + +
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Residues in contact with TYR 221 (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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217B VAL* 3.1 18.7 + - + +
218B TRP* 3.7 4.9 - - - +
219B GLY 3.3 0.2 - - - -
220B ALA* 1.3 76.1 - - - +
222B TRP* 1.3 84.8 + + - +
224B TYR* 3.0 23.3 + + - +
225B LYS* 3.0 47.6 + - + +
233B LEU* 5.1 1.8 - - + +
236B ALA* 4.1 11.5 - - + +
267B THR* 5.8 2.5 - - + -
270B LEU* 3.6 65.8 + - + +
271B LEU* 4.0 21.8 - - + -
273B LYS* 5.2 4.3 - - - +
274B GLU* 3.5 23.9 + - + -
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Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.8 6.7 - - + +
75B TRP* 3.7 50.3 - + + -
78B ILE* 3.8 24.9 - - + -
158B ALA* 3.9 35.2 - - + +
161B ALA* 3.7 5.2 - - + +
162B ALA* 3.8 17.5 - - + -
165B ILE* 4.4 4.7 - - + +
218B TRP* 3.2 54.1 + + - +
219B GLY 4.0 2.7 - - - +
220B ALA 3.3 0.2 - - - -
221B TYR* 1.3 98.5 - + - +
223B LEU* 1.3 58.2 + - - +
225B LYS* 3.3 14.3 + - + +
226B ALA* 3.0 28.6 + - - +
270B LEU* 3.9 16.4 - - + +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA* 4.9 2.9 - - + +
161B ALA* 4.1 12.1 - - + -
179B VAL* 4.5 3.1 - - + +
182B ALA* 3.8 30.1 - - + +
183B LYS* 4.0 18.4 - - + -
186B TYR* 3.4 41.1 - - + -
219B GLY 3.0 16.7 + - - +
220B ALA 3.7 4.5 - - - +
221B TYR 3.2 0.2 - - - -
222B TRP* 1.3 73.4 - - - +
224B TYR* 1.3 55.3 + - - +
226B ALA* 4.4 0.7 - - + +
227B THR* 2.6 51.0 + - + +
232B TYR* 3.7 28.3 - - + +
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Residues in contact with TYR 224 (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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220B ALA 3.0 12.9 + - - +
221B TYR* 3.0 15.5 + + - +
223B LEU* 1.3 77.2 - - - +
225B LYS* 1.3 67.6 + - + +
227B THR* 3.9 2.9 - - - -
228B GLY* 2.6 43.4 + - - -
229B ASP 3.3 18.2 - - - -
230B ASP* 3.8 22.4 + - - -
232B TYR* 3.8 13.6 - - + +
233B LEU* 3.7 50.4 - - + +
274B GLU* 3.5 30.8 + - + +
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Residues in contact with LYS 225 (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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165B ILE* 3.7 23.1 - - + +
221B TYR* 3.0 52.6 + - + +
222B TRP* 3.6 13.9 - - + +
223B LEU 3.3 0.2 - - - -
224B TYR* 1.3 85.1 - - + +
226B ALA* 1.3 59.4 + - - +
228B GLY* 4.5 2.3 + - - -
274B GLU* 3.2 29.7 + - - +
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Residues in contact with ALA 226 (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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146A SER* 5.7 1.6 - - - -
161B ALA* 3.4 22.0 - - + +
164B SER* 3.4 24.3 + - - +
165B ILE* 3.9 8.7 - - - +
179B VAL* 4.1 16.2 - - + +
222B TRP 3.0 14.6 + - - +
223B LEU* 3.9 3.8 - - - +
224B TYR 3.3 0.2 - - - -
225B LYS* 1.3 77.0 - - - +
227B THR* 1.3 62.2 + - + +
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Residues in contact with THR 227 (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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146A SER* 3.3 29.7 - - - +
147A CYS* 3.7 15.6 - - - +
179B VAL* 3.7 24.7 - - + -
183B LYS* 4.2 11.9 - - + -
223B LEU* 2.6 32.7 + - + +
225B LYS 4.9 0.4 - - - -
226B ALA* 1.3 79.9 - - - +
228B GLY* 1.3 59.3 + - - +
229B ASP* 3.1 23.7 + - - +
232B TYR* 3.5 6.0 - - + -
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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