Contacts of the helix formed by residues 195 - 216 (chain D) in PDB entry 2YPT
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 TYR 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193D GLY 3.2 1.2 - - - -
194D ASP* 1.3 90.8 - - + +
196D PHE* 1.4 61.7 + - - +
197D PHE* 3.3 28.5 + + - -
198D ILE* 3.4 30.7 + - + +
199D TYR* 3.3 26.4 - - + +
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Residues in contact with PHE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 4.1 7.5 - - - +
189D ILE* 3.7 41.5 - - + +
192D GLY 3.5 26.2 - - - +
193D GLY* 3.9 2.7 - - - -
194D ASP* 3.3 18.5 - - - -
195D TYR* 1.4 74.3 - - - +
197D PHE* 1.3 64.2 + - - +
199D TYR* 3.4 16.7 + - - +
200D ALA* 3.1 28.8 + - - +
360D PHE* 6.0 0.7 - + - -
363D PHE* 4.0 18.8 - + - -
364D ALA* 3.7 30.7 - - + -
367D ILE* 3.8 19.1 - - + -
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Residues in contact with PHE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D ASP 4.8 2.7 - - - -
195D TYR* 3.8 33.9 - + - -
196D PHE* 1.3 88.5 - - + +
198D ILE* 1.4 81.2 + - + +
200D ALA* 3.8 6.1 - - - +
201D TRP* 2.9 31.2 + - - +
357D PHE* 4.3 16.2 - + - -
360D PHE* 3.3 31.6 - - + +
361D PHE* 3.6 47.8 - + + -
364D ALA* 3.7 22.0 - - + -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D TYR* 3.4 31.6 + - + +
196D PHE 3.3 0.8 - - - -
197D PHE* 1.4 108.2 - - + +
199D TYR* 1.4 66.5 + - + +
201D TRP* 3.5 20.4 + - + +
202D LEU* 3.0 29.6 + - + +
357D PHE* 4.2 13.2 - - + -
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Residues in contact with TYR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 3.8 16.9 - - + +
192D GLY* 4.5 10.1 - - - -
193D GLY 4.0 22.8 + - - -
195D TYR* 3.3 32.5 + - + +
196D PHE* 3.4 20.1 + - - -
198D ILE* 1.4 83.4 - - + +
200D ALA* 1.4 56.0 + - - +
202D LEU* 3.4 6.4 + - - +
203D PHE* 2.9 30.0 + - - +
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LEU* 3.7 9.7 - - + +
188D ILE* 3.6 15.2 - - + +
189D ILE* 4.1 14.8 - - + -
196D PHE* 3.1 19.1 + - + +
197D PHE* 3.8 3.8 - - - +
199D TYR* 1.4 74.3 - - - +
201D TRP* 1.3 61.1 + - - +
203D PHE* 3.6 3.7 + - - +
204D THR* 3.3 28.4 + - - +
360D PHE* 3.8 24.9 - - + -
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Residues in contact with TRP 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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197D PHE 2.9 19.5 + - - +
198D ILE* 3.8 21.1 - - + +
200D ALA* 1.3 75.2 - - - +
202D LEU* 1.4 69.8 + - + +
203D PHE 3.3 0.4 - - - -
204D THR* 2.7 19.0 + - - -
205D LEU* 3.0 40.1 + - + +
353D GLN* 2.8 34.4 + - + -
354D MET* 5.9 0.2 - - - -
356D SER* 3.1 24.1 + - - -
357D PHE* 3.4 49.3 - + + +
360D PHE* 4.0 13.2 - - + -
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Residues in contact with LEU 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 ILE* 3.0 20.7 + - + +
199D TYR* 3.8 7.2 - - - +
201D TRP* 1.4 84.2 - - + +
203D PHE* 1.4 59.9 + - - +
205D LEU* 3.4 15.8 - - + +
206D VAL* 3.1 38.9 + - + +
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Residues in contact with PHE 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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181D VAL* 3.4 30.1 - - + -
184D LEU* 3.5 39.3 - - + -
185D LEU* 3.7 31.2 - - + -
188D ILE* 3.6 20.0 - - + -
199D TYR 2.9 17.5 + - - +
200D ALA 3.8 4.3 - - - +
201D TRP 3.3 0.2 - - - -
202D LEU* 1.4 76.6 - - - +
204D THR* 1.4 60.3 + - + +
206D VAL* 3.3 8.0 + - + +
207D VAL* 2.9 54.2 + - + +
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Residues in contact with THR 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL* 6.2 2.7 - - + -
185D LEU* 3.8 22.0 - - + -
200D ALA 3.3 15.2 + - - +
201D TRP* 2.7 27.7 + - - -
203D PHE* 1.4 77.6 - - + +
205D LEU* 1.4 50.9 + - - +
207D VAL* 3.9 8.1 - - + +
208D SER* 2.6 43.4 + - - -
353D GLN* 4.6 3.1 + - - -
356D SER* 4.8 4.5 + - - -
360D PHE* 3.9 15.8 - - + -
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D TRP* 3.0 46.0 + - + +
202D LEU* 3.4 19.3 - - + +
203D PHE 3.2 0.2 - - - -
204D THR* 1.4 77.4 + - - +
206D VAL* 1.4 64.3 + - + +
208D SER* 3.8 2.3 - - - -
209D LEU* 3.4 22.6 + - + +
353D GLN* 3.4 38.2 + - + +
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Residues in contact with VAL 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 LEU* 3.1 21.0 + - + +
203D PHE* 3.3 10.1 + - + +
205D LEU* 1.4 79.3 - - + +
207D VAL* 1.4 61.5 + - + +
208D SER 3.3 0.5 + - - -
209D LEU* 3.3 5.8 + - - +
210D VAL* 2.9 45.8 + - + +
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D VAL* 4.0 28.5 - - + -
203D PHE* 2.9 52.0 + - + +
204D THR* 3.9 8.5 - - + +
206D VAL* 1.4 75.6 - - + +
208D SER* 1.4 57.8 + - - +
210D VAL* 4.0 5.1 - - - +
211D LEU* 3.0 50.9 + - + +
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Residues in contact with SER 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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204D THR* 2.6 27.1 + - - -
205D LEU 3.8 5.6 - - - -
207D VAL* 1.4 77.1 - - - +
209D LEU* 1.4 57.2 + - - +
211D LEU* 3.9 4.8 - - - +
212D VAL* 3.0 36.3 + - - +
353D GLN* 3.7 20.3 + - - -
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Residues in contact with LEU 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 LEU* 3.4 14.2 + - + +
206D VAL* 3.3 6.3 + - - +
208D SER* 1.4 77.6 - - - +
210D VAL* 1.4 59.2 + - + +
212D VAL* 3.7 8.5 + - - +
213D THR* 2.9 28.1 + - - -
271D PHE* 5.6 3.5 - - + -
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Residues in contact with VAL 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 VAL* 2.9 35.9 + - + +
207D VAL* 4.0 6.5 - - - +
209D LEU* 1.4 76.4 - - + +
211D LEU* 1.4 62.5 + - + +
213D THR* 3.3 6.8 + - - -
214D ILE* 3.0 44.5 + - + +
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Residues in contact with LEU 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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177D ILE* 3.9 34.5 - - + -
181D VAL* 5.0 2.5 - - + -
207D VAL* 3.0 41.0 + - + +
208D SER* 3.9 4.5 - - - +
210D VAL* 1.4 76.2 - - + +
212D VAL* 1.4 59.8 + - - +
214D ILE* 3.9 7.4 - - + -
215D TYR* 3.0 31.9 + - - +
219D ILE* 4.2 21.8 - - + -
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Residues in contact with VAL 212 (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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208D SER* 3.0 23.6 + - - +
209D LEU* 3.8 10.8 - - - +
210D VAL 3.2 0.4 - - - -
211D LEU* 1.4 78.2 - - + +
213D THR* 1.4 64.3 + - - +
215D TYR* 4.1 10.1 + - - +
216D ALA* 4.6 6.2 + - - +
269D TYR* 5.8 3.8 - - - +
270D GLY 5.1 9.2 - - - +
349D ILE* 6.5 0.9 - - + -
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Residues in contact with THR 213 (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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209D LEU 2.9 14.7 + - - -
210D VAL* 3.3 8.3 + - - -
212D VAL* 1.4 79.3 - - - +
214D ILE* 1.3 66.3 + - + +
216D ALA* 4.6 2.1 + - - +
217D ASP* 3.9 21.8 + - - +
218D TYR* 5.3 0.5 - - - -
269D TYR* 5.7 2.4 - - - -
270D GLY 5.1 7.9 + - - +
271D PHE* 3.7 40.6 - - + -
276D ARG* 6.2 1.3 - - - +
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Residues in contact with ILE 214 (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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210D VAL* 3.0 33.9 + - + +
211D LEU* 4.3 7.9 - - + +
212D VAL 3.5 0.2 - - - -
213D THR* 1.3 79.6 - - + +
215D TYR* 1.4 56.1 + - - +
217D ASP 3.1 3.5 + - - -
218D TYR* 2.8 69.8 + - + -
219D ILE* 3.9 19.5 - - + -
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Residues in contact with TYR 215 (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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211D LEU 3.0 20.6 + - - +
212D VAL* 4.1 6.7 - - - +
213D THR 3.6 0.6 - - - -
214D ILE* 1.4 72.7 - - - +
216D ALA* 1.3 66.1 + - + +
219D ILE* 2.9 46.9 + - + +
220D ALA* 2.7 48.9 + - + +
223D PHE* 5.3 6.8 - + - -
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Residues in contact with ALA 216 (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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212D VAL 4.6 6.6 + - - +
213D THR 4.6 1.1 + - - +
214D ILE 3.6 0.6 - - - -
215D TYR* 1.3 83.1 - - + +
217D ASP* 1.3 59.6 + - - +
220D ALA* 3.8 12.0 - - + +
221D PRO* 3.6 16.0 - - - +
226D PHE* 4.3 15.1 - - + -
269D TYR* 3.7 48.9 + - + -
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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