Contacts of the helix formed by residues 195 - 219 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLY 3.2 1.2 - - - -
194A ASP* 1.3 90.8 - - + +
196A PHE* 1.4 60.2 + - - +
197A PHE* 3.2 27.7 + + - -
198A ILE* 3.4 31.5 + - + +
199A TYR* 3.3 26.9 - - + +
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Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ILE* 4.1 7.2 - - - +
189A ILE* 3.7 42.2 - - + +
192A GLY 3.5 26.2 - - - +
193A GLY* 3.9 1.9 - - - -
194A ASP* 3.3 18.5 - - - -
195A TYR* 1.4 74.2 - - - +
197A PHE* 1.3 64.2 + - - +
198A ILE 3.3 0.2 + - - -
199A TYR* 3.4 15.6 + - - +
200A ALA* 3.0 30.4 + - + +
360A PHE* 5.9 0.4 - + - -
363A PHE* 4.0 18.6 - + - -
364A ALA* 3.7 32.5 - - + -
367A ILE* 3.8 19.1 - - + -
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Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP 5.0 2.2 - - - -
195A TYR* 4.0 26.0 - + - -
196A PHE* 1.3 87.0 - - + +
198A ILE* 1.4 87.3 + - + +
200A ALA* 4.0 4.7 - - - -
201A TRP* 3.0 30.0 + - - +
357A PHE* 3.8 26.2 - + - -
360A PHE* 3.4 31.1 - - + +
361A PHE* 3.7 46.4 - + + -
364A ALA* 3.9 19.3 - - + -
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Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A TYR* 3.4 32.9 + - + +
196A PHE 3.2 0.8 - - - -
197A PHE* 1.4 105.8 - - + +
199A TYR* 1.4 69.7 + - + +
201A TRP* 3.5 17.8 + - + +
202A LEU* 3.0 31.2 + - + +
357A PHE* 4.3 11.2 - - + -
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Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ILE* 3.8 16.0 - - + +
192A GLY* 4.4 10.8 - - - -
193A GLY 4.0 22.1 + - - -
195A TYR* 3.3 31.9 + - + +
196A PHE* 3.4 21.0 + - + -
198A ILE* 1.4 81.1 - - + +
200A ALA* 1.4 58.6 + - - +
202A LEU* 3.4 8.2 + - - +
203A PHE* 2.9 29.6 + - - +
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Residues in contact with ALA 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A LEU* 4.1 7.7 - - + +
188A ILE* 3.5 15.8 - - + +
189A ILE* 4.1 14.8 - - + -
196A PHE 3.0 18.9 + - - +
197A PHE* 4.0 3.6 - - - +
199A TYR* 1.4 75.1 - - - +
201A TRP* 1.4 61.8 + - - +
203A PHE* 3.5 5.2 + - - +
204A THR* 3.3 28.9 + - - +
360A PHE* 3.8 25.8 - - + -
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Residues in contact with TRP 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A PHE 3.0 21.1 + - - +
198A ILE* 3.8 13.2 - - + +
199A TYR 3.3 0.2 - - - -
200A ALA* 1.4 73.7 - - - +
202A LEU* 1.4 86.7 + - + +
204A THR* 2.7 19.8 + - - -
205A LEU* 3.0 38.5 + - + +
353A GLN* 2.8 35.7 + - + +
354A MET* 5.7 0.2 - - - -
356A SER* 2.9 25.1 + - - -
357A PHE* 3.3 46.6 - + + +
360A PHE* 4.0 12.3 - + + -
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.0 21.0 + - + +
199A TYR* 3.8 8.1 - - - +
201A TRP* 1.4 96.5 - - + +
203A PHE* 1.4 59.4 + - - +
205A LEU* 3.4 18.6 - - + +
206A VAL* 3.1 39.9 + - + +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 3.4 28.9 - - + -
184A LEU* 3.5 38.4 - - + -
185A LEU* 3.7 31.9 - - + -
188A ILE* 3.6 21.1 - - + -
199A TYR 2.9 18.3 + - - +
200A ALA 3.7 4.3 - - - +
201A TRP 3.3 0.2 - - - -
202A LEU* 1.4 73.3 - - - +
204A THR* 1.4 62.4 + - + +
206A VAL* 3.3 8.0 + - + +
207A VAL* 2.9 53.5 + - + +
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Residues in contact with THR 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL* 6.2 2.2 - - + -
185A LEU* 3.8 22.0 - - + -
200A ALA 3.3 14.8 + - - +
201A TRP* 2.7 27.9 + - - -
203A PHE* 1.4 77.0 - - + +
205A LEU* 1.4 49.9 + - - +
207A VAL* 3.8 8.2 - - + +
208A SER* 2.6 43.2 + - - -
353A GLN* 4.6 2.7 + - - -
356A SER* 4.8 4.3 + - - -
360A PHE* 3.9 15.9 - - + -
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Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A TRP* 3.0 47.6 + - + +
202A LEU* 3.4 22.9 - - + +
203A PHE 3.2 0.2 - - - -
204A THR* 1.4 75.8 + - - +
206A VAL* 1.4 65.2 + - + +
208A SER* 3.8 2.6 - - - -
209A LEU* 3.4 22.8 + - + +
353A GLN* 3.4 38.1 + - + +
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Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LEU* 3.1 22.6 + - + +
203A PHE* 3.3 10.7 + - + +
205A LEU* 1.4 78.8 - - + +
207A VAL* 1.3 62.7 + - + +
208A SER 3.3 0.2 + - - -
209A LEU* 3.3 5.5 + - - +
210A VAL* 2.9 47.8 + - + +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 6.4 0.2 - - + -
181A VAL* 3.9 35.0 - - + -
203A PHE* 2.9 52.2 + - + +
204A THR* 4.0 7.6 - - + +
206A VAL* 1.3 76.1 - - + +
208A SER* 1.4 57.6 + - - +
210A VAL* 4.0 5.7 - - - +
211A LEU* 3.0 33.0 + - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A THR* 2.6 27.9 + - - -
205A LEU 3.8 5.6 - - - -
206A VAL 3.2 0.2 - - - -
207A VAL* 1.4 78.1 - - - +
209A LEU* 1.4 57.2 + - - +
211A LEU* 3.9 3.3 - - - +
212A VAL* 3.0 37.7 + - - +
353A GLN* 3.8 19.6 + - - -
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Residues in contact with LEU 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.4 13.9 + - + +
206A VAL* 3.3 5.9 + - - +
208A SER* 1.4 77.7 - - - +
210A VAL* 1.4 59.9 + - + +
212A VAL* 3.7 8.3 + - - +
213A THR* 2.9 27.7 + - - -
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL* 2.9 36.7 + - + +
207A VAL* 4.0 5.6 - - - +
209A LEU* 1.4 76.2 - - + +
211A LEU* 1.4 57.9 + - - +
213A THR* 3.3 6.8 + - - -
214A ILE* 3.0 44.5 + - + +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 5.9 7.2 - - + -
207A VAL* 3.0 23.3 + - + +
208A SER* 3.9 3.6 - - - +
210A VAL* 1.4 74.5 - - - +
212A VAL* 1.4 59.7 + - + +
214A ILE* 3.9 7.0 - - - -
215A TYR* 3.1 32.1 + - - +
219A ILE* 4.8 6.8 - - + +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A SER* 3.0 23.6 + - - +
209A LEU* 3.8 9.6 - - - +
210A VAL 3.2 0.4 - - - -
211A LEU* 1.4 77.3 - - - +
213A THR* 1.4 63.2 + - - +
215A TYR* 4.1 10.8 + - - +
216A ALA* 4.6 5.5 + - - +
269A TYR* 5.9 3.6 - - - +
270A GLY 5.2 8.3 - - - +
349A ILE* 6.4 1.8 - - + -
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Residues in contact with THR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU 2.9 15.2 + - - -
210A VAL* 3.3 7.0 + - - -
212A VAL* 1.4 79.3 - - - +
214A ILE* 1.3 67.5 + - + +
215A TYR 3.6 0.2 - - - -
216A ALA* 4.6 1.7 + - - +
217A ASP* 3.9 22.0 + - - +
218A TYR* 5.3 0.3 - - - -
269A TYR* 5.7 3.7 - - - -
270A GLY 5.1 8.1 + - - +
271A PHE* 4.4 24.2 - - + +
276A ARG* 6.2 1.8 - - - +
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Residues in contact with ILE 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A VAL* 3.0 34.8 + - + +
211A LEU* 4.2 4.9 - - - +
213A THR* 1.3 80.6 - - + +
215A TYR* 1.4 55.3 + - - +
217A ASP 3.1 3.3 + - - -
218A TYR* 2.8 70.4 + - + -
219A ILE* 3.9 19.5 - - + -
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A LEU 3.1 19.7 + - - +
212A VAL* 4.1 7.4 - - - +
213A THR 3.6 0.6 - - - -
214A ILE* 1.4 72.4 - - - +
216A ALA* 1.3 58.5 + - - +
219A ILE* 2.9 29.4 + - + +
220A ALA* 2.7 32.5 + - + -
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Residues in contact with ALA 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL 4.6 5.3 + - - +
213A THR 4.6 1.3 + - - +
214A ILE 3.6 0.6 - - - -
215A TYR* 1.3 76.6 - - - +
217A ASP* 1.3 59.7 + - - +
220A ALA* 3.8 12.5 - - - +
221A PRO* 3.6 16.5 - - - +
269A TYR* 3.7 49.4 + - + -
278A VAL* 6.0 0.9 - - + -
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.9 14.5 + - - +
214A ILE 3.1 8.5 + - - +
216A ALA* 1.3 80.3 - - - +
218A TYR* 1.4 83.9 + - + +
221A PRO* 3.7 12.1 - - - +
269A TYR* 3.8 15.1 + - - -
276A ARG* 3.1 29.8 + - - -
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Residues in contact with TYR 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR 5.3 0.7 - - - -
214A ILE* 2.8 56.9 + - + +
215A TYR 3.4 0.2 + - - -
217A ASP* 1.4 94.4 - - + +
219A ILE* 1.4 63.5 + - + +
221A PRO* 3.5 9.1 - - - +
222A LEU* 3.4 21.4 - - - +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL* 3.9 18.8 - - + -
177A ILE* 3.9 24.7 - - + -
211A LEU* 4.8 8.5 - - + +
214A ILE* 3.8 21.1 + - + -
215A TYR* 2.9 34.5 + - + +
218A TYR* 1.4 70.6 - - + +
220A ALA* 1.4 63.0 + - - +
222A LEU* 3.4 21.5 + - + +
223A PHE* 3.3 34.4 - - + -
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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