Contacts of the helix formed by residues 203 - 223 (chain A) in PDB entry 1Y7V
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 ASP 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A LYS 3.3 0.7 - - - +
199A GLY* 3.0 12.5 - - - -
200A GLN* 2.5 52.1 + - + +
201A PRO 3.3 0.6 + - - -
202A GLY* 1.3 83.1 - - - +
204A ILE* 1.3 60.4 + - + +
205A TYR* 2.6 37.2 + - + +
206A HIS* 2.8 12.6 + - - -
207A GLN* 2.9 27.8 + - - +
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Residues in contact with ILE 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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142A PHE* 3.7 42.2 - - + -
203A ASP* 1.3 76.8 - - + +
205A TYR* 1.3 87.5 + - + +
207A GLN* 4.2 5.6 - - + +
208A THR* 2.7 37.6 + - - +
211A ARG* 5.0 4.5 - - - +
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Residues in contact with TYR 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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142A PHE* 4.1 21.2 - + - -
184A TRP 4.1 5.8 - - - -
185A LEU* 4.0 29.3 - - + +
197A LEU* 4.6 3.4 - - + +
198A LYS* 3.0 79.3 - - + +
199A GLY* 4.3 3.1 - - - -
203A ASP* 2.6 17.1 + - + +
204A ILE* 1.3 90.5 - - + +
206A HIS* 1.3 57.0 + - + +
208A THR* 3.7 2.1 - - - -
209A TRP* 3.0 29.0 + - - +
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Residues in contact with HIS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.6 26.3 - - + +
198A LYS 3.3 20.2 + - - -
199A GLY 4.0 2.9 - - - -
200A GLN* 3.4 17.5 + - - -
201A PRO* 3.3 20.8 - - + -
202A GLY 3.7 7.0 - - - +
203A ASP* 2.8 16.2 + - - +
205A TYR* 1.3 75.2 - - - +
207A GLN* 1.3 62.8 + - - +
209A TRP* 3.6 5.5 + - - +
210A ALA* 3.2 22.7 + - - +
255A HIS* 2.7 33.5 - + - -
259A PHE* 3.8 12.4 - + - -
263A ASP* 3.1 28.6 - - + +
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Residues in contact with GLN 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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202A GLY* 4.0 8.4 + - - +
203A ASP 2.9 23.9 + - - +
204A ILE* 4.0 7.4 - - + +
205A TYR 3.3 0.4 - - - -
206A HIS* 1.3 75.1 - - - +
208A THR* 1.3 61.1 + - - +
210A ALA* 3.5 3.2 + - - +
211A ARG* 3.0 51.5 + - - +
262A ARG 3.8 4.9 + - - -
263A ASP* 2.4 46.8 + - - +
266A PRO* 6.1 0.6 - - - +
267A THR* 4.1 13.2 + - - +
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Residues in contact with THR 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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142A PHE* 3.3 38.3 + - - +
144A LEU* 3.7 22.7 - - + +
184A TRP* 4.0 12.3 - - + -
185A LEU* 4.1 9.2 - - + -
204A ILE* 2.7 22.6 + - - +
205A TYR 3.7 4.0 - - - -
207A GLN* 1.3 74.9 - - - +
209A TRP* 1.3 66.3 + - - +
211A ARG* 2.9 24.3 + - - +
212A TYR* 2.9 20.8 + - - +
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Residues in contact with TRP 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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178A PRO* 3.9 28.3 - - + -
180A THR 3.9 4.7 - - - -
181A SER* 3.4 43.1 - - - -
182A PRO* 4.4 1.6 - - + -
185A LEU* 4.3 6.2 - - + +
197A LEU* 3.5 35.9 - - + -
205A TYR 3.0 16.6 + - - +
206A HIS 3.9 4.5 - - - +
208A THR* 1.3 76.3 - - - +
210A ALA* 1.3 62.0 + - - +
212A TYR* 3.0 67.0 - + + +
213A PHE* 3.3 19.4 - + - -
232A ALA 5.0 1.2 + - - -
233A GLU* 4.6 2.2 + - - -
249A LEU* 3.5 17.7 - - + +
251A PHE* 4.3 4.0 - - - -
259A PHE* 3.5 21.0 - + + -
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Residues in contact with ALA 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 HIS 3.2 15.9 + - - +
207A GLN 3.8 3.4 - - - +
208A THR 3.3 0.2 - - - -
209A TRP* 1.3 78.3 - - - +
211A ARG* 1.3 62.8 + - - +
213A PHE* 3.0 28.7 + - - +
214A VAL* 3.6 2.4 + - - +
259A PHE* 4.4 3.7 - - + -
263A ASP* 3.8 17.5 - - + +
264A LEU* 4.0 11.4 - - + +
267A THR* 3.5 33.7 - - - +
268A LEU* 5.5 0.2 - - - +
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Residues in contact with ARG 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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142A PHE* 2.8 31.5 + - - +
143A GLN* 4.5 14.9 + - - +
144A LEU* 3.8 12.6 - - + +
204A ILE* 4.6 5.3 + - - +
207A GLN* 3.0 41.7 + - - +
208A THR* 2.9 27.9 + - - +
210A ALA* 1.3 72.8 - - - +
212A TYR* 1.3 57.2 + - - +
214A VAL* 2.8 9.2 + - + +
215A LYS* 2.8 38.9 + - + +
267A THR* 4.3 14.8 - - + -
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Residues in contact with TYR 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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123A MET* 4.5 15.4 + - + -
124A ALA* 3.9 5.0 - - - +
134A THR* 3.6 8.8 - - - -
135A TYR* 3.0 54.0 + + + -
136A ALA 4.2 2.9 - - - -
144A LEU* 3.6 19.0 - - + +
147A PHE* 3.7 18.1 - + - -
180A THR 4.7 2.4 + - - -
182A PRO* 3.6 27.8 - - + -
185A LEU* 5.7 0.7 - - + -
208A THR 2.9 11.2 + - - +
209A TRP* 3.0 51.8 - + + +
211A ARG* 1.3 77.3 - - - +
213A PHE* 1.3 58.3 + + - +
215A LYS* 3.7 4.8 - - - +
216A PHE* 3.0 23.1 + - + +
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Residues in contact with PHE 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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123A MET* 4.0 28.7 - - + -
178A PRO* 3.9 12.6 - - + -
209A TRP* 3.3 43.5 - + - -
210A ALA* 3.0 11.7 + - - +
211A ARG 3.0 0.8 - - - -
212A TYR* 1.3 77.7 - + + +
214A VAL* 1.3 65.4 + - - +
216A PHE* 3.1 4.3 + - - +
217A LEU* 2.9 29.0 + - + +
230A VAL* 4.1 21.3 - - + -
231A THR 3.4 25.8 - - - -
232A ALA 3.9 14.4 - - - -
259A PHE* 4.6 3.1 - + - -
264A LEU* 3.9 25.8 - - + -
268A LEU* 4.4 13.9 - - + -
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Residues in contact with VAL 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 ALA 4.2 2.5 - - - +
211A ARG* 2.8 10.1 + - + +
213A PHE* 1.3 76.2 - - - +
215A LYS* 1.3 55.5 + - + +
217A LEU* 3.0 8.1 + - - +
218A ASP* 2.7 57.7 + - - +
267A THR* 3.9 28.3 - - + +
268A LEU* 4.6 10.3 - - + -
271A SER* 3.9 28.7 - - - +
272A THR* 5.6 0.4 - - - +
273A HIS* 4.0 11.0 - - + -
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Residues in contact with LYS 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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143A GLN 5.1 2.5 + - - +
144A LEU* 3.6 45.3 + - + -
145A HIS* 5.6 2.0 - - - +
147A PHE* 3.7 31.2 - - + -
211A ARG* 2.8 26.8 + - + +
212A TYR 3.7 5.6 - - - +
214A VAL* 1.3 73.5 - - + +
216A PHE* 1.3 56.6 + - - +
218A ASP* 3.2 15.4 + - - +
219A ALA* 2.8 28.6 + - - +
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Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A VAL* 4.4 6.1 - - + -
122A PRO 5.0 0.7 - - - -
123A MET* 3.3 28.7 - - + -
135A TYR* 3.6 34.8 - + + -
147A PHE* 3.6 12.3 - - + -
149A LEU* 4.5 3.4 - - + -
176A ALA* 3.7 25.4 - - + -
212A TYR 3.0 15.0 + - - +
213A PHE 3.3 7.2 - - - +
215A LYS* 1.3 75.5 - - - +
217A LEU* 1.3 73.4 + - + +
219A ALA* 3.1 3.7 + - - +
220A TYR* 2.9 62.7 + + - +
227A PHE* 3.7 26.0 - + - -
230A VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 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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123A MET* 5.9 0.2 - - + -
213A PHE* 2.9 21.7 + - + +
214A VAL* 3.7 0.7 - - - +
216A PHE* 1.3 85.4 - - + +
218A ASP* 1.3 60.8 + - - +
220A TYR* 4.0 2.3 - - - +
221A ALA* 2.9 30.5 + - - +
225A LEU 4.9 1.0 - - - +
227A PHE* 3.7 42.0 - - + +
230A VAL* 4.4 16.2 - - + -
268A LEU* 4.2 19.1 - - + -
273A HIS* 3.5 44.2 - - + +
276A VAL* 4.2 11.7 - - + -
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Residues in contact with ASP 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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214A VAL* 2.7 41.5 + - - +
215A LYS* 3.4 17.8 + - + +
217A LEU* 1.3 73.0 - - - +
219A ALA* 1.3 54.8 + - - +
221A ALA* 3.2 5.4 + - - +
222A GLU* 2.8 47.8 + - - +
272A THR* 4.2 5.2 + - - -
273A HIS* 2.7 27.2 + - - -
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Residues in contact with ALA 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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147A PHE* 4.3 8.1 - - + -
149A LEU* 3.6 34.1 - - + -
215A LYS 2.8 14.1 + - - +
216A PHE 3.1 8.5 + - - +
218A ASP* 1.3 76.2 - - - +
220A TYR* 1.3 64.1 + - - +
222A GLU* 3.1 29.7 + - - +
223A HIS* 3.2 15.0 - - - -
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Residues in contact with TYR 220 (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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121A VAL* 3.8 8.5 - - + +
149A LEU* 4.0 13.7 - - + -
153A ASP* 2.5 29.0 + - - +
157A LYS* 3.7 15.9 - - - +
158A ILE* 3.7 30.5 - - + +
161A ILE* 4.6 6.7 - - + -
216A PHE* 2.9 45.8 + + - +
217A LEU 4.2 2.2 - - - +
219A ALA* 1.3 76.9 - - - +
221A ALA* 1.3 58.9 + - - +
223A HIS* 2.9 21.8 + - - +
224A LYS 3.2 0.2 + - - -
225A LEU* 3.0 45.4 + - + +
227A PHE* 3.5 40.2 - + + -
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Residues in contact with ALA 221 (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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217A LEU 2.9 19.9 + - - +
218A ASP* 3.2 6.3 + - - +
220A TYR* 1.3 76.0 - - - +
222A GLU* 1.3 55.0 + - - +
224A LYS* 2.7 27.0 + - - +
225A LEU 3.6 9.4 + - - +
226A GLN* 3.6 21.5 + - - +
273A HIS* 4.1 14.4 - - + -
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Residues in contact with GLU 222 (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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218A ASP* 2.8 29.6 + - - +
219A ALA* 3.2 16.9 + - - +
221A ALA* 1.3 76.9 - - - +
223A HIS* 1.3 60.5 + - + +
224A LYS* 3.2 8.2 + - - +
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Residues in contact with HIS 223 (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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149A LEU* 4.0 8.2 - - + +
154A THR* 3.9 32.3 - - + +
158A ILE* 3.7 40.0 - - + +
162A HIS* 2.7 39.6 + - - -
219A ALA* 3.2 21.3 + - - +
220A TYR* 2.9 11.9 + - - +
222A GLU* 1.3 82.8 + - + +
224A LYS* 1.3 58.2 + - - +
225A LEU* 3.4 2.1 - - + +
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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