Contacts of the helix formed by residues 198 - 220 (chain D) in PDB entry 2IZZ
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 PRO 198 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B PRO* 3.9 11.6 - - + -
166C LEU* 3.9 24.9 - - + -
196D GLY 3.9 3.8 - - - +
197D LEU* 1.3 86.8 - - + +
199D ARG* 1.3 65.8 + - - +
200D ARG* 3.3 5.1 + - + +
201D LEU* 3.3 16.6 + - + +
202D ALA* 3.0 19.8 + - - +
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Residues in contact with ARG 199 (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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226B GLN* 5.9 2.0 - - - +
228B LYS* 3.1 18.6 - - - +
229B ASP* 2.9 45.3 + - + +
232B SER* 4.1 16.0 + - - +
234B PRO* 4.8 2.4 - - - +
239B ILE* 4.4 1.6 - - - +
186D ASP* 4.1 7.7 + - - -
189D ALA* 3.8 7.9 - - - +
190D ASP* 2.6 43.6 + - - +
193D VAL* 3.6 32.6 - - + +
197D LEU 3.6 1.8 + - - -
198D PRO* 1.3 71.3 - - - +
200D ARG* 1.3 64.5 + - - +
202D ALA* 3.2 1.8 + - - +
203D VAL* 2.9 44.0 + - + +
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Residues in contact with ARG 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D PRO* 3.3 4.7 - - + +
199D ARG* 1.3 80.8 - - - +
201D LEU* 1.3 62.3 + - - +
203D VAL* 3.5 6.4 + - - +
204D ARG* 3.2 23.1 + - + +
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Residues in contact with LEU 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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134C VAL* 4.8 0.2 - - + -
158C PHE* 4.3 10.1 - - + -
160C THR* 3.9 27.1 - - + -
162C VAL* 4.0 21.8 - - + -
166C LEU* 4.2 18.2 - - + -
170C VAL* 4.6 1.6 - - + -
197D LEU* 4.3 13.7 - - + -
198D PRO* 3.3 20.7 + - + +
200D ARG* 1.3 78.2 - - - +
202D ALA* 1.3 57.1 + - - +
204D ARG* 3.4 5.1 + - + +
205D LEU* 2.9 60.5 + - + +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C LEU* 3.4 22.8 - - + +
189D ALA* 3.6 33.6 - - + +
192D GLY* 4.3 1.6 - - - -
193D VAL* 4.3 3.6 - - + -
197D LEU* 4.2 15.7 - - + +
198D PRO 3.0 17.6 + - - +
199D ARG 3.6 4.7 - - - +
201D LEU* 1.3 76.1 - - - +
203D VAL* 1.3 58.2 + - - +
206D GLY* 3.0 27.0 + - - -
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Residues in contact with VAL 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 4.0 31.8 - - + +
218C LEU* 6.5 0.2 - - + -
224C PRO* 5.1 14.8 - - + -
185D LEU* 5.2 3.8 - - + +
189D ALA* 3.7 20.4 - - + -
199D ARG* 2.9 34.6 + - + +
200D ARG* 3.8 5.8 - - - +
202D ALA* 1.3 74.9 - - - +
204D ARG* 1.3 59.2 + - - +
206D GLY* 3.9 0.7 - - - -
207D ALA* 3.0 30.2 + - + +
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Residues in contact with ARG 204 (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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158C PHE* 3.2 58.5 - - + +
218C LEU* 3.5 29.2 - - - +
200D ARG* 3.2 15.9 + - + +
201D LEU* 3.6 7.4 - - - +
203D VAL* 1.3 81.8 - - - +
205D LEU* 1.3 57.1 + - - +
207D ALA* 3.9 1.0 - - - +
208D GLN* 2.9 56.1 + - - +
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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
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132C ALA* 4.1 11.4 - - + -
134C VAL* 4.0 13.5 - - + -
158C PHE* 3.8 29.4 - - + -
170C VAL* 3.6 37.0 - - + -
173C LEU* 4.0 9.0 - - + -
174C SER* 3.8 22.8 - - - +
197D LEU* 4.3 9.6 - - + -
201D LEU* 2.9 37.0 + - + +
204D ARG* 1.3 72.7 - - - +
206D GLY* 1.3 61.6 + - - +
208D GLN* 3.8 3.5 - - - +
209D ALA* 2.9 30.3 + - - +
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Residues in contact with GLY 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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173C LEU* 4.0 19.8 - - - +
185D LEU* 3.4 18.7 - - - +
188D LEU* 4.9 8.3 - - - +
202D ALA 3.0 18.0 + - - -
203D VAL* 3.9 0.9 - - - -
205D LEU* 1.3 75.4 - - - +
207D ALA* 1.3 57.9 + - - +
209D ALA* 3.3 6.6 + - - +
210D LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 207 (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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214C ALA* 3.4 17.0 - - - +
217C LEU* 4.3 20.0 - - + -
218C LEU* 3.6 28.0 - - + -
185D LEU* 3.5 15.5 - - + +
203D VAL* 3.0 19.1 + - + +
206D GLY* 1.3 70.8 - - - +
208D GLN* 1.3 61.3 + - - +
210D LEU 3.4 0.5 + - - -
211D LEU* 2.9 26.3 + - - +
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Residues in contact with GLN 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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130C GLU* 2.8 53.2 + - - +
131C GLY 3.3 19.5 + - - +
132C ALA* 3.8 13.9 - - + -
158C PHE* 4.0 16.7 - - + +
218C LEU* 3.7 14.5 - - - +
204D ARG* 2.9 40.2 + - - +
205D LEU* 3.8 4.3 - - - +
207D ALA* 1.3 77.8 - - - +
209D ALA* 1.3 56.3 + - - +
211D LEU* 3.8 4.6 - - - +
212D GLY* 2.9 28.4 + - - -
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Residues in contact with ALA 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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123C ASN* 4.2 11.9 - - - +
125C PRO* 4.7 0.6 - - - +
132C ALA* 4.6 1.0 - - - +
173C LEU 4.5 0.9 - - - +
174C SER* 4.0 27.6 - - - +
177C GLY* 4.3 16.6 - - - -
178C PRO* 4.4 6.5 - - + +
188D LEU* 6.4 1.1 - - + -
205D LEU 2.9 18.7 + - - +
206D GLY* 3.5 7.6 - - - +
208D GLN* 1.3 75.6 - - - +
210D LEU* 1.3 58.4 + - - +
212D GLY* 3.9 0.6 - - - -
213D ALA* 3.0 30.8 + - - +
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Residues in contact with LEU 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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181C ALA* 3.7 28.9 - - + -
184C ALA* 6.1 0.2 - - + -
210C LEU* 3.8 44.0 - - + +
214C ALA* 4.1 2.2 - - + -
181D ALA* 4.0 25.4 - - + +
184D ALA* 5.7 3.8 - - + -
185D LEU* 4.0 26.2 - - + -
188D LEU* 6.0 2.9 - - + -
206D GLY 3.0 15.4 + - - +
207D ALA 3.8 3.6 - - - +
209D ALA* 1.3 72.7 - - - +
211D LEU* 1.3 66.6 + - - +
213D ALA* 3.4 0.9 + - - +
214D ALA* 3.0 26.6 + - + +
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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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130C GLU* 3.8 35.4 - - + +
211C LEU* 4.1 26.4 - - + +
214C ALA* 3.6 9.3 - - + +
215C LYS* 3.7 31.6 - - + +
218C LEU* 3.7 23.6 - - + -
219C HIS* 6.1 0.4 - - + -
207D ALA 2.9 18.3 + - - +
208D GLN* 3.8 7.4 - - - +
210D LEU* 1.3 75.9 - - - +
212D GLY* 1.3 58.6 + - - +
214D ALA* 3.5 1.9 + - - +
215D LYS* 3.0 27.4 + - + +
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Residues in contact with GLY 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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125C PRO* 3.6 13.1 - - - +
128C VAL* 4.0 0.7 - - - +
130C GLU* 3.5 32.5 - - - -
208D GLN 2.9 12.7 + - - -
209D ALA 4.0 0.7 - - - -
211D LEU* 1.3 76.7 - - - +
213D ALA* 1.3 57.0 + - - +
215D LYS* 3.4 3.2 + - - +
216D MET* 2.9 31.5 + - - +
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Residues in contact with ALA 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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125C PRO* 3.7 6.4 - - - +
178C PRO* 3.8 17.3 - - + -
181C ALA* 3.5 27.6 - - + -
182C PHE* 3.4 25.0 - - + -
185C LEU* 5.0 0.9 - - - -
209D ALA 3.0 19.0 + - - +
210D LEU 3.8 0.7 - - - +
212D GLY* 1.3 73.7 - - - +
214D ALA* 1.3 65.5 + - - +
216D MET* 3.2 1.3 + - - -
217D LEU* 3.0 20.3 + - - +
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Residues in contact with ALA 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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181C ALA* 5.2 0.4 - - - +
185C LEU* 4.3 13.6 - - + +
207C ALA* 3.4 26.5 - - - +
210C LEU* 4.3 7.4 - - + -
211C LEU* 3.6 23.3 - - + +
210D LEU 3.0 18.3 + - - +
211D LEU 3.7 0.9 - - - +
213D ALA* 1.3 74.3 - - - +
215D LYS* 1.3 63.4 + - - +
217D LEU* 3.3 3.8 + - - +
218D LEU* 3.0 26.7 + - - +
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Residues in contact with LYS 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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128C VAL* 2.8 36.5 + - + +
129C ARG* 5.0 2.2 - - - +
130C GLU* 3.6 26.3 + - + +
211C LEU* 3.7 17.6 - - + +
211D LEU* 3.0 21.1 + - + +
212D GLY* 3.6 6.1 - - - +
214D ALA* 1.3 74.3 - - - +
216D MET* 1.3 65.8 + - - +
218D LEU* 3.3 2.5 + - - -
219D HIS* 2.9 59.1 + - + +
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Residues in contact with MET 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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124C THR* 3.5 21.1 - - - +
125C PRO* 3.5 35.4 - - + -
127C VAL* 3.8 27.6 - - + -
128C VAL* 4.0 11.6 - - + +
182C PHE* 3.9 22.2 - - + -
212D GLY 2.9 16.1 + - - +
213D ALA 3.2 7.6 + - - +
215D LYS* 1.3 74.7 - - - +
217D LEU* 1.3 59.8 + - - +
219D HIS* 3.3 2.4 + - - +
220D SER* 2.9 31.8 + - - -
227D LEU* 4.3 19.1 - - + +
230D ASN* 6.1 2.2 - - + +
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Residues in contact with LEU 217 (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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182C PHE* 4.6 4.9 - - + -
185C LEU* 3.4 38.8 - - + -
203C VAL* 4.4 21.9 - - + +
207C ALA* 4.6 6.1 - - + -
213D ALA 3.0 12.5 + - - +
214D ALA 3.6 7.4 - - - +
215D LYS 3.2 0.2 - - - -
216D MET* 1.3 76.3 - - - +
218D LEU* 1.3 63.6 + - - +
220D SER* 3.2 16.5 + - - +
222D GLN 3.9 16.4 - - - +
224D PRO* 4.0 28.9 - - + -
227D LEU* 3.6 25.0 - - + +
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Residues in contact with LEU 218 (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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203C VAL* 5.7 0.9 - - + -
204C ARG* 3.2 47.5 - - - +
207C ALA* 3.7 19.1 - - + -
208C GLN* 4.0 24.7 - - - +
211C LEU* 3.9 24.2 - - + -
214D ALA 3.0 21.4 + - - +
215D LYS* 3.3 4.5 + - - +
217D LEU* 1.3 76.8 - - - +
219D HIS* 1.3 69.1 + - + +
220D SER 3.7 3.1 + - - +
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Residues in contact with HIS 219 (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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128C VAL* 4.3 16.6 - - + -
211C LEU* 6.1 0.2 - - + -
215D LYS* 2.9 56.8 + - + +
216D MET 3.6 3.4 - - - +
218D LEU* 1.3 86.1 - - + +
220D SER* 1.3 59.7 + - - +
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Residues in contact with SER 220 (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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216D MET* 2.9 18.6 + - - -
217D LEU 3.2 13.7 + - - +
218D LEU 4.4 2.8 - - - +
219D HIS* 1.3 80.1 - - - +
221D GLU* 1.3 58.2 + - - +
222D GLN* 2.9 39.6 + - - +
227D LEU* 3.9 17.4 - - - +
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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
------------------------------------------------------------
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