Contacts of the helix formed by residues 193 - 214 (chain D) in PDB entry 7CAL
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 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A THR* 4.5 13.3 + - - -
306A THR* 4.4 18.7 - - + -
307A ARG* 4.3 27.4 + - + +
310A ARG* 4.1 29.5 - - + +
186D GLU* 3.9 36.1 + - + -
191D PHE 3.9 0.2 + - - -
192D ASN* 1.3 83.2 + - - +
194D PHE* 1.3 64.2 + - + +
195D TRP 3.3 1.6 - - - -
196D ILE* 4.0 1.6 - - - +
197D ARG* 3.3 52.9 + - + +
297D ASN* 5.1 3.7 + - - -
298D LEU* 4.6 9.4 - - + -
301D HIS* 3.8 31.4 - + + -
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Residues in contact with PHE 194 (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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314A ARG* 3.9 17.3 - - - -
192D ASN* 3.6 15.9 + - - -
193D TYR* 1.3 80.1 - - + +
195D TRP* 1.3 71.9 + + + +
196D ILE 3.5 0.2 - - - -
197D ARG 4.3 0.9 - - - -
198D CYS* 3.2 30.2 + - - +
298D LEU* 4.0 20.2 - - + -
301D HIS* 3.2 64.4 - + + -
302D TRP* 3.9 52.7 - + + +
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Residues in contact with TRP 195 (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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192D ASN* 3.2 35.5 - - + +
193D TYR 3.3 2.4 - - - +
194D PHE* 1.3 90.1 - - + +
196D ILE* 1.3 67.3 + - - +
198D CYS* 4.4 19.1 - - + +
199D THR* 2.8 21.7 + - - -
302D TRP* 4.4 24.9 - + - -
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Residues in contact with ILE 196 (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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182D PHE* 4.3 26.5 - - + +
185D LEU* 4.0 38.1 - - + +
186D GLU* 3.8 28.0 - - + +
191D PHE* 4.6 10.3 - - + -
192D ASN* 3.2 22.7 - - + +
193D TYR* 3.8 4.7 + - - +
195D TRP* 1.3 84.1 - - - +
197D ARG* 1.3 59.7 + - - +
198D CYS 3.3 1.6 - - - -
199D THR* 3.3 7.1 + - + +
200D LYS* 3.0 27.2 + - - +
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Residues in contact with ARG 197 (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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303A THR* 4.4 11.2 - - - +
186D GLU* 2.8 40.2 + - - -
193D TYR* 3.3 47.1 + - + +
194D PHE 4.8 0.4 - - - +
196D ILE* 1.3 78.0 - - - +
198D CYS* 1.3 58.1 + - - +
200D LYS* 3.3 30.2 + - - +
201D LEU* 3.3 33.8 + - + +
290D TYR* 4.5 4.4 + - - -
294D ASN* 3.0 32.3 - - - +
297D ASN* 6.0 1.2 - - - +
298D LEU* 4.1 22.4 - - + +
701D 3PE 3.1 24.9 + - - -
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Residues in contact with CYS 198 (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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194D PHE 3.2 22.0 + - - +
195D TRP* 4.6 20.2 - - + -
196D ILE 3.3 0.2 - - - -
197D ARG* 1.3 74.8 - - - +
199D THR* 1.3 60.9 + - - +
200D LYS 3.2 0.4 - - - -
201D LEU* 3.6 7.5 - - + +
202D ILE* 2.9 41.4 + - + +
295D MET* 4.6 17.7 - - + -
298D LEU* 3.7 22.9 - - - -
302D TRP* 6.1 2.7 - - - -
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Residues in contact with THR 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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182D PHE* 4.1 20.8 - - + -
195D TRP* 2.8 22.1 + - - -
196D ILE* 3.3 11.9 + - + -
198D CYS* 1.3 77.4 - - - +
200D LYS* 1.3 56.2 - - - +
202D ILE* 4.1 7.0 - - + +
203D SER* 2.9 39.6 + - - +
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Residues in contact with LYS 200 (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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179D SER 5.6 0.9 - - - -
182D PHE* 4.0 40.4 - - + +
183D ALA* 5.9 1.0 - - - +
186D GLU* 4.0 6.1 + - - +
196D ILE 3.0 16.5 + - - +
197D ARG* 3.3 33.4 - - - +
199D THR* 1.3 76.8 - - - +
201D LEU* 1.3 63.2 + - + +
203D SER* 4.4 1.4 - - - -
204D VAL* 3.3 31.0 + - + +
290D TYR* 4.7 5.3 + - - +
701D 3PE 1.3 83.8 + - + +
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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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197D ARG* 3.3 22.6 + - - +
198D CYS* 3.2 8.8 + - - +
200D LYS* 1.3 78.5 - - + +
202D ILE* 1.3 63.0 + - + +
204D VAL* 4.1 2.5 + - - +
205D THR* 3.3 27.5 + - - +
290D TYR* 3.7 37.0 - - + +
291D LEU* 4.0 25.5 - - + +
294D ASN* 3.8 32.3 - - + +
295D MET* 4.6 20.4 - - + +
298D LEU* 4.8 8.5 - - + -
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Residues in contact with ILE 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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701C 3PE 4.6 40.6 - - + -
198D CYS* 2.9 26.9 + - + +
199D THR* 4.1 7.4 - - + +
200D LYS 3.3 0.2 - - - -
201D LEU* 1.3 79.6 - - + +
203D SER* 1.3 60.0 + - - +
204D VAL 3.2 0.2 - - - -
205D THR* 3.1 8.9 + - - +
206D LEU* 2.9 49.6 + - + +
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Residues in contact with SER 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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182D PHE* 4.5 8.6 - - - -
199D THR* 2.9 25.6 + - - +
200D LYS* 4.5 4.3 - - - -
202D ILE* 1.3 79.2 - - - +
204D VAL* 1.3 61.6 + - - +
206D LEU* 4.0 8.6 - - - +
207D PHE* 3.3 16.5 + - - +
701D 3PE 3.4 42.4 - - - +
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Residues in contact with VAL 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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200D LYS* 3.3 20.5 + - + +
201D LEU* 4.4 5.2 - - - +
202D ILE 3.2 0.6 - - - -
203D SER* 1.3 79.1 - - - +
205D THR* 1.3 60.2 + - + +
207D PHE* 3.4 5.7 + - - +
208D ALA* 3.0 25.2 + - + +
283D PHE* 6.0 0.9 - - + -
287D LEU* 4.0 24.5 - - + -
290D TYR* 4.7 11.4 - - + +
291D LEU* 5.5 0.4 - - + -
701D 3PE 3.8 58.3 - - + +
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Residues in contact with THR 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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285C LEU* 5.1 7.1 - - + +
201D LEU 3.3 18.8 + - - +
202D ILE* 3.1 11.0 + - - +
204D VAL* 1.3 76.6 - - + +
206D LEU* 1.3 65.8 + - - +
208D ALA* 3.7 7.5 - - - +
209D ILE* 2.9 43.0 + - - +
258D LEU* 5.0 5.8 - - - -
287D LEU* 4.4 12.6 - - + -
291D LEU* 3.7 33.4 - - + -
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Residues in contact with LEU 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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282C MET* 4.0 26.7 - - - -
701C 3PE 4.3 31.6 - - + -
202D ILE* 2.9 39.0 + - + +
203D SER* 4.3 8.5 - - - +
205D THR* 1.3 80.4 + - - +
207D PHE* 1.3 59.6 + - - +
209D ILE* 4.2 6.9 - - + +
210D HIS* 3.3 17.2 + - - +
701D 3PE 3.3 48.5 - - + +
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Residues in contact with PHE 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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74D ALA* 3.2 30.5 - - + -
78D PRO* 5.0 4.5 - - + -
172D LEU* 3.7 33.7 - - + -
175D LEU* 4.1 14.8 - - + -
203D SER 3.3 17.1 + - - +
204D VAL* 3.8 4.7 - - - +
205D THR 3.2 0.8 - - - -
206D LEU* 1.3 76.9 - - - +
208D ALA* 1.3 61.2 + - - +
210D HIS* 4.5 3.1 - + + -
211D CYS* 3.0 46.7 + - + +
701D 3PE 3.9 37.9 - - + +
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Residues in contact with ALA 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 VAL* 3.0 16.6 + - + +
205D THR* 3.2 8.0 + - - +
207D PHE* 1.3 76.5 - - - +
209D ILE* 1.3 64.8 + - - +
211D CYS* 5.0 2.0 - - - -
212D ALA* 3.3 25.6 + - - +
258D LEU* 4.0 17.4 - - + +
280D PHE* 4.4 1.4 - - - -
283D PHE* 4.0 29.4 - - + -
287D LEU* 4.3 5.2 - - + -
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Residues in contact with ILE 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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278C ILE* 6.2 3.4 - - + -
282C MET* 4.5 17.5 - - + -
285C LEU* 5.7 1.3 - - + -
205D THR* 2.9 28.9 + - - +
206D LEU* 4.2 8.5 - - + +
208D ALA* 1.3 76.4 - - - +
210D HIS* 1.3 59.5 + - - +
213D GLY* 3.0 26.7 + - - -
251D LEU* 3.8 32.7 - - + +
254D SER* 3.8 15.1 - - - +
255D ILE* 3.7 35.7 - - + +
258D LEU* 3.9 22.0 - - + -
701D 3PE 5.3 5.8 - - + -
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Residues in contact with HIS 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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74D ALA 4.7 6.3 - - - -
75D TRP* 3.0 56.9 + + - -
78D PRO* 3.5 24.6 - - + +
79D PHE* 4.1 5.9 - - + +
206D LEU 3.3 18.3 + - - +
207D PHE* 4.1 3.8 - + + +
208D ALA 3.4 0.2 - - - -
209D ILE* 1.3 81.5 - - - +
211D CYS* 1.3 61.7 + - + +
213D GLY* 3.3 1.0 + - - -
214D CYS* 3.2 44.7 + - - -
247D TYR* 3.6 21.4 + + - -
251D LEU* 4.5 6.7 - - - +
701D 3PE 3.7 21.1 - - + +
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Residues in contact with CYS 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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78D PRO* 4.4 12.1 - - + -
172D LEU* 4.7 8.3 - - - -
207D PHE* 3.0 46.2 + - + +
208D ALA* 4.4 2.0 - - - +
210D HIS* 1.3 80.0 - - - +
212D ALA* 1.3 56.9 + - - +
214D CYS 4.2 1.6 - - - -
215D PHE* 3.1 59.2 + - - +
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Residues in contact with ALA 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 ALA 3.3 20.1 + - - +
210D HIS 3.2 0.2 - - - -
211D CYS* 1.3 77.2 - - - +
213D GLY* 1.3 60.9 + - - +
214D CYS 3.4 1.1 - - - -
215D PHE* 4.0 7.6 - - + +
216D ASN* 3.6 10.6 + - - +
253D TRP* 3.6 13.5 - - - -
254D SER* 3.1 9.9 + - - +
276D PHE* 4.2 9.0 - - + -
280D PHE* 3.6 35.2 - - + -
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Residues in contact with GLY 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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83D PHE* 4.3 1.4 - - - -
209D ILE 3.0 16.3 + - - -
210D HIS 3.3 2.4 + - - -
212D ALA* 1.3 76.8 - - - +
214D CYS* 1.3 61.0 + - - +
216D ASN* 4.2 5.0 - - - +
217D TYR* 3.9 10.4 + - - +
250D ALA* 3.3 37.8 - - - +
251D LEU* 4.6 4.9 - - - -
253D TRP* 5.1 0.2 - - - -
254D SER* 3.2 12.1 + - - -
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Residues in contact with CYS 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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78D PRO* 3.4 32.5 - - + +
79D PHE* 4.4 2.7 - - - -
81D PHE* 5.0 0.2 - - - -
82D ALA* 3.3 20.2 - - + +
83D PHE* 3.6 29.4 - - + -
210D HIS* 3.2 40.8 + - - +
213D GLY* 1.3 79.2 - - - +
215D PHE* 1.3 65.9 + - + +
216D ASN 3.3 1.8 - - - -
217D TYR 3.9 2.0 + - - +
218D LEU* 3.7 8.7 + - - +
247D TYR* 4.5 7.2 - - - -
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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