Contacts of the helix formed by residues 192 - 214 (chain D) in PDB entry 7A62
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 GLU 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187D ALA* 3.3 15.1 + - - +
190D MET* 3.2 31.1 - - + +
191D GLN* 1.3 78.7 - - - +
193D ARG* 1.3 65.2 + - - +
194D ASP 3.4 2.0 - - - -
195D THR* 3.3 22.6 + - - +
196D LEU* 3.1 21.8 + - - +
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Residues in contact with ARG 193 (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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191D GLN 3.5 6.4 + - - +
192D GLU* 1.3 73.2 - - - +
194D ASP* 1.3 91.1 + - - +
196D LEU* 3.2 8.7 + - - +
197D LEU* 3.0 37.2 + - - +
319D PHE* 6.3 2.2 - - - -
325D ASP* 2.7 42.5 + - - +
327D GLY* 3.9 15.0 - - - +
328D LEU* 4.2 17.4 - - + +
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Residues in contact with ASP 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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192D GLU 3.4 0.2 - - - -
193D ARG* 1.3 108.3 + - - +
195D THR* 1.3 63.7 + - - +
197D LEU* 3.2 8.3 + - + +
198D LYS* 2.9 26.3 + - - +
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Residues in contact with THR 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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183D THR* 4.2 17.5 - - + -
187D ALA* 3.6 18.8 - - + -
192D GLU* 3.3 24.1 + - + +
194D ASP* 1.3 79.8 - - - +
196D LEU* 1.3 61.8 + - - +
198D LYS* 3.6 6.6 + - - +
199D ALA* 3.1 21.7 + - - +
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Residues in contact with LEU 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D VAL* 3.7 35.9 - - + +
187D ALA* 3.7 13.4 - - + +
188D MET* 4.7 9.9 - - + +
192D GLU 3.1 13.1 + - - +
193D ARG* 3.2 8.0 + - - +
195D THR* 1.3 77.3 - - - +
197D LEU* 1.3 58.7 + - - +
199D ALA* 3.2 3.9 + - - +
200D LEU* 2.9 39.0 + - + +
316D VAL* 5.2 3.8 - - + -
319D PHE* 4.0 25.4 - - + -
320D VAL* 4.7 6.5 - - + -
328D LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 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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193D ARG* 3.0 35.9 + - - +
194D ASP* 3.2 7.2 + - - +
196D LEU* 1.3 75.5 - - - +
198D LYS* 1.3 69.7 + - + +
200D LEU* 3.1 6.0 + - - +
201D LEU* 3.0 39.5 + - + +
327D GLY* 3.1 42.4 - - - +
328D LEU* 3.7 16.8 - - + +
331D ALA* 4.2 7.9 - - + -
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Residues in contact with LYS 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 ASP 2.9 16.7 + - - +
195D THR* 4.0 5.4 - - - +
197D LEU* 1.3 83.0 - - + +
199D ALA* 1.3 57.1 + - - +
201D LEU* 3.4 8.7 + - + +
202D GLU* 3.0 29.6 + - + +
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Residues in contact with ALA 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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180D VAL* 3.7 21.8 - - + +
183D THR* 4.2 14.8 - - + -
184D VAL* 3.9 15.7 - - + +
195D THR 3.1 17.5 + - - +
196D LEU* 3.5 7.0 - - - +
197D LEU 3.1 0.2 - - - -
198D LYS* 1.3 74.7 - - - +
200D LEU* 1.3 66.3 + - - +
202D GLU* 3.3 5.5 + - - +
203D ILE* 3.0 28.3 + - - +
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Residues in contact with LEU 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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184D VAL* 4.6 11.2 - - + -
196D LEU* 2.9 40.8 + - + +
197D LEU 3.1 4.9 + - - +
199D ALA* 1.3 76.8 - - - +
201D LEU* 1.3 64.3 + - - +
203D ILE* 3.2 6.8 + - + +
204D ALA* 3.0 19.6 + - - +
276D LEU* 5.7 2.5 - - + -
277D LEU* 5.0 6.7 - - + -
316D VAL* 4.5 16.8 - - + -
320D VAL* 4.7 7.4 - - + -
328D LEU* 4.4 12.8 - - + +
331D ALA* 3.8 18.4 - - + +
332D TYR* 4.0 26.5 - - + +
335D CYS* 3.1 24.2 - - - -
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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 LEU* 3.0 38.7 + - + +
198D LYS* 3.7 7.4 - - + +
200D LEU* 1.3 76.2 - - - +
202D GLU* 1.3 58.6 + - - +
204D ALA* 3.3 4.7 + - + +
205D SER* 2.8 29.3 + - - -
330D GLU* 5.3 1.6 - - + -
331D ALA* 3.5 28.0 - - + +
334D ALA* 4.6 11.4 - - + -
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Residues in contact with GLU 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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176D SER* 4.8 2.1 - - - +
179D LYS* 6.0 1.4 - - - -
180D VAL* 3.9 23.3 - - + +
198D LYS* 3.0 20.2 + - + +
199D ALA* 3.6 8.3 - - - +
200D LEU 3.2 0.2 - - - -
201D LEU* 1.3 76.8 - - - +
203D ILE* 1.3 56.9 + - - +
205D SER* 3.1 12.3 + - - -
206D CYS* 2.8 50.5 + - - -
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Residues in contact with ILE 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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177D ALA* 3.6 29.1 - - + +
180D VAL* 3.9 11.7 - - + -
181D ILE* 4.6 3.8 - - + -
184D VAL* 4.0 20.4 - - + -
199D ALA 3.0 18.7 + - - +
200D LEU* 3.2 11.9 + - + +
202D GLU* 1.3 75.5 - - - +
204D ALA* 1.3 57.5 + - - +
206D CYS* 3.2 2.9 + - - +
207D LEU* 2.8 36.6 + - + +
273D PHE* 3.8 25.1 - - + -
276D LEU* 3.9 24.2 - - + -
335D CYS* 3.7 15.3 - - + -
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Residues in contact with ALA 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 LEU 3.0 12.3 + - - +
201D LEU* 3.6 8.7 - - + +
203D ILE* 1.3 77.2 - - - +
205D SER* 1.3 57.5 + - - +
207D LEU* 3.3 6.9 + - - +
208D GLU* 2.8 41.9 + - - +
334D ALA* 3.6 46.0 - - + +
335D CYS* 3.8 5.6 - - - +
338D ALA* 4.1 1.2 - - - +
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Residues in contact with SER 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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201D LEU 2.8 18.1 + - - -
202D GLU* 3.4 15.5 + - - -
204D ALA* 1.3 76.3 - - - +
206D CYS* 1.3 63.5 + - - +
208D GLU* 3.3 17.6 + - - +
209D LYS* 3.2 43.5 + - - +
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Residues in contact with CYS 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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173D ALA 4.5 7.6 - - - +
176D SER* 3.5 33.2 - - - -
177D ALA* 3.7 19.3 - - + +
202D GLU* 2.8 42.3 + - - +
203D ILE 3.8 3.1 - - - +
205D SER* 1.3 78.8 - - - +
207D LEU* 1.3 63.7 + - - +
209D LYS* 3.0 26.6 + - - +
210D ALA* 3.0 13.5 + - - +
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Residues in contact with LEU 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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174D ALA* 5.0 9.0 - - + -
177D ALA* 4.2 8.3 - - + -
203D ILE* 2.8 26.2 + - + +
204D ALA* 3.3 1.3 + - - +
206D CYS* 1.3 77.8 - - - +
208D GLU* 1.3 61.7 + - - +
210D ALA* 3.4 10.7 + - + +
211D LEU* 3.3 19.8 + - - +
269D VAL* 5.4 2.2 - - + -
273D PHE* 4.0 49.8 - - + -
277D LEU* 6.1 0.4 - - + -
335D CYS* 4.5 10.5 - - + +
338D ALA* 3.5 26.8 - - + +
339D LEU* 4.6 8.7 - - + +
342D LEU* 4.1 23.3 - - + +
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Residues in contact with GLU 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 ALA* 2.8 33.6 + - - +
205D SER* 3.5 16.2 - - - +
206D CYS 3.2 0.2 - - - -
207D LEU* 1.3 76.5 - - - +
209D LYS* 1.3 62.9 + - + +
211D LEU* 3.4 18.0 + - + +
212D GLN* 3.4 16.9 + - - +
334D ALA* 4.7 7.8 - - - +
338D ALA* 4.3 11.9 - - + -
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Residues in contact with LYS 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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173D ALA* 5.4 4.3 - - + +
205D SER* 3.2 32.6 + - - +
206D CYS* 3.0 18.1 + - - +
208D GLU* 1.3 73.9 - - + +
210D ALA* 1.3 66.1 + - - +
211D LEU 3.1 2.0 - - - -
212D GLN* 2.9 19.8 + - - +
213D VAL* 3.0 18.4 + - + +
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Residues in contact with ALA 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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170D VAL* 4.1 19.1 - - + +
173D ALA* 3.7 27.7 - - + +
174D ALA* 4.4 9.0 - - + +
206D CYS 3.0 11.2 + - - +
207D LEU* 3.4 15.4 + - + +
209D LYS* 1.3 75.2 - - - +
211D LEU* 1.3 62.2 + - - +
213D VAL* 3.3 3.5 + - - +
214D PHE* 3.0 22.9 + - - +
342D LEU* 4.0 11.1 - - + +
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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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207D LEU 3.3 8.1 + - - +
208D GLU* 3.4 15.0 - - + +
209D LYS 3.1 0.8 - - - -
210D ALA* 1.3 81.2 - - - +
212D GLN* 1.3 74.5 + - - +
214D PHE* 3.2 16.2 + - + +
215D HIS* 3.5 11.2 + - + -
338D ALA* 5.6 0.7 - - - +
341D SER* 3.8 29.6 - - - +
342D LEU* 3.5 23.3 - - + +
345D TYR* 3.5 40.4 - - + -
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Residues in contact with GLN 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 GLU 3.4 11.3 + - - +
209D LYS* 2.9 11.8 + - - +
211D LEU* 1.3 87.6 - - - +
213D VAL* 1.3 66.4 + - + +
215D HIS* 2.9 54.7 + - - +
216D GLN* 4.3 1.9 + - - +
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Residues in contact with VAL 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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166D VAL* 4.2 4.1 - - + +
169D LEU* 3.7 41.3 - - + +
170D VAL* 3.9 7.0 - - + +
173D ALA* 4.1 15.7 - - + -
209D LYS* 3.0 15.0 + - + +
210D ALA* 3.3 9.4 + - - +
212D GLN* 1.3 74.3 - - + +
214D PHE* 1.3 62.5 + - - +
215D HIS 2.9 1.6 + - - -
216D GLN* 3.1 33.7 + - - +
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Residues in contact with PHE 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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166D VAL* 4.5 2.9 - - + +
170D VAL* 3.9 16.8 - - + +
210D ALA 3.0 11.7 + - - +
211D LEU 3.2 15.7 - - - +
212D GLN 3.1 0.4 - - - -
213D VAL* 1.3 77.8 - - - +
215D HIS* 1.3 60.7 + - - +
216D GLN 3.2 0.5 + - - -
217D ILE* 3.2 26.3 + - + +
270D PHE* 4.9 6.5 - + - -
342D LEU* 4.3 21.3 - - + -
345D TYR* 3.8 19.1 - + + -
346D HIS* 3.9 34.1 - + + -
349D ILE* 4.0 17.0 - - + -
504D HEM 3.7 52.7 - + + -
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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