Contacts of the helix formed by residues 186 - 204 (chain D) in PDB entry 6ACQ
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 VAL 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D GLU* 3.2 7.2 + - - +
177D VAL* 6.0 0.4 - - + -
179D VAL* 4.2 17.7 - - + -
184D GLY 3.7 0.4 - - - -
185D PHE* 1.3 86.1 - - - +
187D VAL* 1.3 65.7 + - - +
188D ASN 3.5 0.4 - - - -
189D ARG* 3.5 2.0 + - - +
190D ILE* 3.2 41.1 + - + +
201E ILE* 4.4 13.5 - - + -
207E ALA* 4.0 25.8 - - + -
211E ASP 5.3 0.7 - - - +
212E ILE* 4.2 21.3 - - + +
215E ALA* 3.9 22.9 - - + -
216E MET* 4.4 2.7 - - - -
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Residues in contact with VAL 187 (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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140D PHE* 3.7 35.2 - - + -
148D LEU* 4.0 5.4 - - + -
150D GLU* 3.0 17.4 + - - +
184D GLY 3.8 0.2 + - - -
186D VAL* 1.3 72.8 - - - +
188D ASN* 1.3 70.3 + - - +
190D ILE* 3.2 2.8 + - - +
191D LEU* 2.8 50.9 + - + +
215E ALA* 3.5 29.6 - - + +
216E MET* 3.9 11.8 - - + +
219E GLY* 4.3 10.5 - - - +
220E ALA 5.0 0.2 - - - +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D SER* 3.9 28.5 + - - -
138D HIS* 4.4 14.0 - - - -
140D PHE* 5.4 2.1 - - - -
150D GLU* 5.0 0.8 + - - -
184D GLY* 3.4 19.2 + - - +
185D PHE* 5.6 1.0 - - - -
187D VAL* 1.3 88.9 - - - +
189D ARG* 1.3 62.3 + - - +
191D LEU* 4.7 1.7 - - - +
192D ILE* 3.1 42.2 + - + +
193D PRO* 3.3 5.7 - - - +
241D ILE* 3.7 33.3 - - + +
245D LEU* 4.5 1.6 - - - +
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Residues in contact with ARG 189 (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 ALA* 5.0 4.2 - - - +
183D PRO* 3.2 45.1 + - - +
184D GLY* 3.0 10.9 + - - +
185D PHE 3.4 21.3 - - - +
186D VAL 3.6 4.0 - - - +
187D VAL 3.1 0.2 - - - -
188D ASN* 1.3 77.6 - - - +
190D ILE* 1.3 55.8 + - - +
193D PRO* 3.4 18.9 - - - +
245D LEU* 3.9 14.8 - - - +
249D THR* 4.2 9.8 - - - +
254D TYR* 2.9 34.1 + - - -
197E GLU* 2.7 26.0 + - - +
200E GLY 6.3 1.2 - - - -
201E ILE* 3.7 26.1 - - + +
204E GLU* 4.6 13.7 + - - -
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Residues in contact with ILE 190 (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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186D VAL* 3.2 21.9 + - + +
187D VAL 3.2 3.0 + - - +
188D ASN 3.1 0.4 - - - -
189D ARG* 1.3 79.9 - - - +
191D LEU* 1.3 63.8 + - - +
192D ILE 3.6 0.7 - - - -
193D PRO* 3.7 7.0 - - - +
194D MET* 3.7 13.0 + - - +
194E MET* 3.4 37.4 - - + +
197E GLU* 4.0 13.2 - - + +
198E ALA* 4.0 26.2 - - + -
201E ILE* 3.9 19.7 - - + -
212E ILE* 4.5 1.8 - - + -
216E MET* 3.7 37.5 - - + -
226E PRO* 4.1 3.1 - - + -
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Residues in contact with LEU 191 (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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187D VAL* 2.8 32.4 + - + +
188D ASN* 4.7 2.0 - - - +
190D ILE* 1.3 75.4 - - - +
192D ILE* 1.3 67.4 + - + +
194D MET* 3.0 46.8 - - + +
195D ILE* 3.2 8.5 + - + +
229D LEU* 4.0 24.0 - - + -
233D ILE* 4.4 15.7 - - + -
216E MET* 4.3 5.8 - - + -
219E GLY 5.5 1.1 - - - +
220E ALA* 3.6 32.3 - - + -
222E HIS* 4.0 11.4 - - + +
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Residues in contact with ILE 192 (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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188D ASN* 3.1 25.3 + - - +
191D LEU* 1.3 82.7 - - + +
193D PRO* 1.3 64.6 - - + +
195D ILE* 2.9 21.9 + - + +
196D ASN* 2.9 24.1 + - - +
233D ILE* 4.6 12.3 - - + -
238D CYS* 3.4 43.5 - - + +
241D ILE* 3.7 35.7 - - + -
242D MET* 3.6 13.5 - - + -
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Residues in contact with PRO 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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188D ASN 3.3 13.7 - - - +
189D ARG 3.4 18.8 - - - +
190D ILE 3.7 4.7 - - - +
191D LEU 3.6 2.5 - - - -
192D ILE* 1.3 94.0 - - + +
194D MET* 1.3 54.7 + - - +
196D ASN* 3.4 5.6 + - + +
197D GLU* 2.8 30.8 + - - +
242D MET* 3.7 24.7 - - + -
245D LEU* 3.9 11.4 - - + -
254D TYR* 4.4 11.7 - - + -
197E GLU* 5.6 2.9 - - + +
253E LYS* 5.5 2.7 + - - -
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Residues in contact with MET 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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190D ILE 3.7 8.9 + - - +
191D LEU* 3.0 41.9 + - + +
193D PRO* 1.3 77.1 - - - +
195D ILE* 1.3 62.4 - - + +
197D GLU* 3.5 7.4 + - - +
198D ALA* 3.2 19.2 + - - +
216D MET* 5.8 0.4 - - + -
222D HIS* 4.4 18.6 - - + +
224D MET 6.0 1.1 - - - +
226D PRO* 4.2 23.7 - - + +
229D LEU* 4.6 9.9 - - + -
190E ILE* 3.2 30.1 - - + +
194E MET* 2.3 42.6 - - + -
222E HIS* 4.5 1.3 - - - +
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Residues in contact with ILE 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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191D LEU* 3.9 14.1 - - + +
192D ILE* 2.9 15.7 + - + +
194D MET* 1.3 75.9 - - + +
196D ASN* 1.3 67.2 + - - +
198D ALA* 3.0 13.5 + - - +
199D VAL* 3.0 23.2 + - + +
226D PRO* 3.4 35.0 - - + +
227D LEU* 5.3 4.0 - - + -
229D LEU* 4.0 15.7 - - + -
230D GLY* 4.1 13.0 - - - -
233D ILE* 3.9 27.4 - - + -
235D LEU* 5.3 5.2 - - + -
238D CYS* 4.1 22.0 - - + -
260D LEU* 6.0 3.1 - - + -
277D PHE* 5.5 0.7 - - + -
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Residues in contact with ASN 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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192D ILE 2.9 12.4 + - - +
193D PRO* 3.4 13.0 + - + +
195D ILE* 1.3 79.3 - - - +
197D GLU* 1.3 61.4 + - - +
199D VAL* 3.4 11.1 + - - +
200D GLY* 3.3 16.8 + - - -
242D MET* 3.7 21.4 - - + +
253D LYS 5.6 0.6 + - - -
255D ARG 3.2 21.8 + - - -
256D PRO* 3.4 4.5 - - - +
257D HIS* 2.9 31.8 + - - +
260D LEU* 3.9 14.2 - - + +
253E LYS* 4.3 14.6 + - - +
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Residues in contact with GLU 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 PRO 2.8 16.0 + - - +
194D MET* 3.7 9.4 - - - +
196D ASN* 1.3 77.6 - - - +
198D ALA* 1.3 61.9 + - - +
200D GLY* 3.1 5.1 + - - -
201D ILE* 3.1 21.4 + - - +
189E ARG* 2.8 49.3 + - - +
190E ILE* 4.0 12.3 - - + -
193E PRO* 5.7 2.8 - - + +
253E LYS* 2.7 35.6 + - - +
254E TYR* 2.6 28.1 + - - -
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Residues in contact with ALA 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 MET 3.2 5.9 + - - +
195D ILE 3.0 9.7 + - - +
197D GLU* 1.3 77.4 - - - +
199D VAL* 1.3 63.5 + - - +
201D ILE* 3.3 8.0 + - - +
202D LEU* 3.1 21.5 + - - +
212D ILE* 3.8 9.3 - - + +
226D PRO* 3.7 31.4 - - + -
227D LEU* 3.7 15.7 - - + +
190E ILE* 3.9 14.0 - - + +
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Residues in contact with VAL 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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195D ILE* 3.0 24.1 + - + +
196D ASN* 3.6 11.9 - - - +
198D ALA* 1.3 73.9 - - - +
200D GLY* 1.3 54.6 + - - +
202D LEU* 3.1 8.7 + - - +
203D ALA* 2.7 33.8 + - - +
227D LEU* 3.9 6.9 - - + +
257D HIS* 3.5 31.4 - - + +
259D LEU* 4.1 8.3 - - + +
260D LEU* 4.0 25.4 - - + +
277D PHE* 4.0 26.0 - - + -
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Residues in contact with GLY 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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196D ASN 3.3 5.3 + - - -
197D GLU* 3.1 9.8 + - - -
199D VAL* 1.3 79.0 - - - +
201D ILE* 1.3 61.9 + - - +
203D ALA* 3.8 0.5 - - - +
204D GLU* 2.9 35.9 + - - +
257D HIS* 3.4 26.7 - - - -
189E ARG* 5.2 3.1 - - - -
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Residues in contact with ILE 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 GLU 3.1 13.1 + - - +
198D ALA* 3.6 6.3 - - - +
199D VAL 3.3 0.2 - - - -
200D GLY* 1.3 73.0 - - - +
202D LEU* 1.3 65.0 + - - +
204D GLU* 3.5 1.7 + - - -
205D GLY 3.5 2.4 + - - -
206D ILE* 3.1 52.2 + - + +
207D ALA* 4.0 4.2 + - + +
212D ILE* 3.7 22.2 - - + -
185E PHE 4.2 11.2 - - - +
186E VAL* 4.2 14.6 - - + +
189E ARG* 3.8 27.1 - - + +
190E ILE* 3.8 35.4 - - + -
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Residues in contact with LEU 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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198D ALA 3.1 13.6 + - - +
199D VAL* 3.3 7.9 - - - +
201D ILE* 1.3 75.8 - - - +
203D ALA* 1.3 65.5 + - - +
205D GLY* 3.0 15.1 + - - -
207D ALA 3.7 20.1 - - - +
208D SER* 4.2 2.5 - - - -
209D VAL* 3.7 36.3 - - + +
212D ILE* 3.8 5.1 - - + +
227D LEU* 4.8 3.1 - - + -
259D LEU* 4.1 13.2 - - + -
263D TYR* 4.6 5.8 - - - +
277D PHE* 3.8 34.5 - - + -
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Residues in contact with ALA 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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204A GLU* 3.9 27.1 - - + +
199D VAL 2.7 19.5 + - - +
200D GLY 3.8 2.2 - - - +
201D ILE 3.4 0.2 - - - -
202D LEU* 1.3 74.6 - - - +
204D GLU* 1.3 60.0 + - + +
205D GLY 3.5 0.5 + - - -
257D HIS* 3.3 33.9 - - + +
259D LEU* 3.8 18.4 - - + +
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Residues in contact with GLU 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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203A ALA* 3.8 23.7 - - + +
204A GLU* 4.9 12.5 - - + +
257A HIS* 4.1 23.2 + - - -
258A THR* 5.1 6.1 - - - +
200D GLY* 2.9 21.3 + - - +
201D ILE* 3.5 1.8 + - - +
202D LEU 3.2 1.0 - - - -
203D ALA* 1.3 78.2 - - + +
205D GLY* 1.3 61.6 + - - +
206D ILE* 3.3 23.9 + - + +
257D HIS* 5.5 3.6 + - - +
189E ARG* 4.8 14.4 + - - +
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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