Contacts of the helix formed by residues 218 - 230 (chain D) in PDB entry 4RZR
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 GLY 218 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214D LYS 2.8 17.2 + - - -
215D GLY 4.6 0.6 + - - -
216D MET 3.8 0.8 - - - -
217D ILE* 1.3 80.2 - - - +
219D GLU* 1.3 68.3 + - - -
220D ALA 3.2 3.5 + - - -
221D LYS 3.4 1.6 + - - -
222D ALA* 3.1 21.1 + - - +
11E G 3.5 26.2 - - - -
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Residues in contact with GLU 219 (chain D).
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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210D PHE* 5.0 6.2 - - + -
214D LYS* 3.8 43.7 + - + +
218D GLY* 1.3 71.2 - - - -
220D ALA* 1.3 58.8 + - - +
222D ALA* 3.4 2.6 + - - +
223D LYS* 3.0 62.4 + - + +
11E G 3.2 14.4 + - - +
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Residues in contact with ALA 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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218D GLY 3.3 1.0 - - - -
219D GLU* 1.3 81.3 - - + +
221D LYS* 1.3 58.6 + - - +
223D LYS* 3.5 7.6 + - - +
224D TYR* 3.0 29.2 + - - +
10E G 4.2 28.7 - - - +
11E G 3.5 11.9 + - - +
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Residues in contact with LYS 221 (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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185D GLY* 2.8 32.2 + - - +
186D ILE* 3.9 15.9 - - + -
190D THR* 4.4 14.4 - - - -
217D ILE* 3.4 44.4 - - + +
218D GLY 3.4 0.8 + - - +
219D GLU 3.4 0.2 - - - -
220D ALA* 1.3 77.5 - - - +
222D ALA* 1.3 58.6 + - - +
224D TYR* 3.2 13.8 - - + +
225D LEU* 2.9 29.5 + - + +
11E G 5.0 0.6 + - - -
11F G 5.2 1.9 + - - -
12F T 3.9 14.8 - - - -
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Residues in contact with ALA 222 (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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210D PHE* 4.0 16.2 - - + -
213D LEU* 3.5 33.2 - - + -
214D LYS* 4.0 11.4 - - - -
217D ILE* 3.8 4.6 - - + +
218D GLY 3.1 13.2 + - - +
219D GLU 3.7 7.0 - - - +
220D ALA 3.3 0.2 - - - -
221D LYS* 1.3 76.4 - - - +
223D LYS* 1.3 57.6 + - - +
225D LEU* 3.2 2.5 + - - +
226D ILE* 2.9 35.3 + - - +
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Residues in contact with LYS 223 (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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210D PHE* 4.3 20.8 - - + -
219D GLU* 3.0 48.4 + - + +
220D ALA* 3.8 7.2 - - - +
222D ALA* 1.3 72.2 - - - +
224D TYR* 1.3 66.4 + - - +
226D ILE* 4.0 5.1 - - - +
227D SER* 2.9 28.6 + - - -
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Residues in contact with TYR 224 (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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149D VAL* 3.3 26.1 - - + +
183D VAL* 4.1 6.1 - - + -
184D PRO* 2.7 32.7 + - - +
185D GLY* 4.8 6.1 - - - -
186D ILE* 5.1 1.1 - - + -
220D ALA 3.0 15.1 + - - +
221D LYS* 3.2 20.6 - - + +
223D LYS* 1.3 78.9 - - - +
225D LEU* 1.3 73.9 + - + +
227D SER* 3.2 6.8 + - - -
228D LEU* 3.2 37.8 + - + +
233D TYR* 3.7 33.2 - + - -
406D GOL 4.9 7.2 + - - -
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Residues in contact with LEU 225 (chain D).
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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180D ILE* 4.3 3.6 - - + -
183D VAL* 4.2 7.0 - - + -
186D ILE* 3.9 28.3 - - + -
194D LEU* 3.8 24.0 - - + -
202D LEU* 3.9 21.9 - - + +
205D THR* 4.1 25.1 - - + -
213D LEU* 4.9 1.8 - - + -
217D ILE* 3.7 26.9 - - + -
221D LYS 2.9 15.5 + - - +
222D ALA* 3.2 4.2 + - - +
224D TYR* 1.3 85.6 - - + +
226D ILE* 1.3 58.5 + - - +
228D LEU* 3.2 6.1 + - + +
229D ALA* 2.9 29.6 + - - +
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Residues in contact with ILE 226 (chain D).
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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205D THR* 4.3 25.6 - - - +
206D LEU* 4.2 8.3 - - + -
208D ILE 6.1 0.2 - - - +
210D PHE* 3.3 41.3 - - + -
213D LEU* 4.3 10.8 - - + -
222D ALA 2.9 18.9 + - - +
223D LYS* 4.0 4.3 - - - +
225D LEU* 1.3 77.6 - - - +
227D SER* 1.3 58.1 + - - +
229D ALA* 3.2 1.2 + - - +
230D ARG* 2.9 67.4 + - - +
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Residues in contact with SER 227 (chain D).
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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223D LYS 2.9 16.0 + - - -
224D TYR* 3.2 10.4 + - - -
226D ILE* 1.3 77.3 - - - +
228D LEU* 1.3 60.5 + - - +
230D ARG* 3.7 4.8 + - - +
231D ASP 3.3 1.6 + - - -
232D GLU* 2.8 37.3 + - - -
233D TYR* 3.0 33.3 + - - +
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Residues in contact with LEU 228 (chain D).
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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147D ASN* 4.3 2.5 - - - +
149D VAL* 3.8 25.4 - - + -
150D PHE* 4.0 22.9 - - + -
175D ILE* 3.5 13.1 - - - +
183D VAL* 4.0 17.0 - - + -
202D LEU* 4.2 13.9 - - + -
224D TYR* 3.2 49.6 + - + +
225D LEU* 3.4 10.1 - - - +
226D ILE 3.1 0.2 - - - -
227D SER* 1.3 75.6 - - - +
229D ALA* 1.3 61.2 + - - +
231D ASP* 2.9 20.0 + - - +
233D TYR* 3.7 25.4 - - + -
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Residues in contact with ALA 229 (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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175D ILE* 3.5 24.6 - - + +
202D LEU* 3.2 36.8 - - + +
203D VAL* 4.3 1.5 - - - +
205D THR* 3.5 12.1 - - - +
206D LEU* 3.9 23.3 - - + +
225D LEU 2.9 14.0 + - - +
226D ILE 3.9 2.0 - - - +
228D LEU* 1.3 74.1 - - - +
230D ARG* 1.3 59.7 + - - +
231D ASP* 3.2 1.4 + - - +
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Residues in contact with ARG 230 (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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206D LEU* 3.9 23.5 - - + +
226D ILE* 2.9 42.9 + - - +
227D SER* 4.2 3.4 - - - +
229D ALA* 1.3 75.6 - - - +
231D ASP* 1.3 71.1 + - - +
232D GLU* 3.3 36.5 + - + +
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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