Contacts of the helix formed by residues 213 - 228 (chain E) in PDB entry 1R4N
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 213 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E TYR* 4.1 13.5 - - - +
211E HIS 4.1 3.6 - - - +
212E THR* 1.3 96.2 - - + +
214E TRP* 1.3 64.6 + - - +
215E ILE 3.3 0.7 + - - +
216E VAL* 3.4 12.5 + - + -
217E ILE* 3.2 16.3 + - - +
332E MET* 3.2 24.9 - - + -
333E ILE 4.2 1.3 - - - +
334E ALA* 3.6 24.8 - - + -
338E LYS* 4.3 20.6 - - + +
339E TYR* 4.3 3.1 - - - +
342E LEU* 3.7 16.6 - - + -
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Residues in contact with TRP 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E GLU* 6.1 0.4 - - + -
183E LEU* 4.7 12.4 - - + +
185E LEU* 6.0 0.4 - - - +
212E THR 3.3 2.7 + - - -
213E PRO* 1.3 68.6 - - - +
215E ILE* 1.3 79.5 + - + +
217E ILE* 3.2 12.7 - - - +
218E ILE* 3.0 35.5 + - + +
264E ASN* 4.1 7.6 - - + +
267E GLU* 3.7 21.3 - - + +
268E ALA* 3.9 18.6 - - + +
271E ASN* 2.9 48.5 - - + +
275E ALA* 4.7 6.6 - - + +
330E PRO* 3.7 30.1 - - + -
331E ASP 3.5 20.6 - - - -
332E MET* 3.2 34.8 - - + +
333E ILE 4.6 1.8 + - - -
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Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E LEU* 3.7 26.5 - - + -
185E LEU* 3.8 20.6 - - + -
196E PHE* 3.6 28.0 - - + -
213E PRO 3.1 0.8 - - - -
214E TRP* 1.3 91.7 - - + +
216E VAL* 1.3 58.3 + - - +
218E ILE* 2.6 8.3 + - - +
219E ALA 2.5 33.8 + - - -
329E ILE* 4.8 3.8 - - + -
332E MET* 3.7 28.5 - - + -
342E LEU* 3.9 14.1 - - + -
346E TYR* 3.7 21.5 - - + +
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Residues in contact with VAL 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS* 4.7 6.5 - - - +
196E PHE* 4.2 21.1 - - + +
199E TYR* 3.3 57.4 - - + +
212E THR* 4.1 7.0 - - + -
213E PRO* 3.7 25.8 - - + +
215E ILE* 1.3 78.5 - - - +
217E ILE* 1.3 56.4 + - + +
219E ALA* 2.9 9.1 + - - +
220E LYS* 2.7 42.3 + - + +
342E LEU* 4.8 4.3 - - + -
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Residues in contact with ILE 217 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E HIS* 5.4 3.4 - - + -
212E THR* 3.5 33.4 - - + +
213E PRO 3.2 14.8 - - - +
214E TRP* 3.2 12.6 - - - +
216E VAL* 1.3 78.2 - - + +
218E ILE* 1.3 60.8 + - - +
220E LYS* 3.9 2.9 - - - +
221E TYR* 3.3 31.3 + - + +
247E ILE* 4.2 16.6 - - + -
264E ASN* 4.4 4.9 - - - +
265E PHE* 3.5 41.1 - - + -
268E ALA* 3.9 17.9 - - + -
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Residues in contact with ILE 218 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 4.0 20.0 - - + -
214E TRP* 3.0 26.1 + - + +
215E ILE* 2.6 13.0 + - - +
217E ILE* 1.3 70.7 - - - +
219E ALA* 1.3 58.2 + - - +
221E TYR 3.7 0.9 - - - +
222E LEU* 2.8 35.4 + - + +
243E PHE* 3.7 19.3 - - + -
247E ILE* 4.1 7.4 - - + -
268E ALA* 3.1 37.9 - - + +
271E ASN* 4.0 0.2 - - + -
272E VAL* 3.6 22.2 - - + +
275E ALA* 4.0 15.5 - - + -
276E LEU* 4.8 7.4 - - + -
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Residues in contact with ALA 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 3.9 12.5 - - + +
196E PHE* 3.7 48.5 - - + -
215E ILE 2.5 16.3 + - - +
216E VAL 3.3 7.9 - - - +
218E ILE* 1.3 75.3 - - - +
220E LYS* 1.3 56.4 + - - +
222E LEU* 3.3 8.8 + - - +
223E ALA* 2.8 28.9 + - - +
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Residues in contact with LYS 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E PHE* 2.7 39.0 + - + +
197E GLN* 3.8 9.9 + - - +
199E TYR* 3.9 28.5 - - + -
216E VAL* 2.7 25.3 + - + +
217E ILE* 3.9 5.4 - - - +
219E ALA* 1.3 69.6 - - + +
221E TYR* 1.3 68.0 + - + +
222E LEU 2.9 8.9 + - - -
223E ALA* 2.9 19.6 + - + +
224E GLN* 3.0 14.3 + - - +
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Residues in contact with TYR 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E ILE* 3.3 22.8 + - + +
220E LYS* 1.3 86.9 - - + +
222E LEU* 1.3 58.6 + - - +
224E GLN* 4.0 17.2 - - - +
225E TRP* 3.5 11.8 + - - +
243E PHE* 2.8 22.9 - - + -
246E LEU* 3.2 45.3 - - + +
247E ILE* 3.4 36.1 - - + -
249E GLN 4.5 1.5 + - - -
250E GLY* 2.9 30.7 + - - -
265E PHE* 4.3 13.3 - + - -
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Residues in contact with LEU 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E LEU* 4.1 33.9 - - + +
186E ASP* 5.9 0.4 - - - -
218E ILE* 2.8 20.7 + - + +
219E ALA* 3.4 9.9 - - - +
221E TYR* 1.3 77.5 - - - +
223E ALA* 1.3 66.5 + - - +
224E GLN 3.1 1.6 - - - -
225E TRP* 3.0 7.5 + - + +
226E TYR* 3.0 21.1 + - + +
232E ARG* 4.5 7.4 - - - +
233E ILE* 3.3 31.9 - - + -
243E PHE* 3.5 7.6 - - + -
276E LEU* 4.3 15.3 - - + -
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Residues in contact with ALA 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ALA 2.8 15.4 + - - +
220E LYS* 3.3 15.5 - - + +
222E LEU* 1.3 78.9 - - - +
224E GLN* 1.3 60.5 + - - +
226E TYR* 3.1 21.6 - - - +
227E SER* 3.6 7.3 + - - -
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Residues in contact with GLN 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E LYS 3.0 13.4 + - - +
221E TYR* 4.1 17.8 - - - +
222E LEU 3.1 0.2 - - - -
223E ALA* 1.3 73.1 - - - +
225E TRP* 1.3 58.4 + - - +
226E TYR 2.8 10.2 + - - -
227E SER* 2.8 19.8 + - - -
228E GLU* 3.3 36.6 + - + +
246E LEU* 3.6 31.1 - - - +
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Residues in contact with TRP 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E TYR 3.5 13.0 + - - +
222E LEU* 3.0 11.1 + - + +
224E GLN* 1.3 79.7 - - - +
226E TYR* 1.3 61.5 + - - +
228E GLU* 4.2 10.5 - - - +
229E THR* 3.5 31.8 + - + -
230E ASN 4.0 0.2 + - - -
231E GLY* 3.9 16.3 - - - -
232E ARG* 3.8 6.6 - - - +
233E ILE* 3.2 37.3 - - + +
239E GLU* 3.9 42.8 - - + -
242E ASP* 4.7 9.6 - - + -
243E PHE* 4.0 32.3 - + + -
246E LEU* 4.3 15.7 - - + +
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Residues in contact with TYR 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222E LEU* 3.0 10.9 + - + +
223E ALA* 3.1 18.2 - - - +
224E GLN 2.8 0.8 + - - -
225E TRP* 1.3 81.8 - - - +
227E SER* 1.3 57.0 + - - +
230E ASN* 2.6 60.2 + - + +
231E GLY 3.4 16.6 - - - -
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Residues in contact with SER 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E ALA 3.6 5.7 + - - -
224E GLN* 2.8 11.6 + - - -
226E TYR* 1.3 78.3 - - - +
228E GLU* 1.3 56.6 + - - -
229E THR* 2.6 18.6 + - - -
230E ASN* 4.8 6.8 + - - +
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Residues in contact with GLU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E GLN* 3.3 40.0 + - + +
225E TRP* 4.0 10.0 + - - +
226E TYR 3.6 0.2 - - - -
227E SER* 1.3 73.9 - - - +
229E THR* 1.3 67.4 + - - +
246E LEU* 5.1 5.5 - - - +
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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