Contacts of the strand formed by residues 201 - 216 (chain E) in PDB entry 5IXM
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 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191E LYS* 4.0 8.7 + - - +
192E PHE 3.5 7.2 - - - +
193E THR* 3.5 36.0 - - + +
194E SER 4.5 11.2 - - - +
199E ASN 3.8 6.0 + - - +
200E PRO* 1.3 77.4 - - - +
202E ALA* 1.3 66.4 + - - +
235E GLN* 3.4 4.0 - - - +
236E ASP* 2.7 53.5 + - - +
238E PRO* 4.9 0.2 - - - +
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Residues in contact with ALA 202 (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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190E ALA 4.0 0.3 - - - +
191E LYS* 3.4 8.1 - - - +
192E PHE* 2.9 43.3 + - + +
201E GLU* 1.3 77.5 - - - +
203E SER* 1.3 65.1 + - - +
233E TYR* 4.9 4.5 - - + -
234E GLN 3.2 5.8 - - - +
235E GLN* 3.8 12.3 - - + -
236E ASP* 3.8 1.1 + - - -
303E TYR* 3.4 37.2 - - + +
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Residues in contact with SER 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190E ALA 3.6 6.5 - - - -
191E LYS* 3.3 26.7 + - - +
202E ALA* 1.3 71.7 - - - +
204E ARG* 1.3 59.6 + - - +
205E PHE* 4.2 22.4 + - - -
232E HIS 3.9 1.2 - - - +
233E TYR* 3.8 2.1 - - - -
234E GLN* 2.9 45.1 + - - +
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Residues in contact with ARG 204 (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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168E GLN* 5.2 1.2 + - - -
188E GLN* 2.5 32.6 + - - +
189E ALA* 3.4 4.7 - - - -
190E ALA* 2.9 38.7 + - - +
192E PHE* 3.3 32.7 - - + -
202E ALA 4.1 0.4 - - - -
203E SER* 1.3 73.7 - - - +
205E PHE* 1.3 68.3 + - - +
206E HIS* 4.3 0.9 - - + +
231E THR* 4.2 9.0 - - + -
232E HIS 3.6 5.6 - - - +
233E TYR* 3.2 37.4 + - + -
304E ASP* 2.9 43.0 + - - -
323E GLY* 5.1 0.2 - - - -
324E LEU* 3.6 28.0 - - - +
325E ASP* 2.9 15.8 + - - -
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Residues in contact with PHE 205 (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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188E GLN 3.5 3.1 - - - +
189E ALA* 3.9 26.0 - - + -
190E ALA 5.9 0.4 - - - -
203E SER* 4.2 27.1 - - - -
204E ARG* 1.3 76.3 - - - +
206E HIS* 1.3 62.0 + - - +
231E THR* 3.5 3.1 - - - +
232E HIS* 2.9 66.7 + + + +
234E GLN* 5.6 1.6 - - + -
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Residues in contact with HIS 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E TYR* 4.3 13.0 - + - -
187E GLY* 3.2 5.2 - - - -
188E GLN* 2.9 41.8 + - + +
204E ARG* 5.2 3.1 - - + +
205E PHE* 1.3 76.0 - - - +
207E ILE* 1.3 66.1 + - - +
208E GLU* 3.2 33.2 + - + +
229E LEU* 3.9 16.8 - - + -
230E ALA 3.1 15.6 + - - -
231E THR* 2.8 31.8 + - + +
256E ARG* 5.0 0.7 - - - -
324E LEU* 3.5 45.0 - - + +
327E ILE* 6.0 0.4 - - + -
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Residues in contact with ILE 207 (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 VAL* 3.7 22.7 - - + -
186E TYR 3.5 15.3 - - - +
187E GLY* 4.1 9.4 - - - -
206E HIS* 1.3 75.4 - - - +
208E GLU* 1.3 63.3 + - - +
209E PRO* 4.0 9.0 - - + -
228E LEU 3.5 0.9 - - - +
230E ALA* 2.9 53.8 + - + +
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Residues in contact with GLU 208 (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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184E HIS* 3.7 5.4 + - - +
185E VAL* 3.5 3.2 - - - -
186E TYR* 2.9 54.8 + - + +
206E HIS* 3.2 22.6 + - + +
207E ILE* 1.3 79.4 - - - +
209E PRO* 1.3 61.1 - - - +
210E THR* 4.2 4.2 + - - +
227E LYS* 3.3 35.9 + - + +
228E LEU 3.1 11.0 - - - +
229E LEU* 3.3 20.1 - - + +
319E ARG* 3.7 11.7 + - - -
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Residues in contact with PRO 209 (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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184E HIS 3.8 4.0 - - - +
185E VAL* 4.2 18.6 - - + -
207E ILE* 4.0 12.8 - - + +
208E GLU* 1.3 89.0 - - - +
210E THR* 1.3 64.8 + - - +
211E VAL* 5.7 2.7 - - + -
226E ALA 4.1 0.2 - - - +
227E LYS* 3.4 0.9 - - - +
228E LEU* 2.9 61.8 + - + +
230E ALA* 5.9 0.2 - - + -
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Residues in contact with THR 210 (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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182E ASP 3.9 0.3 - - - +
183E MET* 3.4 5.9 - - - +
184E HIS* 2.9 54.3 + - + +
185E VAL* 5.0 0.4 - - - +
208E GLU* 4.2 6.4 + - - -
209E PRO* 1.3 78.0 + - - +
211E VAL* 1.3 67.9 + - - +
212E ASN* 5.0 4.7 - - + +
225E GLU* 3.8 35.4 - - + +
226E ALA 3.4 5.6 - - - +
227E LYS* 3.3 22.2 - - - +
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Residues in contact with VAL 211 (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 PHE* 3.7 37.7 - - + -
182E ASP 3.7 2.2 - - - +
183E MET* 4.2 24.9 - - + -
209E PRO* 5.7 2.7 - - + -
210E THR* 1.3 79.2 - - - +
212E ASN* 1.3 64.5 + - - +
224E THR 4.1 0.3 - - - +
225E GLU* 3.6 3.6 - - - +
226E ALA* 2.9 42.4 + - + +
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Residues in contact with ASN 212 (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 PHE* 3.2 10.2 - - - -
182E ASP* 2.9 51.6 + - + +
210E THR* 5.2 6.3 - - + -
211E VAL* 1.3 76.7 - - - +
213E LEU* 1.3 58.4 + - - +
214E PRO* 3.2 14.4 - - - +
223E ASN* 2.8 44.8 + - - +
224E THR 3.0 8.6 - - - +
225E GLU* 3.5 14.4 - - - +
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Residues in contact with LEU 213 (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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180E PRO* 3.7 24.0 - - + +
181E PHE* 3.9 20.0 - - + -
212E ASN* 1.3 70.7 - - - +
214E PRO* 1.3 63.2 - - + +
215E LEU* 3.9 20.4 + - + +
222E ILE 4.0 0.3 - - - +
223E ASN* 3.1 5.6 - - - +
224E THR* 2.8 51.0 + - - +
601E C8E 3.8 43.3 - - - +
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Residues in contact with PRO 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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180E PRO 3.8 15.3 - - - +
182E ASP* 3.6 24.9 - - - +
212E ASN* 3.2 19.7 - - - +
213E LEU* 1.3 85.8 - - + +
215E LEU* 1.3 68.5 + - - +
216E SER* 4.0 2.5 + - - -
222E ILE 3.9 2.0 - - - +
223E ASN* 3.5 13.7 - - + +
601E C8E 5.5 0.5 - - - +
37F ARG* 4.4 7.6 - - - +
38F LEU* 5.4 11.9 - - + -
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Residues in contact with LEU 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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213E LEU* 4.7 18.4 - - + +
214E PRO* 1.3 80.6 - - - +
216E SER* 1.3 60.5 + - - +
221E SER* 3.3 5.8 - - - -
222E ILE* 2.9 62.1 + - + +
601E C8E 3.5 51.6 - - - +
38F LEU* 5.6 1.3 - - - +
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Residues in contact with SER 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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214E PRO* 4.0 2.9 + - - -
215E LEU* 1.3 74.6 - - - +
217E ASN* 1.3 70.6 + - - +
221E SER* 4.0 6.7 - - - -
37F ARG 5.0 1.3 - - - -
38F LEU* 2.1 48.6 + - - +
40F ASN* 3.3 23.7 + - - +
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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