Contacts of the strand formed by residues 181 - 193 (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 PHE 181 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177E ASP* 3.3 2.1 + - - -
178E VAL* 2.9 37.7 + - - +
179E GLY 3.3 1.4 - - - -
180E PRO* 1.3 99.3 - - + +
182E ASP* 1.3 67.0 - - - +
183E MET* 4.6 11.2 - - + -
211E VAL* 3.7 27.8 - - + -
212E ASN 3.2 16.6 - - - +
213E LEU* 3.9 20.4 - - + -
601E C8E 3.6 35.4 - - - -
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Residues in contact with ASP 182 (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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175E LYS 3.8 3.1 - - - -
176E ASN* 3.5 15.6 - - - +
177E ASP* 3.1 14.6 + - - -
180E PRO 4.3 0.5 + - - +
181E PHE* 1.3 73.6 - - - +
183E MET* 1.3 62.5 + - - +
210E THR 3.9 0.7 - - - +
211E VAL* 3.7 1.0 - - - -
212E ASN* 2.9 47.0 + - + +
214E PRO* 3.6 15.4 - - - +
37F ARG* 2.4 47.3 + - - -
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Residues in contact with MET 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E TYR* 4.7 2.5 - - + -
174E TYR* 3.7 1.6 - - - +
175E LYS* 2.9 41.6 + - + +
176E ASN* 5.0 1.6 - - - +
178E VAL* 3.7 40.2 - - + +
181E PHE* 4.6 10.8 - - + -
182E ASP* 1.3 79.0 - - - +
184E HIS* 1.3 62.9 + - - +
185E VAL* 5.9 3.4 - - + -
210E THR 3.4 4.9 - - - +
211E VAL* 4.2 33.7 - - + -
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Residues in contact with HIS 184 (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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172E ASN* 3.0 26.3 + - - -
173E TYR* 3.3 13.2 - - - -
174E TYR* 3.3 36.8 - + + -
183E MET* 1.3 77.4 - - - +
185E VAL* 1.3 73.3 + - - +
186E TYR* 3.8 15.5 - - + +
208E GLU* 3.7 4.9 - - - +
209E PRO 3.7 0.3 - - - -
210E THR* 2.9 50.6 + - + +
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Residues in contact with VAL 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E MET 4.6 0.2 - - - -
172E ASN* 3.5 2.9 - - - -
173E TYR* 2.9 52.6 + - + +
183E MET* 5.8 2.9 - - + -
184E HIS* 1.3 81.7 - - - +
186E TYR* 1.3 63.1 + - - +
207E ILE* 3.7 28.5 - - + -
208E GLU 3.5 9.2 - - - +
209E PRO* 4.2 16.8 - - + -
210E THR 5.0 0.4 - - - +
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Residues in contact with TYR 186 (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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170E ASP* 2.7 32.1 + - + -
171E MET 3.2 14.6 - - - -
172E ASN* 3.2 32.8 - - - +
184E HIS* 3.8 12.7 + - + +
185E VAL* 1.3 75.6 - - - +
187E GLY* 1.3 71.2 + - - +
188E GLN* 2.8 19.8 + - + -
206E HIS* 4.3 17.0 - + - -
207E ILE* 3.5 6.0 - - - +
208E GLU* 2.9 61.6 + - + +
319E ARG* 6.3 0.2 - - - -
324E LEU* 5.0 4.5 - - + -
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Residues in contact with GLY 187 (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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169E LEU 4.4 0.2 - - - -
170E ASP* 3.6 0.3 - - - -
171E MET* 2.9 42.3 + - - +
186E TYR* 1.3 84.1 - - - +
188E GLN* 1.3 61.7 + - - +
206E HIS 3.2 9.9 - - - -
207E ILE* 4.1 9.2 - - - +
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Residues in contact with GLN 188 (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* 3.0 22.7 + - + +
169E LEU 3.1 7.2 - - - +
170E ASP* 2.9 16.1 + - - +
186E TYR* 2.8 30.4 + - + +
187E GLY* 1.3 75.5 - - - +
189E ALA* 1.3 68.9 + - - +
190E ALA* 4.2 2.8 - - - +
204E ARG* 2.5 41.3 + - - +
205E PHE* 3.5 3.6 - - - +
206E HIS* 2.9 44.4 + - + +
304E ASP* 5.5 0.2 + - - -
324E LEU* 3.8 10.5 - - + +
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Residues in contact with ALA 189 (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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167E PRO 3.9 1.4 - - - +
168E GLN* 3.5 1.9 - - - -
169E LEU* 2.9 50.2 + - + +
188E GLN* 1.3 74.9 - - - +
190E ALA* 1.3 60.9 + - - +
204E ARG 3.4 4.7 - - - -
205E PHE* 3.9 25.8 - - + -
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Residues in contact with ALA 190 (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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165E ALA* 5.3 0.4 - - + -
167E PRO 3.5 4.0 - - - -
168E GLN* 4.2 16.6 - - + -
188E GLN* 4.2 13.4 - - - +
189E ALA* 1.3 76.3 - - - +
191E LYS* 1.3 61.1 + - - +
192E PHE* 3.7 33.0 - - + -
202E ALA 4.0 0.3 - - - +
203E SER* 3.6 3.5 - - - -
204E ARG* 2.9 36.7 + - - +
205E PHE* 5.7 0.9 - - - -
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Residues in contact with LYS 191 (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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164E ARG 3.2 2.9 - - - +
165E ALA* 3.7 0.2 - - - -
166E GLN* 2.9 52.1 + - - +
167E PRO* 3.1 13.8 + - + +
190E ALA* 1.3 73.3 - - - +
192E PHE* 1.3 60.2 + - - +
193E THR* 3.7 26.4 + - + -
201E GLU* 4.0 13.6 + - - -
202E ALA 3.4 21.6 + - - +
203E SER* 3.3 25.7 + - - +
236E ASP* 4.1 10.1 + - - -
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Residues in contact with PHE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E TYR* 4.2 6.1 - - + -
164E ARG 3.2 15.5 - - - +
165E ALA* 4.3 10.3 - - + -
168E GLN* 5.9 1.6 - - - -
190E ALA* 3.7 21.5 - - + -
191E LYS* 1.3 71.2 - - - +
193E THR* 1.3 66.8 + - - +
201E GLU* 3.5 3.6 - - - -
202E ALA* 2.9 46.6 + - + +
204E ARG* 3.3 59.5 - - + -
233E TYR* 5.6 0.2 - + - -
303E TYR* 3.7 38.8 - + + -
304E ASP* 3.9 11.4 - - + -
114F LEU* 3.9 23.3 - - + -
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Residues in contact with THR 193 (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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162E ALA 4.1 0.5 - - - +
163E TYR* 3.5 7.1 - - - -
164E ARG* 2.9 37.0 + - - +
166E GLN* 4.7 14.5 - - + +
191E LYS* 3.7 22.8 + - + -
192E PHE* 1.3 79.6 - - - +
194E SER* 1.3 61.0 + - - +
201E GLU* 3.5 35.7 - - - +
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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