Contacts of the strand formed by residues 200 - 209 (chain E) in PDB entry 1R8Y
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 LYS 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E TYR* 4.1 27.5 - - + -
36E ASP* 4.7 4.5 - - - -
188E PRO* 4.5 14.6 - - + +
189E GLY* 4.2 15.9 - - - +
196E SER* 4.1 23.1 + - - -
198E LEU* 3.5 14.7 + - + +
199E THR* 1.3 80.9 - - - +
201E ASP* 1.3 65.9 + - - +
202E ILE* 4.0 13.2 - - + +
220E TYR* 3.7 36.6 - - + -
221E THR 3.5 6.1 - - - +
222E VAL* 3.6 22.7 - - + -
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Residues in contact with ASP 201 (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 PRO* 5.5 0.9 - - - -
200E LYS* 1.3 78.7 - - - +
202E ILE* 1.3 76.3 + - - +
203E THR* 5.6 0.2 + - - -
219E ASP 3.4 2.3 - - - +
220E TYR* 3.4 3.6 - - - -
221E THR* 2.6 56.7 + - + +
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Residues in contact with ILE 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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175E ARG* 5.9 1.6 - - - +
186E ALA 3.6 21.1 - - - +
187E PRO 4.8 1.3 - - - +
188E PRO* 3.7 40.6 - - + +
200E LYS* 4.0 7.0 - - + +
201E ASP* 1.3 90.8 + - - +
203E THR* 1.3 72.7 + - - +
204E THR* 4.3 1.7 + - - +
218E LEU* 4.3 22.4 - - + -
219E ASP 3.7 1.6 - - - +
220E TYR* 3.4 40.8 - - + -
210H ASN* 3.9 8.3 + - - +
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Residues in contact with THR 203 (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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201E ASP* 5.6 0.3 + - - -
202E ILE* 1.3 75.8 + - - +
204E THR* 1.3 59.2 + - - +
205E SER* 3.7 1.1 + - - +
217E THR 3.6 1.6 - - - +
218E LEU* 3.5 4.9 - - - -
219E ASP* 3.2 49.9 + - - +
209H VAL* 3.5 22.9 - - + -
210H ASN* 3.1 23.2 + - - +
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Residues in contact with THR 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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180E ILE* 4.4 2.5 - - + -
184E GLY 3.4 23.3 - - - +
185E CYS* 3.2 5.1 - - - +
186E ALA* 2.6 37.9 + - + +
202E ILE* 4.3 2.4 + - - +
203E THR* 1.3 70.9 - - - +
205E SER* 1.3 60.2 + - - +
206E VAL* 4.4 8.7 - - + -
216E VAL* 4.1 14.1 - - + -
218E LEU* 3.9 18.3 - - + +
208H THR 3.6 0.7 - - - +
209H VAL* 3.2 1.6 - - - +
210H ASN* 2.4 50.2 + - - -
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Residues in contact with SER 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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203E THR 4.3 0.2 + - - -
204E THR* 1.3 75.1 - - - +
206E VAL* 1.3 63.0 + - - +
207E LEU 4.0 0.3 + - - -
215E MET 3.8 0.5 - - - +
216E VAL* 3.4 3.0 - - - -
217E THR* 2.8 54.8 + - - -
219E ASP* 4.0 13.9 + - - -
239E ARG* 4.7 4.9 + - - -
5F TYR* 5.3 2.8 + - - -
207H LEU* 4.1 15.4 - - - +
208H THR 3.2 3.6 - - - -
209H VAL* 3.7 28.1 - - - +
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Residues in contact with VAL 206 (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 ILE* 5.4 1.3 - - + -
181E LEU* 3.8 28.0 - - + +
184E GLY* 4.5 15.9 - - - +
204E THR* 4.4 13.0 - - + -
205E SER* 1.3 74.7 - - - +
207E LEU* 1.3 63.1 + - - +
208E THR* 3.9 18.1 - - - +
213E ALA* 5.1 2.7 - - + -
215E MET 3.5 8.1 - - - +
216E VAL* 4.3 11.4 - - + -
206H VAL 3.5 1.0 - - - +
207H LEU* 3.4 4.2 - - - +
208H THR* 2.5 56.2 + - + +
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Residues in contact with LEU 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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205E SER 4.0 0.8 + - - -
206E VAL* 1.3 74.2 - - - +
208E THR* 1.3 61.6 + - - +
209E VAL* 4.3 12.6 - - + -
213E ALA* 3.9 0.5 - - - -
214E HIS* 2.9 39.4 + - + -
215E MET* 2.8 43.3 + - + +
5F TYR* 4.7 7.6 - - - +
5G TYR* 4.1 35.0 - - + +
205H SER* 4.2 10.1 - - - -
206H VAL 3.4 20.0 - - - +
207H LEU* 4.0 16.8 - - + -
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Residues in contact with THR 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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206E VAL* 3.9 12.7 + - - +
207E LEU* 1.3 75.4 + - - +
209E VAL* 1.3 58.7 + - - +
210E ASN 3.9 0.3 + - - -
211E ASN* 3.4 41.4 + - - +
212E LYS 3.7 5.8 - - - +
213E ALA* 3.9 9.2 - - - +
184H GLY* 5.1 2.0 - - - +
204H THR 3.8 1.0 - - - +
205H SER* 3.5 0.7 - - - -
206H VAL* 2.7 54.3 + - + +
208H THR* 6.1 1.2 - - - -
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Residues in contact with VAL 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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207E LEU* 4.0 12.5 + - + -
208E THR* 1.3 69.5 - - - +
210E ASN* 1.3 78.1 + - + +
211E ASN 3.1 1.6 - - - -
212E LYS* 2.8 29.8 + - - +
214E HIS* 4.3 24.9 - - + +
203H THR* 3.8 23.3 - - + -
204H THR 3.4 8.5 - - - +
205H SER* 3.8 21.3 - - - +
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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