Contacts of the strand formed by residues 207 - 214 (chain E) in PDB entry 6D6U
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 ARG 207 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E SER* 5.6 0.6 - - - -
206E LEU* 1.3 85.3 - - - +
208E ASN* 1.3 68.9 + - - +
209E THR* 4.9 6.2 - - + +
225E VAL* 3.7 10.4 - - - +
226E TYR* 2.9 82.0 + - + +
228E ASP* 3.9 24.9 + - - -
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Residues in contact with ASN 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E TRP* 4.8 18.6 - - + +
186E SER 4.8 5.1 + - - -
187E SER* 4.6 13.3 + - - -
188E VAL* 5.2 6.9 - - + +
206E LEU* 5.8 2.1 - - + +
207E ARG* 1.3 82.1 - - - +
209E THR* 1.3 69.7 + - - +
210E THR* 5.9 0.2 - - - -
224E SER 3.7 5.6 - - - -
225E VAL* 4.1 16.4 - - + +
226E TYR* 5.2 0.9 - - - +
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Residues in contact with THR 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E TRP* 4.6 1.4 + - - -
207E ARG* 4.9 6.5 - - + +
208E ASN* 1.3 82.1 - - - +
210E THR* 1.3 69.1 + - - +
211E GLU* 4.7 11.4 + - - +
224E SER* 2.9 48.1 + - - +
226E TYR* 3.7 31.2 - - + +
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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
----------------------------------------------------------
182E GLN* 6.0 1.1 - - - -
183E TRP* 4.0 14.8 - - + -
208E ASN 5.9 0.2 - - - -
209E THR* 1.3 80.4 - - - +
211E GLU* 1.3 69.7 + - - +
222E VAL 4.1 4.9 - - - -
223E MET* 3.6 36.1 - - + -
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Residues in contact with GLU 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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168E GLU* 5.4 4.2 - - - +
209E THR* 4.7 12.6 + - - +
210E THR* 1.3 82.4 - - - +
212E VAL* 1.3 73.2 + - - +
213E VAL* 4.7 13.2 - - + +
221E VAL* 3.9 5.0 - - - +
222E VAL* 3.3 34.0 + - + +
223E MET* 5.4 0.9 - - - +
224E SER* 5.7 5.2 - - - -
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Residues in contact with VAL 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E ARG* 3.8 31.9 - - - +
211E GLU* 1.3 83.1 - - - +
213E VAL* 1.3 69.2 + - - +
214E LYS 4.3 0.7 + - - -
219E ASP* 4.4 18.6 - - + -
220E TYR 3.8 8.5 - - - +
221E VAL* 4.5 14.1 - - + -
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Residues in contact with VAL 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ARG* 5.2 7.2 - - - +
211E GLU* 4.7 12.6 - - - +
212E VAL* 1.3 81.6 - - - +
214E LYS* 1.3 71.1 + - - +
215E THR* 3.9 15.4 + - + +
218E GLY 4.0 0.3 - - - +
219E ASP* 3.5 2.5 - - - -
220E TYR* 2.9 34.3 + - + +
222E VAL* 3.6 33.9 - - + -
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Residues in contact with LYS 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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212E VAL* 4.3 0.6 + - + -
213E VAL* 1.3 75.1 - - - +
215E THR* 1.3 80.2 + - - +
218E GLY* 3.4 11.7 + - - +
219E ASP* 3.3 22.6 + - - +
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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