Contacts of the strand formed by residues 208 - 213 (chain E) in PDB entry 2I3T
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 GLY 208 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E LEU* 3.8 13.2 - - - +
202E LEU* 3.4 18.7 + - - +
207E GLU* 1.3 78.1 + - - +
209E TYR* 1.3 73.8 + - - +
221E GLU 3.1 12.3 - - - -
223E PHE* 4.3 11.0 - - - -
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Residues in contact with TYR 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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164E ILE* 3.6 26.2 - - + -
172E VAL* 3.4 25.8 - - + +
174E TRP* 5.3 6.1 - + - -
188E GLU* 3.1 22.0 + - - -
189E GLU 3.5 11.3 + - - -
190E SER* 3.7 6.5 - - - -
199E VAL* 4.2 3.6 - - + -
200E ALA 3.4 15.0 - - - +
201E LEU* 4.2 4.3 - - + -
202E LEU* 3.4 11.9 - - - +
208E GLY* 1.3 81.8 - - - +
210E ALA* 1.3 70.3 + - - +
211E CYS* 3.9 21.5 - - - -
219E ALA 5.2 0.9 - - - -
220E VAL* 3.3 3.7 - - - +
221E GLU* 2.8 59.8 + - + -
223E PHE* 5.1 3.4 - + - -
235E ARG* 3.8 2.1 + - - -
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Residues in contact with ALA 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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199E VAL* 3.4 2.9 - - - +
200E ALA 2.8 35.4 + - - +
202E LEU* 4.5 1.1 - - + -
209E TYR* 1.3 76.9 - - - +
211E CYS* 1.3 63.1 + - - +
218E VAL* 4.7 1.1 - - + -
219E ALA 3.2 10.1 - - - +
220E VAL* 4.0 15.0 - - + +
257E ILE* 3.6 14.5 - - + +
259E PHE* 4.2 20.9 - - + -
266E LEU* 4.4 8.3 - - + -
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Residues in contact with CYS 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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172E VAL* 4.9 2.0 - - + -
190E SER* 3.6 30.3 - - - -
192E LEU* 3.5 22.2 - - + +
196E ILE* 4.5 6.1 - - + -
198E ASP 3.2 14.6 - - - +
199E VAL* 4.1 11.9 - - + -
209E TYR* 3.9 14.8 - - + -
210E ALA* 1.3 76.4 - - - +
212E SER* 1.3 60.4 + - - +
218E VAL* 3.4 3.8 - - - -
219E ALA* 2.9 36.6 + - - -
257E ILE* 3.9 5.1 - - - +
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Residues in contact with SER 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E LEU* 3.6 4.3 - - - +
196E ILE* 3.5 4.3 - - - -
197E ARG 2.7 30.8 + - - -
198E ASP* 2.9 19.3 + - - +
211E CYS* 1.3 74.6 - - - +
213E SER* 1.3 54.2 + - - +
217E ARG 3.5 7.0 - - - -
218E VAL* 4.2 2.7 - - - -
254E VAL* 2.8 46.4 + - - -
257E ILE* 3.6 18.7 - - - +
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Residues in contact with SER 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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192E LEU* 3.7 20.1 - - - +
193E LYS 5.3 0.2 - - - -
194E TYR 4.3 8.3 - - - -
195E GLN 3.1 15.7 - - - -
197E ARG* 4.1 5.1 - - - +
212E SER* 1.3 75.8 - - - +
214E ILE* 1.3 61.9 + - - +
215E ASP* 3.2 24.9 + - - -
217E ARG* 3.1 23.9 + - - +
254E VAL* 3.0 28.6 + - - +
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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