Contacts of the strand formed by residues 213 - 218 (chain E) in PDB entry 3IT8
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 ILE 213 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TYR* 4.3 15.7 - - + +
100E THR* 4.1 20.4 - - + +
103E LEU* 3.5 36.8 - - + -
211E ASP* 6.2 0.2 - - + -
212E VAL* 1.3 85.3 - - - +
214E THR* 1.3 72.9 + - - +
215E LYS* 4.9 4.0 - - + -
245E PRO* 4.7 11.7 - - + +
246E GLY* 4.4 19.3 - - - +
252E TRP* 4.0 20.6 - - + +
283E VAL* 3.8 1.7 - - - -
284E PHE* 2.8 38.8 + - + +
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Residues in contact with THR 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202E CYS* 4.2 2.6 - - - +
204E VAL* 5.5 0.3 - - - +
212E VAL* 5.4 0.4 - - - -
213E ILE* 1.3 80.2 - - - +
215E LYS* 1.3 64.6 + - - +
216E TRP* 3.9 10.8 + - + +
239E ARG* 5.5 3.6 - - - +
252E TRP* 3.5 28.4 - - + -
265E LEU* 5.1 8.8 - - - +
267E ASP* 2.9 34.7 - - - +
281E CYS* 3.3 27.2 - - - -
282E VAL 3.4 4.0 + - - -
283E VAL* 4.2 6.8 - - - +
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Residues in contact with LYS 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 4.2 23.1 - - - +
213E ILE* 4.9 4.0 - - + -
214E THR* 1.3 77.9 - - - +
216E TRP* 1.3 63.6 + - - +
217E ILE* 3.9 9.9 - - + -
228E TYR* 3.9 20.8 + - + +
236E GLU* 3.2 43.0 + - + +
280E VAL 3.6 0.3 - - - +
281E CYS* 3.8 0.9 - - - -
282E VAL* 2.8 45.9 + - + +
284E PHE* 3.4 33.4 - - + -
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Residues in contact with TRP 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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188E VAL* 4.0 9.0 - - + -
200E LEU* 3.8 34.5 - - + -
202E CYS* 3.4 37.9 - - + -
214E THR* 3.9 8.4 - - + +
215E LYS* 1.3 74.8 - - - +
217E ILE* 1.3 60.2 - - - +
236E GLU 2.7 33.9 + - - +
237E TRP* 3.4 20.3 + - + +
239E ARG* 5.2 8.1 - - + -
267E ASP* 2.7 35.0 + - - -
269E VAL* 3.0 31.2 - - + +
279E PRO* 3.7 29.8 - - + -
280E VAL 3.5 13.2 - - - -
281E CYS* 3.8 20.4 - - + -
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Residues in contact with ILE 217 (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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215E LYS* 3.8 8.3 + - + +
216E TRP* 1.3 82.0 - - - +
218E GLU* 1.3 78.7 + - - +
221E HIS* 3.9 14.4 - - + -
222E PHE* 3.7 19.3 - - + -
228E TYR* 4.0 16.4 - - + -
234E TYR* 3.8 25.1 - - + -
235E PRO 3.5 21.8 - - - +
236E GLU* 4.2 8.5 - - + +
279E PRO* 3.8 4.3 - - - -
280E VAL* 2.8 39.9 + - + +
282E VAL* 3.9 21.8 - - + -
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Residues in contact with GLU 218 (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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217E ILE* 1.3 76.2 - - - +
219E SER* 1.3 65.1 + - - +
220E GLU* 3.0 22.8 + - + +
221E HIS* 3.1 34.7 + - + +
222E PHE* 4.0 1.2 - - - -
235E PRO 5.1 0.6 + - - -
237E TRP* 3.7 37.2 - - + +
275E MET* 3.8 20.8 - - + +
276E SER* 3.5 15.5 + - - -
277E SER* 3.5 16.5 + - - +
278E GLN 4.6 2.7 - - - +
279E PRO* 4.0 8.4 - - - +
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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
------------------------------------------------------------
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